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Oberhofer G, Johnson ML, Ivy T, Antoshechkin I, Hay BA. Cleave and Rescue gamete killers create conditions for gene drive in plants. NATURE PLANTS 2024:10.1038/s41477-024-01701-3. [PMID: 38886522 DOI: 10.1038/s41477-024-01701-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/16/2024] [Indexed: 06/20/2024]
Abstract
Gene drive elements promote the spread of linked traits and can be used to change the composition or fate of wild populations. Cleave and Rescue (ClvR) drive elements sit at a fixed chromosomal position and include a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene and a recoded version of the essential gene resistant to cleavage. ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. Here we demonstrate the essential features of the ClvR gene drive in the plant Arabidopsis thaliana through killing of gametes that fail to inherit a ClvR that targets the essential gene YKT61. Resistant alleles, which can slow or prevent drive, were not observed. Modelling shows plant ClvRs are robust to certain failure modes and can be used to rapidly drive population modification or suppression. Possible applications are discussed.
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Affiliation(s)
- Georg Oberhofer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michelle L Johnson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tobin Ivy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Bruce A Hay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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2
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Kefi M, Cardoso-Jaime V, Saab SA, Dimopoulos G. Curing mosquitoes with genetic approaches for malaria control. Trends Parasitol 2024; 40:487-499. [PMID: 38760256 DOI: 10.1016/j.pt.2024.04.010] [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: 03/12/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
Malaria remains a persistent global public health challenge because of the limitations of current prevention tools. The use of transgenic mosquitoes incapable of transmitting malaria, in conjunction with existing methods, holds promise for achieving elimination of malaria and preventing its reintroduction. In this context, population modification involves the spread of engineered genetic elements through mosquito populations that render them incapable of malaria transmission. Significant progress has been made in this field over the past decade in revealing promising targets, optimizing genetic tools, and facilitating the transition from the laboratory to successful field deployments, which are subject to regulatory scrutiny. This review summarizes recent advances and ongoing challenges in 'curing' Anopheles vectors of the malaria parasite.
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Affiliation(s)
- Mary Kefi
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Victor Cardoso-Jaime
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Sally A Saab
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - George Dimopoulos
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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3
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Chae K, Contreras B, Romanowski JS, Dawson C, Myles KM, Adelman ZN. Transgene removal using an in cis programmed homing endonuclease via single-strand annealing in the mosquito Aedes aegypti. Commun Biol 2024; 7:660. [PMID: 38811748 PMCID: PMC11137009 DOI: 10.1038/s42003-024-06348-6] [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: 12/06/2023] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
While gene drive strategies have been proposed to aid in the control of mosquito-borne diseases, additional genome engineering technologies may be required to establish a defined end-of-product-life timeline. We previously demonstrated that single-strand annealing (SSA) was sufficient to program the scarless elimination of a transgene while restoring a disrupted gene in the disease vector mosquito Aedes aegypti. Here, we extend these findings by establishing that complete transgene removal (four gene cassettes comprising ~8-kb) can be programmed in cis. Reducing the length of the direct repeat from 700-bp to 200-bp reduces, but does not eliminate, SSA activity. In contrast, increasing direct repeat length to 1.5-kb does not increase SSA rates, suggesting diminishing returns above a certain threshold size. Finally, we show that while the homing endonuclease Y2-I-AniI triggered both SSA and NHEJ at significantly higher rates than I-SceI at one genomic locus (P5-EGFP), repair events are heavily skewed towards NHEJ at another locus (kmo), suggesting the nuclease used and the genomic region targeted have a substantial influence on repair outcomes. Taken together, this work establishes the feasibility of engineering temporary transgenes in disease vector mosquitoes, while providing critical details concerning important operational parameters.
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Affiliation(s)
- Keun Chae
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Bryan Contreras
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Joseph S Romanowski
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Chanell Dawson
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Kevin M Myles
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Zach N Adelman
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA.
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4
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Connolly JB, Burt A, Christophides G, Diabate A, Habtewold T, Hancock PA, James AA, Kayondo JK, Lwetoijera DW, Manjurano A, McKemey AR, Santos MR, Windbichler N, Randazzo F. Considerations for first field trials of low-threshold gene drive for malaria vector control. Malar J 2024; 23:156. [PMID: 38773487 PMCID: PMC11110314 DOI: 10.1186/s12936-024-04952-9] [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: 11/29/2023] [Accepted: 04/15/2024] [Indexed: 05/23/2024] Open
Abstract
Sustainable reductions in African malaria transmission require innovative tools for mosquito control. One proposal involves the use of low-threshold gene drive in Anopheles vector species, where a 'causal pathway' would be initiated by (i) the release of a gene drive system in target mosquito vector species, leading to (ii) its transmission to subsequent generations, (iii) its increase in frequency and spread in target mosquito populations, (iv) its simultaneous propagation of a linked genetic trait aimed at reducing vectorial capacity for Plasmodium, and (v) reduced vectorial capacity for parasites in target mosquito populations as the gene drive system reaches fixation in target mosquito populations, causing (vi) decreased malaria incidence and prevalence. Here the scope, objectives, trial design elements, and approaches to monitoring for initial field releases of such gene dive systems are considered, informed by the successful implementation of field trials of biological control agents, as well as other vector control tools, including insecticides, Wolbachia, larvicides, and attractive-toxic sugar bait systems. Specific research questions to be addressed in initial gene drive field trials are identified, and adaptive trial design is explored as a potentially constructive and flexible approach to facilitate testing of the causal pathway. A fundamental question for decision-makers for the first field trials will be whether there should be a selective focus on earlier points of the pathway, such as genetic efficacy via measurement of the increase in frequency and spread of the gene drive system in target populations, or on wider interrogation of the entire pathway including entomological and epidemiological efficacy. How and when epidemiological efficacy will eventually be assessed will be an essential consideration before decisions on any field trial protocols are finalized and implemented, regardless of whether initial field trials focus exclusively on the measurement of genetic efficacy, or on broader aspects of the causal pathway. Statistical and modelling tools are currently under active development and will inform such decisions on initial trial design, locations, and endpoints. Collectively, the considerations here advance the realization of developer ambitions for the first field trials of low-threshold gene drive for malaria vector control within the next 5 years.
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Affiliation(s)
- John B Connolly
- Department of Life Sciences, Silwood Park, Imperial College London, London, UK.
| | - Austin Burt
- Department of Life Sciences, Silwood Park, Imperial College London, London, UK
| | - George Christophides
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, UK
| | - Abdoulaye Diabate
- Institut de Recherche en Sciences de la Santé/Centre Muraz, Bobo-Dioulasso, Burkina Faso
| | - Tibebu Habtewold
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, UK
- Environmental Health and Ecological Science Department, Ifakara Health Institute, Ifakara, Tanzania
| | - Penelope A Hancock
- MRC Centre for Global Infectious Disease Analysis, St. Mary's Campus, Imperial College London, London, UK
| | - Anthony A James
- Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry, University of California, Irvine, USA
| | - Jonathan K Kayondo
- Entomology Department, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Alphaxard Manjurano
- Malaria Research Unit and Laboratory Sciences, Mwanza Medical Research Centre, National Institute for Medical Research, Mwanza, Tanzania
| | - Andrew R McKemey
- Department of Life Sciences, Silwood Park, Imperial College London, London, UK
| | - Michael R Santos
- Foundation for the National Institutes of Health, North Bethesda, MD, USA
| | - Nikolai Windbichler
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, UK
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5
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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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6
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Ambrose L, Allen SL, Iro'ofa C, Butafa C, Beebe NW. Genetic and geographic population structure in the malaria vector, Anopheles farauti, provides a candidate system for pioneering confinable gene-drive releases. Heredity (Edinb) 2024; 132:232-246. [PMID: 38494530 DOI: 10.1038/s41437-024-00677-2] [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: 11/19/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024] Open
Abstract
Indoor insecticide applications are the primary tool for reducing malaria transmission in the Solomon Archipelago, a region where Anopheles farauti is the only common malaria vector. Due to the evolution of behavioural resistance in some An. farauti populations, these applications have become less effective. New malaria control interventions are therefore needed in this region, and gene-drives provide a promising new technology. In considering developing a population-specific (local) gene-drive in An. farauti, we detail the species' population genetic structure using microsatellites and whole mitogenomes, finding many spatially confined populations both within and between landmasses. This strong population structure suggests that An. farauti would be a useful system for developing a population-specific, confinable gene-drive for field release, where private alleles can be used as Cas9 targets. Previous work on Anopheles gambiae has used the Cardinal gene for the development of a global population replacement gene-drive. We therefore also analyse the Cardinal gene to assess whether it may be a suitable target to engineer a gene-drive for the modification of local An. farauti populations. Despite the extensive population structure observed in An. farauti for microsatellites, only one remote island population from Vanuatu contained fixed and private alleles at the Cardinal locus. Nonetheless, this study provides an initial framework for further population genomic investigations to discover high-frequency private allele targets in localized An. farauti populations. This would enable the development of gene-drive strains for modifying localised populations with minimal chance of escape and may provide a low-risk route to field trial evaluations.
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Affiliation(s)
- Luke Ambrose
- School of the Environment, University of Queensland, St Lucia, Brisbane, QLD, Australia.
| | - Scott L Allen
- School of the Environment, University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Charlie Iro'ofa
- Solomon Islands Ministry of Health, Honiara, Guadalcanal, Solomon Islands
| | - Charles Butafa
- Solomon Islands Ministry of Health, Honiara, Guadalcanal, Solomon Islands
| | - Nigel W Beebe
- School of the Environment, University of Queensland, St Lucia, Brisbane, QLD, Australia.
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7
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Dong Y, Xu X, Qian L, Kou Z, Andongma AA, Zhou L, Huang Y, Wang Y. Genome-wide identification of yellow gene family in Hermetia illucens and functional analysis of yellow-y by CRISPR/Cas9. INSECT SCIENCE 2024. [PMID: 38685755 DOI: 10.1111/1744-7917.13371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 05/02/2024]
Abstract
The yellow gene family plays a crucial role in insect pigmentation. It has potential for use as a visible marker gene in genetic manipulation and transgenic engineering in several model and non-model insects. Sadly, yellow genes have rarely been identified in Stratiomyidae species and the functions of yellow genes are relatively unknown. In the present study, we first manually annotated and curated 10 yellow genes in the black soldier fly (BSF), Hermetia illucens (Stratiomyidae). Then, the conserved amino acids in the major royal jelly proteins (MRJPs) domain, structural architecture and phylogenetic relationship of yellow genes in BSF were analyzed. We found that the BSF yellow-y, yellow-c and yellow-f genes are expressed at all developmental stages, especially in the prepupal stage. Using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, we successfully disrupted yellow-y, yellow-c and yellow-f in the BSF. Consequently, the mutation of yellow-y clearly resulted in a pale-yellow body color in prepupae, pupae and adults, instead of the typical black body color of the wild type. However, the mutation of yellow-c or yellow-f genes did not result in any change in color of the insects, when compared with the wild type. Our study indicates that the BSF yellow-y gene plays a role in body pigmentation, providing an optimal marker gene for the genetic manipulation of BSF.
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Affiliation(s)
- Yongcheng Dong
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Xiaomiao Xu
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Lansa Qian
- Chinese Academy of Sciences (CAS) Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, CAS, Shanghai, China
| | - Zongqing Kou
- Chinese Academy of Sciences (CAS) Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, CAS, Shanghai, China
| | - Awawing A Andongma
- Insect and Parasite Ecology Group, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Lijun Zhou
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yongping Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yaohui Wang
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, College of Plant Protection, Anhui Agricultural University, Hefei, China
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D'Amato R, Taxiarchi C, Galardini M, Trusso A, Minuz RL, Grilli S, Somerville AGT, Shittu D, Khalil AS, Galizi R, Crisanti A, Simoni A, Müller R. Anti-CRISPR Anopheles mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages. Nat Commun 2024; 15:952. [PMID: 38296981 PMCID: PMC10830555 DOI: 10.1038/s41467-024-44907-x] [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: 04/18/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
CRISPR-based gene drives have the potential to spread within populations and are considered as promising vector control tools. A doublesex-targeting gene drive was able to suppress laboratory Anopheles mosquito populations in small and large cages, and it is considered for field application. Challenges related to the field-use of gene drives and the evolving regulatory framework suggest that systems able to modulate or revert the action of gene drives, could be part of post-release risk-mitigation plans. In this study, we challenge an AcrIIA4-based anti-drive to inhibit gene drive spread in age-structured Anopheles gambiae population under complex feeding and behavioural conditions. A stochastic model predicts the experimentally-observed genotype dynamics in age-structured populations in medium-sized cages and highlights the necessity of large-sized cage trials. These experiments and experimental-modelling framework demonstrate the effectiveness of the anti-drive in different scenarios, providing further corroboration for its use in controlling the spread of gene drive in Anopheles.
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Affiliation(s)
- Rocco D'Amato
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy
| | | | - Marco Galardini
- Biological Design Center, Boston University, Boston, MA, USA
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - Alessandro Trusso
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy
| | - Roxana L Minuz
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy
| | - Silvia Grilli
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Dammy Shittu
- Department of Life Sciences, Imperial College London, London, UK
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, UK
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alekos Simoni
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
| | - Ruth Müller
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy.
- Unit of Entomology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
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9
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Gebhardt CM, Niopek D. Anti-CRISPR Proteins and Their Application to Control CRISPR Effectors in Mammalian Systems. Methods Mol Biol 2024; 2774:205-231. [PMID: 38441767 DOI: 10.1007/978-1-0716-3718-0_14] [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] [Indexed: 03/07/2024]
Abstract
CRISPR-Cas effectors are powerful tools for genome and transcriptome targeting and editing. Naturally, these protein-RNA complexes are part of the microbial innate immune system, which emerged from the evolutionary arms race between microbes and phages. This coevolution has also given rise to so-called anti-CRISPR (Acr) proteins that counteract the CRISPR-Cas adaptive immunity. Acrs constitutively block cognate CRISPR-Cas effectors, e.g., by interfering with guide RNA binding, target DNA/RNA recognition, or target cleavage. In addition to their important role in microbiology and evolution, Acrs have recently gained particular attention for being useful tools and switches to regulate or fine-tune the activity of CRISPR-Cas effectors. Due to their commonly small size, high inhibition potency, and structural and mechanistic versatility, Acrs offer a wide range of potential applications for controlling CRISPR effectors in heterologous systems, including mammalian cells.Here, we review the diverse applications of Acrs in mammalian cells and organisms and discuss the underlying engineering strategies. These applications include (i) persistent blockage of CRISPR-Cas function to create write-protected cells, (ii) reduction of CRISPR-Cas off-target editing, (iii) focusing CRISPR-Cas activity to specific cell types and tissues, (iv) spatiotemporal control of CRISPR effectors based on engineered, opto-, or chemogenetic Acrs, and (v) the use of Acrs for selective binding and detection of CRISPR-Cas effectors in complex samples. We will also highlight potential future applications of Acrs in a biomedical context and point out present challenges that need to be overcome on the way.
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Affiliation(s)
- Carolin Maja Gebhardt
- Centre for Synthetic Biology, Department of Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Dominik Niopek
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Faculty of Engineering Sciences, Heidelberg University, Heidelberg, Germany.
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10
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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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11
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Chennuri PR, Zapletal J, Monfardini RD, Ndeffo-Mbah ML, Adelman ZN, Myles KM. Repeat mediated excision of gene drive elements for restoring wild-type populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.23.568397. [PMID: 38045402 PMCID: PMC10690251 DOI: 10.1101/2023.11.23.568397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
We demonstrate here that single strand annealing (SSA) repair can be co-opted for the precise autocatalytic excision of a drive element. Although SSA is not the predominant form of DNA repair in eukaryotic organisms, we increased the likelihood of its use by engineering direct repeats at sites flanking the drive allele, and then introducing a double-strand DNA break (DSB) at a second endonuclease target site encoded within the drive allele. We have termed this technology Re peat M ediated E xcision of a D rive E lement (ReMEDE). Incorporation of ReMEDE into the previously described mutagenic chain reaction (MCR) gene drive, targeting the yellow gene of Drosophila melanogaster , replaced drive alleles with wild-type alleles demonstrating proof-of-principle. Although the ReMEDE system requires further research and development, the technology has a number of attractive features as a gene drive mitigation strategy, chief among these the potential to restore a wild-type population without releasing additional transgenic organisms or large-scale environmental engineering efforts.
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12
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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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13
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Du S, Tong X, Lai ACK, Chan CK, Mason CE, Lee PKH. Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution. Nat Commun 2023; 14:2676. [PMID: 37160974 PMCID: PMC10169181 DOI: 10.1038/s41467-023-38400-0] [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: 11/02/2022] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
Viruses in built environments (BEs) raise public health concerns, yet they are generally less studied than bacteria. To better understand viral dynamics in BEs, this study assesses viromes from 11 habitats across four types of BEs with low to high occupancy. The diversity, composition, metabolic functions, and lifestyles of the viromes are found to be habitat dependent. Caudoviricetes species are ubiquitous on surface habitats in the BEs, and some of them are distinct from those present in other environments. Antimicrobial resistance genes are identified in viruses inhabiting surfaces frequently touched by occupants and in viruses inhabiting occupants' skin. Diverse CRISPR/Cas immunity systems and anti-CRISPR proteins are found in bacterial hosts and viruses, respectively, consistent with the strongly coupled virus-host links. Evidence of viruses potentially aiding host adaptation in a specific-habitat manner is identified through a unique gene insertion. This work illustrates that virus-host interactions occur frequently in BEs and that viruses are integral members of BE microbiomes.
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Affiliation(s)
- Shicong Du
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, P. R. China
| | - Alvin C K Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Chak K Chan
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
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14
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Kraus C, Sontheimer EJ. Applications of Anti-CRISPR Proteins in Genome Editing and Biotechnology. J Mol Biol 2023; 435:168120. [PMID: 37100169 DOI: 10.1016/j.jmb.2023.168120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
In the ten years since the discovery of the first anti-CRISPR (Acr) proteins, the number of validated Acrs has expanded rapidly, as has our understanding of the diverse mechanisms they employ to suppress natural CRISPR-Cas immunity. Many, though not all, function via direct, specific interaction with Cas protein effectors. The abilities of Acr proteins to modulate the activities and properties of CRISPR-Cas effectors have been exploited for an ever-increasing spectrum of biotechnological uses, most of which involve the establishment of control over genome editing systems. This control can be used to minimize off-target editing, restrict editing based on spatial, temporal, or conditional cues, limit the spread of gene drive systems, and select for genome-edited bacteriophages. Anti-CRISPRs have also been developed to overcome bacterial immunity, facilitate viral vector production, control synthetic gene circuits, and other purposes. The impressive and ever-growing diversity of Acr inhibitory mechanisms will continue to allow the tailored applications of Acrs.
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Affiliation(s)
| | - Erik J Sontheimer
- RNA Therapeutics Institute; Program in Molecular Medicine, and; Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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15
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Nourani L, Mehrizi AA, Pirahmadi S, Pourhashem Z, Asadollahi E, Jahangiri B. CRISPR/Cas advancements for genome editing, diagnosis, therapeutics, and vaccine development for Plasmodium parasites, and genetic engineering of Anopheles mosquito vector. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 109:105419. [PMID: 36842543 DOI: 10.1016/j.meegid.2023.105419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/30/2023] [Accepted: 02/21/2023] [Indexed: 02/28/2023]
Abstract
Malaria as vector-borne disease remains important health concern with over 200 million cases globally. Novel antimalarial medicines and more effective vaccines must be developed to eliminate and eradicate malaria. Appraisal of preceding genome editing approaches confirmed the CRISPR/Cas nuclease system as a novel proficient genome editing system and a tool for species-specific diagnosis, and drug resistance researches for Plasmodium species, and gene drive to control Anopheles population. CRISPR/Cas technology, as a handy tool for genome editing can be justified for the production of transgenic malaria parasites like Plasmodium transgenic lines expressing Cas9, chimeric Plasmodium transgenic lines, knockdown and knockout transgenic parasites, and transgenic parasites expressing alternative alleles, and also mutant strains of Anopheles such as only male mosquito populations, generation of wingless mosquitoes, and creation of knock-out/ knock-in mutants. Though, the incorporation of traditional methods and novel molecular techniques could noticeably enhance the quality of results. The striking development of a CRISPR/Cas-based diagnostic kit that can specifically diagnose the Plasmodium species or drug resistance markers is highly required in malaria settings with affordable cost and high-speed detection. Furthermore, the advancement of genome modifications by CRISPR/Cas technologies resolves contemporary restrictions to culturing, maintaining, and analyzing these parasites, and the aptitude to investigate parasite genome functions opens up new vistas in the better understanding of pathogenesis.
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Affiliation(s)
- Leila Nourani
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Akram Abouie Mehrizi
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Sakineh Pirahmadi
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Zeinab Pourhashem
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Elahe Asadollahi
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Babak Jahangiri
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
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16
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Marino ND. Phage Against the Machine: Discovery and Mechanism of Type V Anti-CRISPRs. J Mol Biol 2023; 435:168054. [PMID: 36934807 DOI: 10.1016/j.jmb.2023.168054] [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: 12/14/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
The discovery of diverse bacterial CRISPR-Cas systems has reignited interest in understanding bacterial defense pathways while yielding exciting new tools for genome editing. CRISPR-Cas systems are widely distributed in prokaryotes, found in 40% of bacteria and 90% of archaea, where they function as adaptive immune systems against bacterial viruses (phage) and other mobile genetic elements. In turn, phage have evolved inhibitors, called anti-CRISPR proteins, to prevent targeting. Type V CRISPR-Cas12 systems have emerged as a particularly exciting arena in this co-evolutionary arms race. Type V anti-CRISPRs have highly diverse and novel mechanisms of action, some of which appear to be unusually potent or widespread. In this review, we discuss the discovery and mechanism of these anti-CRISPRs as well as future areas for exploration.
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Affiliation(s)
- Nicole D Marino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
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17
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Hwang S, Maxwell KL. Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins. J Mol Biol 2023; 435:168041. [PMID: 36893938 DOI: 10.1016/j.jmb.2023.168041] [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: 12/13/2022] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) systems provide bacteria and archaea with an adaptive immune response against invasion by mobile genetic elements like phages, plasmids, and transposons. These systems have been repurposed as very powerful biotechnological tools for gene editing applications in both bacterial and eukaryotic systems. The discovery of natural off-switches for CRISPR-Cas systems, known as anti-CRISPR proteins, provided a mechanism for controlling CRISPR-Cas activity and opened avenues for the development of more precise editing tools. In this review, we focus on the inhibitory mechanisms of anti-CRISPRs that are active against type II CRISPR-Cas systems and briefly discuss their biotechnological applications.
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Affiliation(s)
- Sungwon Hwang
- Department of Biochemistry. University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON M5G 1M1, Canada. https://twitter.com/s1hwang_21
| | - Karen L Maxwell
- Department of Biochemistry. University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON M5G 1M1, Canada.
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18
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Contreras B, Adelman ZN, Chae K. Evaluating the Mating Competency of Genetically Modified Male Mosquitoes in Laboratory Conditions. FRONTIERS IN TROPICAL DISEASES 2023; 4:1106671. [PMID: 37860147 PMCID: PMC10586724 DOI: 10.3389/fitd.2023.1106671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023] Open
Abstract
Efforts to eradicate mosquito-borne diseases have increased the demand for genetic control strategies, many of which involve the release of genetically modified (GM) mosquito males into natural populations. The first hurdle for GM males is to compete with their wild-type counterparts for access to females. Here, we introduce an eye color-based mating assay, in which both Lvp wild-type and kynurenine 3-monooxygenase (kmo)-null males compete for access to kmo-null females, and therefore the eye color phenotype (black or white) of the progeny is dependent on the parental mating pair. A series of tests addressed that male mating competitiveness between the two strains can significantly be influenced by adult density, light intensity, and mating duration. Interestingly, the mating competitiveness of males was not correlated with body size, which was negatively influenced by a high larval density. Lastly, this eye color-associated assay was applied to characterize GM mosquitoes in their mating competitiveness, establishing this method as a fast and precise way of benchmarking this fitness parameter for laboratory-raised males.
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Affiliation(s)
- Bryan Contreras
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Zach N. Adelman
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Keun Chae
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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19
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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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20
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Dong M, Liu J, Liu C, Wang H, Sun W, Liu B. CRISPR/CAS9: A promising approach for the research and treatment of cardiovascular diseases. Pharmacol Res 2022; 185:106480. [PMID: 36191879 DOI: 10.1016/j.phrs.2022.106480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 10/31/2022]
Abstract
The development of gene-editing technology has been one of the biggest advances in biomedicine over the past two decades. Not only can it be used as a research tool to build a variety of disease models for the exploration of disease pathogenesis at the genetic level, it can also be used for prevention and treatment. This is done by intervening with the expression of target genes and carrying out precise molecular targeted therapy for diseases. The simple and flexible clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene-editing technology overcomes the limitations of zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). For this reason, it has rapidly become a preferred method for gene editing. As a new gene intervention method, CRISPR/Cas9 has been widely used in the clinical treatment of tumours and rare diseases; however, its application in the field of cardiovascular diseases is currently limited. This article reviews the application of the CRISPR/Cas9 editing technology in cardiovascular disease research and treatment, and discusses the limitations and prospects of this technology.
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Affiliation(s)
- Mengying Dong
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041
| | - Jiangen Liu
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041
| | - Caixia Liu
- Department of Neurology, The Liaoning Province People's Hospital, 33 Wenyi Road, ShenYang, China, 110016
| | - He Wang
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041
| | - Wei Sun
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041.
| | - Bin Liu
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041.
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21
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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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22
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Chennuri PR, Adelman ZN, Myles KM. Genetic Approaches for Controlling CRISPR-based Autonomous Homing Gene Drives. Front Bioeng Biotechnol 2022; 10:897231. [PMID: 35782500 PMCID: PMC9240394 DOI: 10.3389/fbioe.2022.897231] [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: 03/15/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR-based autonomous homing gene drives are a potentially transformative technology with the power to reduce the prevalence of, or even eliminate, vector-borne diseases, agricultural pests, and invasive species. However, there are a number of regulatory, ethical, environmental, and sociopolitical concerns surrounding the potential use of gene drives, particularly regarding the possibility for any unintended outcomes that might result from such a powerful technology. Therefore, there is an imminent need for countermeasures or technologies capable of exerting precise spatiotemporal control of gene drives, if their transformative potential is ever to be fully realized. This review summarizes the current state of the art in the development of technologies to prevent the uncontrolled spread of CRISPR-based autonomous homing gene drives.
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23
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Abstract
Insects have evolved highly diverse genetic sex-determination mechanisms and a relatively balanced male to female sex ratio is generally expected. However, selection may shift the optimal sex ratio while meiotic drive and endosymbiont manipulation can result in sex ratio distortion (SRD). Recent advances in sex chromosome genomics and CRISPR/Cas9-mediated genome editing brought significant insights into the molecular regulators of sex determination in an increasing number of insects and provided new ways to engineer SRD. We review these advances and discuss both naturally occurring and engineered SRD in the context of the Anthropocene. We emphasize SRD-mediated biological control of insects to help improve One Health, sustain agriculture, and conserve endangered species.
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Affiliation(s)
- Austin Compton
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Zhijian Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
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24
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Yang E, Metzloff M, Langmüller AM, Xu X, Clark AG, Messer PW, Champer J. A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance alleles. G3 (BETHESDA, MD.) 2022; 12:jkac081. [PMID: 35394026 PMCID: PMC9157102 DOI: 10.1093/g3journal/jkac081] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/30/2022] [Indexed: 11/14/2022]
Abstract
Gene drives are engineered alleles that can bias inheritance in their favor, allowing them to spread throughout a population. They could potentially be used to modify or suppress pest populations, such as mosquitoes that spread diseases. CRISPR/Cas9 homing drives, which copy themselves by homology-directed repair in drive/wild-type heterozygotes, are a powerful form of gene drive, but they are vulnerable to resistance alleles that preserve the function of their target gene. Such resistance alleles can prevent successful population suppression. Here, we constructed a homing suppression drive in Drosophila melanogaster that utilized multiplexed gRNAs to inhibit the formation of functional resistance alleles in its female fertility target gene. The selected gRNA target sites were close together, preventing reduction in drive conversion efficiency. The construct reached a moderate equilibrium frequency in cage populations without apparent formation of resistance alleles. However, a moderate fitness cost prevented elimination of the cage population, showing the importance of using highly efficient drives in a suppression strategy, even if resistance can be addressed. Nevertheless, our results experimentally demonstrate the viability of the multiplexed gRNAs strategy in homing suppression gene drives.
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Affiliation(s)
- Emily Yang
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Matthew Metzloff
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Anna M Langmüller
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
- Vienna Graduate School of Population Genetics, 1210 Wien, Austria
| | - Xuejiao Xu
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jackson Champer
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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25
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Chae K, Dawson C, Valentin C, Contreras B, Zapletal J, Myles KM, Adelman ZN. Engineering a self-eliminating transgene in the yellow fever mosquito, Aedes aegypti. PNAS NEXUS 2022; 1:pgac037. [PMID: 36713320 PMCID: PMC9802104 DOI: 10.1093/pnasnexus/pgac037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023]
Abstract
Promising genetics-based approaches are being developed to reduce or prevent the transmission of mosquito-vectored diseases. Less clear is how such transgenes can be removed from the environment, a concern that is particularly relevant for highly invasive gene drive transgenes. Here, we lay the groundwork for a transgene removal system based on single-strand annealing (SSA), a eukaryotic DNA repair mechanism. An SSA-based rescuer strain (kmoRG ) was engineered to have direct repeat sequences (DRs) in the Aedes aegypti kynurenine 3-monooxygenase (kmo) gene flanking the intervening transgenic cargo genes, DsRED and EGFP. Targeted induction of DNA double-strand breaks (DSBs) in the DsRED transgene successfully triggered complete elimination of the entire cargo from the kmoRG strain, restoring the wild-type kmo gene, and thereby, normal eye pigmentation. Our work establishes the framework for strategies to remove transgene sequences during the evaluation and testing of modified strains for genetics-based mosquito control.
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Affiliation(s)
- Keun Chae
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Chanell Dawson
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Collin Valentin
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Bryan Contreras
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Josef Zapletal
- Department of Industrial and Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Kevin M Myles
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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26
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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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27
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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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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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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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St. Leger RJ. From the Lab to the Last Mile: Deploying Transgenic Approaches Against Mosquitoes. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.804066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ingenious exploitation of transgenic approaches to produce malaria resistant or sterile mosquitoes, or hypervirulent mosquito pathogens, has produced many potential solutions to vector borne diseases. However, in spite of technological feasibility, it has not been determined how well these new methods will work, and how they should be tested and regulated. Some self-limiting transgenic fungal pathogens and mosquitoes are almost field ready, and may be easier to regulate than self-sustaining strategies. However, they require repeat sales and so must show business viability; low-cost mass production is just one of a number of technical constraints that are sometimes treated as an afterthought in technology deployment. No transgenic self-sustaining approach to anopheline control has ever been deployed because of unresolved ethical, social and regulatory issues. These overlapping issues include: 1) the transparency challenge, which requires public discourse, particularly in Africa where releases are proposed, to determine what society is willing to risk given the potential benefits; 2) the transboundary challenge, self-sustaining mosquitoes or pathogens are potentially capable of crossing national boundaries and irreversibly altering ecosystems, and 3) the risk assessment challenge. The polarized debate as to whether these technologies will ever be used to save lives is ongoing; they will founder without a political answer as to how do we interpret the precautionary principle, as exemplified in the Cartagena protocol, in the global context of technological changes.
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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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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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