1
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Johnson ML, Hay BA, Maselko M. Altering traits and fates of wild populations with Mendelian DNA sequence modifying Allele Sails. Nat Commun 2024; 15:6665. [PMID: 39138152 PMCID: PMC11322531 DOI: 10.1038/s41467-024-50992-9] [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: 04/05/2024] [Accepted: 07/26/2024] [Indexed: 08/15/2024] Open
Abstract
Population-scale genome modification can alter the composition or fate of wild populations. Synthetic gene drives provide one set of tools, but their use is complicated by scientific, regulatory, and social issues associated with transgene persistence and flow. Here we propose an alternative approach. An Allele Sail consists of a genome editor (the Wind) that introduces DNA sequence edits, and is inherited in a Mendelian fashion. Meanwhile, the edits (the Sail) experience an arithmetic, Super-Mendelian increase in frequency. We model this system and identify contexts in which a single, low frequency release of an editor brings edits to a very high frequency. We also identify conditions in which manipulation of sex determination can bring about population suppression. In regulatory frameworks that distinguish between transgenics (GMO) and their edited non-transgenic progeny (non-GMO) Allele Sails may prove useful since the spread and persistence of the GM component can be limited.
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Affiliation(s)
- Michelle L Johnson
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, MC156-29, Pasadena, CA, 91125, USA
| | - Bruce A Hay
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, MC156-29, Pasadena, CA, 91125, USA.
| | - Maciej Maselko
- Applied BioSciences, Macquarie University, North Ryde, NSW, 2109, Australia.
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2
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Collier TC, Lee Y, Mathias DK, López Del Amo V. CRISPR-Cas9 and Cas12a target site richness reflects genomic diversity in natural populations of Anopheles gambiae and Aedes aegypti mosquitoes. BMC Genomics 2024; 25:700. [PMID: 39020310 PMCID: PMC11253549 DOI: 10.1186/s12864-024-10597-4] [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: 05/28/2024] [Accepted: 07/04/2024] [Indexed: 07/19/2024] Open
Abstract
Due to limitations in conventional disease vector control strategies including the rise of insecticide resistance in natural populations of mosquitoes, genetic control strategies using CRISPR gene drive systems have been under serious consideration. The identification of CRISPR target sites in mosquito populations is a key aspect for developing efficient genetic vector control strategies. While genome-wide Cas9 target sites have been explored in mosquitoes, a precise evaluation of target sites focused on coding sequence (CDS) is lacking. Additionally, target site polymorphisms have not been characterized for other nucleases such as Cas12a, which require a different DNA recognition site (PAM) and would expand the accessibility of mosquito genomes for genetic engineering. We undertook a comprehensive analysis of potential target sites for both Cas9 and Cas12a nucleases within the genomes of natural populations of Anopheles gambiae and Aedes aegypti from multiple continents. We demonstrate that using two nucleases increases the number of targets per gene. Also, we identified differences in nucleotide diversity between North American and African Aedes populations, impacting the abundance of good target sites with a minimal degree of polymorphisms that can affect the binding of gRNA. Lastly, we screened for gRNAs targeting sex-determination genes that could be widely applicable for developing field genetic control strategies. Overall, this work highlights the utility of employing both Cas9 and Cas12a nucleases and underscores the importance of designing universal genetic strategies adaptable to diverse mosquito populations.
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Affiliation(s)
| | - Yoosook Lee
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32962, USA
| | - Derrick K Mathias
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32962, USA
| | - Víctor López Del Amo
- Center for Infectious Diseases, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, 77030, USA.
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3
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Adedeji EO, Beder T, Damiani C, Cappelli A, Accoti A, Tapanelli S, Ogunlana OO, Fatumo S, Favia G, Koenig R, Adebiyi E. Combination of computational techniques and RNAi reveal targets in Anopheles gambiae for malaria vector control. PLoS One 2024; 19:e0305207. [PMID: 38968330 PMCID: PMC11226046 DOI: 10.1371/journal.pone.0305207] [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: 01/05/2024] [Accepted: 05/25/2024] [Indexed: 07/07/2024] Open
Abstract
Increasing reports of insecticide resistance continue to hamper the gains of vector control strategies in curbing malaria transmission. This makes identifying new insecticide targets or alternative vector control strategies necessary. CLassifier of Essentiality AcRoss EukaRyote (CLEARER), a leave-one-organism-out cross-validation machine learning classifier for essential genes, was used to predict essential genes in Anopheles gambiae and selected predicted genes experimentally validated. The CLEARER algorithm was trained on six model organisms: Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Saccharomyces cerevisiae and Schizosaccharomyces pombe, and employed to identify essential genes in An. gambiae. Of the 10,426 genes in An. gambiae, 1,946 genes (18.7%) were predicted to be Cellular Essential Genes (CEGs), 1716 (16.5%) to be Organism Essential Genes (OEGs), and 852 genes (8.2%) to be essential as both OEGs and CEGs. RNA interference (RNAi) was used to validate the top three highly expressed non-ribosomal predictions as probable vector control targets, by determining the effect of these genes on the survival of An. gambiae G3 mosquitoes. In addition, the effect of knockdown of arginase (AGAP008783) on Plasmodium berghei infection in mosquitoes was evaluated, an enzyme we computationally inferred earlier to be essential based on chokepoint analysis. Arginase and the top three genes, AGAP007406 (Elongation factor 1-alpha, Elf1), AGAP002076 (Heat shock 70kDa protein 1/8, HSP), AGAP009441 (Elongation factor 2, Elf2), had knockdown efficiencies of 91%, 75%, 63%, and 61%, respectively. While knockdown of HSP or Elf2 significantly reduced longevity of the mosquitoes (p<0.0001) compared to control groups, Elf1 or arginase knockdown had no effect on survival. However, arginase knockdown significantly reduced P. berghei oocytes counts in the midgut of mosquitoes when compared to LacZ-injected controls. The study reveals HSP and Elf2 as important contributors to mosquito survival and arginase as important for parasite development, hence placing them as possible targets for vector control.
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Affiliation(s)
- Eunice O. Adedeji
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Biochemistry, Covenant University, Ota, Ogun State, Nigeria
- School of Biosciences & Veterinary Medicine, University of Camerino, Camerino, Italy
- Department of Biology, University of York, York, United Kingdom
| | - Thomas Beder
- Medical Department II, Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein, University Medical Center Schleswig-Holstein, Kiel and Lübeck, Germany
- Institute for Infectious Diseases and Infection Control (IIMK, RG Systemsbiology), Jena University Hospital, Jena, Germany
| | - Claudia Damiani
- School of Biosciences & Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Alessia Cappelli
- School of Biosciences & Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Anastasia Accoti
- School of Biosciences & Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sofia Tapanelli
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Olubanke O. Ogunlana
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Biochemistry, Covenant University, Ota, Ogun State, Nigeria
- African Center of Excellence in Bioinformatics & Data Intensive Science, Makerere University, Kampala, Uganda
| | - Segun Fatumo
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Guido Favia
- School of Biosciences & Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Rainer Koenig
- Institute for Infectious Diseases and Infection Control (IIMK, RG Systemsbiology), Jena University Hospital, Jena, Germany
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- African Center of Excellence in Bioinformatics & Data Intensive Science, Makerere University, Kampala, Uganda
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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4
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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; 10:936-953. [PMID: 38886522 DOI: 10.1038/s41477-024-01701-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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5
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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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6
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.13.562303. [PMID: 37873352 PMCID: PMC10592828 DOI: 10.1101/2023.10.13.562303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Gene drive elements promote the spread of linked traits, even when their presence confers a fitness cost to carriers, 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 (the Cleaver/Toxin) that disrupts endogenous versions of an essential gene, and a recoded version of the essential gene resistant to cleavage (the Rescue/Antidote). ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. We demonstrate the essential features of ClvR gene drive in the plant Arabidopsis thaliana through killing of gametes that fail to inherit a ClvR that targets the essential gene YKT61, whose expression is required in male and female gametes for their survival. Resistant (uncleavable but functional) alleles, which can slow or prevent drive, were not observed. Modeling shows plant ClvRs are likely to be robust to certain failure modes and can be used to rapidly drive population modification or suppression. Possible applications in plant breeding, weed control, and conservation are discussed.
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Affiliation(s)
- Georg Oberhofer
- California Institute of Technology. Division of Biology and Biological Engineering. 1200 East California Boulevard, MC156-29, Pasadena, CA 91125
| | - Michelle L. Johnson
- California Institute of Technology. Division of Biology and Biological Engineering. 1200 East California Boulevard, MC156-29, Pasadena, CA 91125
| | - Tobin Ivy
- California Institute of Technology. Division of Biology and Biological Engineering. 1200 East California Boulevard, MC156-29, Pasadena, CA 91125
| | - Igor Antoshechkin
- California Institute of Technology. Division of Biology and Biological Engineering. 1200 East California Boulevard, MC156-29, Pasadena, CA 91125
| | - Bruce A. Hay
- California Institute of Technology. Division of Biology and Biological Engineering. 1200 East California Boulevard, MC156-29, Pasadena, CA 91125
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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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Pan M, Champer J. Making waves: Comparative analysis of gene drive spread characteristics in a continuous space model. Mol Ecol 2023; 32:5673-5694. [PMID: 37694511 DOI: 10.1111/mec.17131] [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: 11/11/2022] [Revised: 08/16/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023]
Abstract
With their ability to rapidly increase in frequency, gene drives can be used to modify or suppress target populations after an initial release of drive individuals. Recent advances have revealed many possibilities for different types of drives, and several of these have been realized in experiments. These drives have advantages and disadvantages related to their ease of construction, confinement and capacity to be used for modification or suppression. Though characteristics of these drives have been explored in modelling studies, assessment in continuous space environments has been limited, often focusing on outcomes rather than fundamental properties. Here, we conduct a comparative analysis of many different gene drive types that have the capacity to form a wave of advance in continuous space using individual-based simulations in continuous space. We evaluate the drive wave speed as a function of drive performance and ecological parameters, which reveals substantial differences between drive performance in panmictic versus spatial environments. In particular, we find that suppression drive waves are uniquely vulnerable to fitness costs and undesired CRISPR cleavage activity in embryos by maternal deposition. Some drives, however, retain robust performance even with widely varying efficiency parameters. To gain a better understanding of drive waves, we compare their panmictic performance and find that the rate of wild-type allele removal is correlated with drive wave speed, though this is also affected by other factors. Overall, our results provide a useful resource for understanding the performance of drives in spatially continuous environments, which may be most representative of potential drive deployment in many relevant scenarios.
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Affiliation(s)
- Mingzuyu Pan
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
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9
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Auradkar A, Guichard A, Kaduwal S, Sneider M, Bier E. tgCRISPRi: efficient gene knock-down using truncated gRNAs and catalytically active Cas9. Nat Commun 2023; 14:5587. [PMID: 37696787 PMCID: PMC10495392 DOI: 10.1038/s41467-023-40836-3] [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: 03/09/2023] [Accepted: 08/14/2023] [Indexed: 09/13/2023] Open
Abstract
CRISPR-interference (CRISPRi), a highly effective method for silencing genes in mammalian cells, employs an enzymatically dead form of Cas9 (dCas9) complexed with one or more guide RNAs (gRNAs) with 20 nucleotides (nt) of complementarity to transcription initiation sites of target genes. Such gRNA/dCas9 complexes bind to DNA, impeding transcription of the targeted locus. Here, we present an alternative gene-suppression strategy using active Cas9 complexed with truncated gRNAs (tgRNAs). Cas9/tgRNA complexes bind to specific target sites without triggering DNA cleavage. When targeted near transcriptional start sites, these short 14-15 nts tgRNAs efficiently repress expression of several target genes throughout somatic tissues in Drosophila melanogaster without generating any detectable target site mutations. tgRNAs also can activate target gene expression when complexed with a Cas9-VPR fusion protein or modulate enhancer activity, and can be incorporated into a gene-drive, wherein a traditional gRNA sustains drive while a tgRNA inhibits target gene expression.
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Affiliation(s)
- Ankush Auradkar
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Annabel Guichard
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Saluja Kaduwal
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Marketta Sneider
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA.
- Tata Institute for Genetics and Society - UCSD, La Jolla, USA.
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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: 2] [Impact Index Per Article: 2.0] [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)
| | | | - Jackson Champer
- 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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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: 12] [Impact Index Per Article: 6.0] [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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13
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Ellis DA, Avraam G, Hoermann A, Wyer CAS, Ong YX, Christophides GK, Windbichler N. Testing non-autonomous antimalarial gene drive effectors using self-eliminating drivers in the African mosquito vector Anopheles gambiae. PLoS Genet 2022; 18:e1010244. [PMID: 35653396 PMCID: PMC9197043 DOI: 10.1371/journal.pgen.1010244] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/14/2022] [Accepted: 05/09/2022] [Indexed: 11/19/2022] Open
Abstract
Gene drives for mosquito population modification are novel tools for malaria control. Strategies to safely test antimalarial effectors in the field are required. Here, we modified the Anopheles gambiae zpg locus to host a CRISPR/Cas9 integral gene drive allele (zpgD) and characterized its behaviour and resistance profile. We found that zpgD dominantly sterilizes females but can induce efficient drive at other loci when it itself encounters resistance. We combined zpgD with multiple previously characterized non-autonomous payload drives and found that, as zpgD self-eliminates, it leads to conversion of mosquito cage populations at these loci. Our results demonstrate how self-eliminating drivers could allow safe testing of non-autonomous effector-traits by local population modification. They also suggest that after engendering resistance, gene drives intended for population suppression could nevertheless serve to propagate subsequently released non-autonomous payload genes, allowing modification of vector populations initially targeted for suppression. Gene drive is a method that allows the genetic modification of entire populations of harmful organisms. Their application to tackle invasive species, agricultural pests or insect disease vectors has been suggested. For example, they could reduce the capacity of malaria mosquitoes to transmit this deadly disease to humans by producing effector molecules inhibiting the development of the Plasmodium parasite in the mosquito vector. We describe a strategy to modularize and test multiple transgenes destined for release, and to introduce only the minimal set of modifications needed into a mosquito population. We show how some elements, once no longer needed, can be made to self-eliminate from populations and we also study how several independent gene drive traits, located in different parts of the genome, can interact and propagate at the level of mosquito cage populations.
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Affiliation(s)
- David A. Ellis
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - George Avraam
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Astrid Hoermann
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Claudia A. S. Wyer
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Yi Xin Ong
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
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14
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Metzloff M, Yang E, Dhole S, Clark AG, Messer PW, Champer J. Experimental demonstration of tethered gene drive systems for confined population modification or suppression. BMC Biol 2022; 20:119. [PMID: 35606745 PMCID: PMC9128227 DOI: 10.1186/s12915-022-01292-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Homing gene drives hold great promise for the genetic control of natural populations. However, current homing systems are capable of spreading uncontrollably between populations connected by even marginal levels of migration. This could represent a substantial sociopolitical barrier to the testing or deployment of such drives and may generally be undesirable when the objective is only local population control, such as suppression of an invasive species outside of its native range. Tethered drive systems, in which a locally confined gene drive provides the CRISPR nuclease needed for a homing drive, could provide a solution to this problem, offering the power of a homing drive and confinement of the supporting drive. RESULTS Here, we demonstrate the engineering of a tethered drive system in Drosophila, using a regionally confined CRISPR Toxin-Antidote Recessive Embryo (TARE) drive to support modification and suppression homing drives. Each drive was able to bias inheritance in its favor, and the TARE drive was shown to spread only when released above a threshold frequency in experimental cage populations. After the TARE drive had established in the population, it facilitated the spread of a subsequently released split homing modification drive (to all individuals in the cage) and of a homing suppression drive (to its equilibrium frequency). CONCLUSIONS Our results show that the tethered drive strategy is a viable and easily engineered option for providing confinement of homing drives to target populations.
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Affiliation(s)
- Matthew Metzloff
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Emily Yang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Sumit Dhole
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - 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.
- Present Address: Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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15
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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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16
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Liu Y, Champer J. Modelling homing suppression gene drive in haplodiploid organisms. Proc Biol Sci 2022; 289:20220320. [PMID: 35414240 PMCID: PMC9006016 DOI: 10.1098/rspb.2022.0320] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/21/2022] [Indexed: 01/13/2023] Open
Abstract
Gene drives have shown great promise for suppression of pest populations. These engineered alleles can function by a variety of mechanisms, but the most common is the CRISPR homing drive, which converts wild-type alleles to drive alleles in the germline of heterozygotes. Some potential target species are haplodiploid, in which males develop from unfertilized eggs and thus have only one copy of each chromosome. This prevents drive conversion, a substantial disadvantage compared to diploids where drive conversion can take place in both sexes. Here, we study homing suppression gene drives in haplodiploids and find that a drive targeting a female fertility gene could still be successful. However, such drives are less powerful than in diploids and suffer more from functional resistance alleles. They are substantially more vulnerable to high resistance allele formation in the embryo owing to maternally deposited Cas9 and guide RNA and also to somatic cleavage activity. Examining spatial models where organisms move over a continuous landscape, we find that haplodiploid suppression drives surprisingly perform nearly as well as in diploids, possibly owing to their ability to spread further before inducing strong suppression. Together, these results indicate that gene drive can potentially be used to effectively suppress haplodiploid populations.
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Affiliation(s)
- Yiran Liu
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 People's Republic of China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 People's Republic of China
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17
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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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18
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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: 7] [Impact Index Per Article: 3.5] [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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19
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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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20
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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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21
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Oberhofer G, Ivy T, Hay BA. Gene drive that results in addiction to a temperature-sensitive version of an essential gene triggers population collapse in Drosophila. Proc Natl Acad Sci U S A 2021; 118:e2107413118. [PMID: 34845012 PMCID: PMC8670509 DOI: 10.1073/pnas.2107413118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
One strategy for population suppression seeks to use gene drive to spread genes that confer conditional lethality or sterility, providing a way of combining population modification with suppression. Stimuli of potential interest could be introduced by humans, such as an otherwise benign virus or chemical, or occur naturally on a seasonal basis, such as a change in temperature. Cleave and Rescue (ClvR) selfish genetic elements use Cas9 and guide RNAs (gRNAs) to disrupt endogenous versions of an essential gene while also including a Rescue version of the essential gene resistant to disruption. ClvR spreads by creating loss-of-function alleles of the essential gene that select against those lacking it, resulting in populations in which the Rescue provides the only source of essential gene function. As a consequence, if function of the Rescue, a kind of Trojan horse now omnipresent in a population, is condition dependent, so too will be the survival of that population. To test this idea, we created a ClvR in Drosophila in which Rescue activity of an essential gene, dribble, requires splicing of a temperature-sensitive intein (TS-ClvRdbe ). This element spreads to transgene fixation at 23 °C, but when populations now dependent on Ts-ClvRdbe are shifted to 29 °C, death and sterility result in a rapid population crash. These results show that conditional population elimination can be achieved. A similar logic, in which Rescue activity is conditional, could also be used in homing-based drive and to bring about suppression and/or killing of specific individuals in response to other stimuli.
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Affiliation(s)
- Georg Oberhofer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Tobin Ivy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Bruce A Hay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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22
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Adelman ZN. Demystifying the Risk Assessment Process for Laboratory-Based Experiments Utilizing Invasive Genetic Elements: It Is More Than Gene Drive. APPLIED BIOSAFETY 2021; 26:154-163. [PMID: 36035544 PMCID: PMC9134331 DOI: 10.1089/apb.20.0074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Advances in recombinant DNA approaches have resulted in the development of transgene architectures that severely bias their own inheritance, a process commonly referred to as "gene drive." The rapid pace of development, combined with the complexity of many gene drive approaches, threatens to overwhelm those responsible for ensuring its safe use in the laboratory, as even identifying that a specific transgene is capable of gene drive may not be intuitive. Although currently gene drive experiments have been limited to just a few species (mosquitoes, flies, mice, and yeast), the range of organisms used in gene drive research is expected to increase substantially in the coming years. Here the defining features of different gene drive approaches are discussed. Although this will start with a focus on identifying when gene drive could or could not occur, the emphasis will also be on establishing risk profiles based on anticipated level of invasiveness and persistence of transgenes in the surrounding environment. Attention is also called to the fact that transgenes can be considered invasive without being considered gene drive (and vice versa). This further supports the notion that adequate risk assessment requires information regarding the specific circumstances a given transgene or set of transgenes is capable of invading a corresponding population. Finally, challenges in the review and evaluation of work involving gene drive organisms are discussed.
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Affiliation(s)
- Zach N. Adelman
- Department of Entomology and Agrilife Research, Texas A&M University, College Station, Texas, USA
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23
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Verma P, Reeves RG, Gokhale CS. A common gene drive language eases regulatory process and eco-evolutionary extensions. BMC Ecol Evol 2021; 21:156. [PMID: 34372763 PMCID: PMC8351217 DOI: 10.1186/s12862-021-01881-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 07/12/2021] [Indexed: 02/08/2023] Open
Abstract
Background Synthetic gene drive technologies aim to spread transgenic constructs into wild populations even when they impose organismal fitness disadvantages. The extraordinary diversity of plausible drive mechanisms and the range of selective parameters they may encounter makes it very difficult to convey their relative predicted properties, particularly where multiple approaches are combined. The sheer number of published manuscripts in this field, experimental and theoretical, the numerous techniques resulting in an explosion in the gene drive vocabulary hinder the regulators’ point of view. We address this concern by defining a simplified parameter based language of synthetic drives. Results Employing the classical population dynamics approach, we show that different drive construct (replacement) mechanisms can be condensed and evaluated on an equal footing even where they incorporate multiple replacement drives approaches. Using a common language, it is then possible to compare various model properties, a task desired by regulators and policymakers. The generalization allows us to extend the study of the invasion dynamics of replacement drives analytically and, in a spatial setting, the resilience of the released drive constructs. The derived framework is available as a standalone tool. Conclusion Besides comparing available drive constructs, our tool is also useful for educational purpose. Users can also explore the evolutionary dynamics of future hypothetical combination drive scenarios. Thus, our results appraise the properties and robustness of drives and provide an intuitive and objective way for risk assessment, informing policies, and enhancing public engagement with proposed and future gene drive approaches.
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Affiliation(s)
- Prateek Verma
- Research Group for Theoretical Models of Eco-evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - R Guy Reeves
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Chaitanya S Gokhale
- Research Group for Theoretical Models of Eco-evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
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24
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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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25
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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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26
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Hoermann A, Tapanelli S, Capriotti P, Del Corsano G, Masters EK, Habtewold T, Christophides GK, Windbichler N. Converting endogenous genes of the malaria mosquito into simple non-autonomous gene drives for population replacement. eLife 2021; 10:58791. [PMID: 33845943 PMCID: PMC8043746 DOI: 10.7554/elife.58791] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 03/21/2021] [Indexed: 12/15/2022] Open
Abstract
Gene drives for mosquito population replacement are promising tools for malaria control. However, there is currently no clear pathway for safely testing such tools in endemic countries. The lack of well-characterized promoters for infection-relevant tissues and regulatory hurdles are further obstacles for their design and use. Here we explore how minimal genetic modifications of endogenous mosquito genes can convert them directly into non-autonomous gene drives without disrupting their expression. We co-opted the native regulatory sequences of three midgut-specific loci of the malaria vector Anopheles gambiae to host a prototypical antimalarial molecule and guide-RNAs encoded within artificial introns that support efficient gene drive. We assess the propensity of these modifications to interfere with the development of Plasmodium falciparum and their effect on fitness. Because of their inherent simplicity and passive mode of drive such traits could form part of an acceptable testing pathway of gene drives for malaria eradication.
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Affiliation(s)
- Astrid Hoermann
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Sofia Tapanelli
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Paolo Capriotti
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Ellen Kg Masters
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tibebu Habtewold
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, London, United Kingdom
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27
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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: 29] [Impact Index Per Article: 9.7] [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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28
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Oberhofer G, Ivy T, Hay BA. Split versions of Cleave and Rescue selfish genetic elements for measured self limiting gene drive. PLoS Genet 2021; 17:e1009385. [PMID: 33600432 PMCID: PMC7951863 DOI: 10.1371/journal.pgen.1009385] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 03/11/2021] [Accepted: 01/28/2021] [Indexed: 12/26/2022] Open
Abstract
Gene drive elements promote the spread of linked traits, providing methods for changing the composition or fate of wild populations. Drive mechanisms that are self-limiting are attractive because they allow control over the duration and extent of trait spread in time and space, and are reversible through natural selection as drive wanes. Self-sustaining Cleave and Rescue (ClvR) elements include a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene, a tightly linked recoded version of the essential gene resistant to cleavage (the Rescue), and a Cargo. ClvR spreads by creating loss-of-function (LOF) conditions in which those without ClvR die because they lack functional copies of the essential gene. We use modeling to show that when the Rescue-Cargo and one or both components required for LOF allele creation (Cas9 and gRNA) reside at different locations (split ClvR), drive of Rescue-Cargo is self-limiting due to a progressive decrease in Cas9 frequency, and thus opportunities for creation of LOF alleles, as spread occurs. Importantly, drive strength and duration can be extended in a measured manner-which is still self-limiting-by moving the two components close enough to each other that they experience some degree of linkage. With linkage, Cas9 transiently experiences drive by hitchhiking with Rescue-Cargo until linkage disequilibrium between the two disappears, a function of recombination frequency and number of generations, creating a novel point of control. We implement split ClvR in Drosophila, with key elements on different chromosomes. Cargo/Rescue/gRNAs spreads to high frequency in a Cas9-dependent manner, while the frequency of Cas9 decreases. These observations show that measured, transient drive, coupled with a loss of future drive potential, can be achieved using the simple toolkit that make up ClvR elements-Cas9 and gRNAs and a Rescue/Cargo.
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Affiliation(s)
- Georg Oberhofer
- California Institute of Technology, Pasadena, California, United States of America
| | - Tobin Ivy
- California Institute of Technology, Pasadena, California, United States of America
| | - Bruce A. Hay
- California Institute of Technology, Pasadena, California, United States of America
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29
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Hay BA, Oberhofer G, Guo M. Engineering the Composition and Fate of Wild Populations with Gene Drive. ANNUAL REVIEW OF ENTOMOLOGY 2021; 66:407-434. [PMID: 33035437 DOI: 10.1146/annurev-ento-020117-043154] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Insects play important roles as predators, prey, pollinators, recyclers, hosts, parasitoids, and sources of economically important products. They can also destroy crops; wound animals; and serve as vectors for plant, animal, and human diseases. Gene drive-a process by which genes, gene complexes, or chromosomes encoding specific traits are made to spread through wild populations, even if these traits result in a fitness cost to carriers-provides new opportunities for altering populations to benefit humanity and the environment in ways that are species specific and sustainable. Gene drive can be used to alter the genetic composition of an existing population, referred to as population modification or replacement, or to bring about population suppression or elimination. We describe technologies under consideration, progress that has been made, and remaining technological hurdles, particularly with respect to evolutionary stability and our ability to control the spread and ultimate fate of genes introduced into populations.
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Affiliation(s)
- Bruce A Hay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA; ,
- St. John's College, University of Cambridge, Cambridge CB2 1TP, United Kingdom
| | - Georg Oberhofer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA; ,
| | - Ming Guo
- Departments of Neurology and Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA;
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30
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Naegeli H, Bresson J, Dalmay T, Dewhurst IC, Epstein MM, Guerche P, Hejatko J, Moreno FJ, Mullins E, Nogué F, Rostoks N, Sánchez Serrano JJ, Savoini G, Veromann E, Veronesi F, Bonsall MB, Mumford J, Wimmer EA, Devos Y, Paraskevopoulos K, Firbank LG. Adequacy and sufficiency evaluation of existing EFSA guidelines for the molecular characterisation, environmental risk assessment and post-market environmental monitoring of genetically modified insects containing engineered gene drives. EFSA J 2020; 18:e06297. [PMID: 33209154 PMCID: PMC7658669 DOI: 10.2903/j.efsa.2020.6297] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Advances in molecular and synthetic biology are enabling the engineering of gene drives in insects for disease vector/pest control. Engineered gene drives (that bias their own inheritance) can be designed either to suppress interbreeding target populations or modify them with a new genotype. Depending on the engineered gene drive system, theoretically, a genetic modification of interest could spread through target populations and persist indefinitely, or be restricted in its spread or persistence. While research on engineered gene drives and their applications in insects is advancing at a fast pace, it will take several years for technological developments to move to practical applications for deliberate release into the environment. Some gene drive modified insects (GDMIs) have been tested experimentally in the laboratory, but none has been assessed in small-scale confined field trials or in open release trials as yet. There is concern that the deliberate release of GDMIs in the environment may have possible irreversible and unintended consequences. As a proactive measure, the European Food Safety Authority (EFSA) has been requested by the European Commission to review whether its previously published guidelines for the risk assessment of genetically modified animals (EFSA, 2012 and 2013), including insects (GMIs), are adequate and sufficient for GDMIs, primarily disease vectors, agricultural pests and invasive species, for deliberate release into the environment. Under this mandate, EFSA was not requested to develop risk assessment guidelines for GDMIs. In this Scientific Opinion, the Panel on Genetically Modified Organisms (GMO) concludes that EFSA's guidelines are adequate, but insufficient for the molecular characterisation (MC), environmental risk assessment (ERA) and post-market environmental monitoring (PMEM) of GDMIs. While the MC,ERA and PMEM of GDMIs can build on the existing risk assessment framework for GMIs that do not contain engineered gene drives, there are specific areas where further guidance is needed for GDMIs.
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31
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Dhole S, Lloyd AL, Gould F. Gene Drive Dynamics in Natural Populations: The Importance of Density Dependence, Space, and Sex. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2020; 51:505-531. [PMID: 34366722 PMCID: PMC8340601 DOI: 10.1146/annurev-ecolsys-031120-101013] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The spread of synthetic gene drives is often discussed in the context of panmictic populations connected by gene flow and described with simple deterministic models. Under such assumptions, an entire species could be altered by releasing a single individual carrying an invasive gene drive, such as a standard homing drive. While this remains a theoretical possibility, gene drive spread in natural populations is more complex and merits a more realistic assessment. The fate of any gene drive released in a population would be inextricably linked to the population's ecology. Given the uncertainty often involved in ecological assessment of natural populations, understanding the sensitivity of gene drive spread to important ecological factors is critical. Here we review how different forms of density dependence, spatial heterogeneity, and mating behaviors can impact the spread of self-sustaining gene drives. We highlight specific aspects of gene drive dynamics and the target populations that need further research.
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Affiliation(s)
- Sumit Dhole
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Alun L Lloyd
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, North Carolina 27695-8213, USA
- Genetic Engineering and Society Center, North Carolina State University, Raleigh, North Carolina 27695-7565, USA
| | - Fred Gould
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695, USA
- Genetic Engineering and Society Center, North Carolina State University, Raleigh, North Carolina 27695-7565, USA
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