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Hou S, Chen J, Feng R, Xu X, Liang N, Champer J. A homing rescue gene drive with multiplexed gRNAs reaches high frequency in cage populations but generates functional resistance. J Genet Genomics 2024; 51:836-843. [PMID: 38599514 DOI: 10.1016/j.jgg.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
CRISPR homing gene drives have considerable potential for managing populations of medically and agriculturally significant insects. They operate by Cas9 cleavage followed by homology-directed repair, copying the drive allele to the wild-type chromosome and thus increasing in frequency and spreading throughout a population. However, resistance alleles formed by end-joining repair pose a significant obstacle. To address this, we create a homing drive targeting the essential hairy gene in Drosophila melanogaster. Nonfunctional resistance alleles are recessive lethal, while drive carriers have a recoded "rescue" version of hairy. The drive inheritance rate is moderate, and multigenerational cage studies show drive spread to 96%-97% of the population. However, the drive does not reach 100% due to the formation of functional resistance alleles despite using four gRNAs. These alleles have a large deletion but likely utilize an alternate start codon. Thus, revised designs targeting more essential regions of a gene may be necessary to avoid such functional resistance. Replacement of the rescue element's native 3' UTR with a homolog from another species increases drive inheritance by 13%-24%. This was possibly because of reduced homology between the rescue element and surrounding genomic DNA, which could also be an important design consideration for rescue gene drives.
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Affiliation(s)
- Shibo Hou
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jingheng Chen
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ruobing Feng
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuejiao Xu
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Nan Liang
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jackson Champer
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China.
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2
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Asad M, Liao J, Chen J, Munir F, Pang S, Abbas AN, Yang G. Exploring the role of the ovary-serine protease gene in the female fertility of the diamondback moth using CRISPR/Cas9. PEST MANAGEMENT SCIENCE 2024; 80:3194-3206. [PMID: 38348909 DOI: 10.1002/ps.8022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/24/2023] [Accepted: 02/11/2024] [Indexed: 03/01/2024]
Abstract
BACKGROUND Oogenesis is a complex pathway necessary for proper female reproduction in insects. Ovary-serine protease (Osp) is a homologous gene of serine protease Nudel (SpNudel) and plays an essential role in the oogenesis and ovary development of Drosophila melanogaster. However, the function of Osp is not determined in Plutella xylostella, a highly destructive pest of cruciferous crops. RESULTS The PxOsp gene comprises a 5883-bp open-reading frame that encodes a protein consisting of 1994 amino acids, which contain four conserved domains. PxOsp exhibited a high relative expression in adult females with a specific expression in the ovary. Through the utilization of CRISPR/Cas9 technology, homozygous mutants of PxOsp were generated. These homozygous mutant females produced fewer eggs (average of 56 eggs/female) than wild-type (WT) females (average of 97 eggs/female) when crossed with WT males, and these eggs failed to hatch. Conversely, mutant males produced normal progeny when crossed with WT females. The ovarioles in homozygous mutant females were significantly shorter (5.02 mm in length) and contained fewer eggs (average of 3 eggs/ovariole) than WT ovarioles (8.09 mm in length with an average of 8 eggs/ovariole). Moreover, eggs laid by homozygous mutant females were fragile, with irregular shapes, and were unable to maintain structural integrity due to eggshell ruptures. However, no significant differences were observed between WT and mutant individuals regarding developmental duration, pupal weight, and mating behavior. CONCLUSION Our study suggesteds that PxOsp plays a vital role in female reproduction, particularly in ovary and egg development. Disrupting PxOsp results in recessive female sterility while leaving the male reproductive capability unaffected. This report represents the first study of a haplosufficient gene responsible for female fertility in lepidopteran insects. Additionally, these findings emphasize PxOsp as a potential target for genetically-based pest management of P. xylostella. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Muhammad Asad
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Jianying Liao
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Jing Chen
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Faisal Munir
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Senbo Pang
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Anam Noreen Abbas
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian/Taiwan Crops and College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
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3
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Zhang S, Champer J. Performance characteristics allow for confinement of a CRISPR toxin-antidote gene drive for population suppression in a reaction-diffusion model. Proc Biol Sci 2024; 291:20240500. [PMID: 38889790 DOI: 10.1098/rspb.2024.0500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/26/2024] [Indexed: 06/20/2024] Open
Abstract
Gene drive alleles that can bias their own inheritance could engineer populations for control of disease vectors, invasive species and agricultural pests. There are successful examples of suppression drives and confined modification drives, but developing confined suppression drives has proven more difficult. However, CRISPR-based toxin-antidote dominant embryo (TADE) suppression drive may fill this niche. It works by targeting and disrupting a haplolethal target gene in the germline with its gRNAs while rescuing this target. It also disrupts a female fertility gene by driving insertion or additional gRNAs. Here, we used a reaction-diffusion model to assess drive performance in continuous space, where outcomes can be substantially different from those in panmictic populations. We measured drive wave speed and found that moderate fitness costs or target gene disruption in the early embryo from maternally deposited nuclease can eliminate the drive's ability to form a wave of advance. We assessed the required release size, and finally we investigated migration corridor scenarios. It is often possible for the drive to suppress one population and then persist in the corridor without invading the second population, a potentially desirable outcome. Thus, even imperfect variants of TADE suppression drive may be excellent candidates for confined population suppression.
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Affiliation(s)
- Shijie Zhang
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University , Beijing 100871, People's Republic of China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University , Beijing 100871, People's Republic of China
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4
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Du J, Chen W, Jia X, Xu X, Yang E, Zhou R, Zhang Y, Metzloff M, Messer PW, Champer J. Germline Cas9 promoters with improved performance for homing gene drive. Nat Commun 2024; 15:4560. [PMID: 38811556 PMCID: PMC11137117 DOI: 10.1038/s41467-024-48874-1] [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: 07/24/2023] [Accepted: 05/16/2024] [Indexed: 05/31/2024] Open
Abstract
Gene drive systems could be a viable strategy to prevent pathogen transmission or suppress vector populations by propagating drive alleles with super-Mendelian inheritance. CRISPR-based homing gene drives convert wild type alleles into drive alleles in heterozygotes with Cas9 and gRNA. It is thus desirable to identify Cas9 promoters that yield high drive conversion rates, minimize the formation rate of resistance alleles in both the germline and the early embryo, and limit somatic Cas9 expression. In Drosophila, the nanos promoter avoids leaky somatic expression, but at the cost of high embryo resistance from maternally deposited Cas9. To improve drive efficiency, we test eleven Drosophila melanogaster germline promoters. Some achieve higher drive conversion efficiency with minimal embryo resistance, but none completely avoid somatic expression. However, such somatic expression often does not carry detectable fitness costs for a rescue homing drive targeting a haplolethal gene, suggesting somatic drive conversion. Supporting a 4-gRNA suppression drive, one promoter leads to a low drive equilibrium frequency due to fitness costs from somatic expression, but the other outperforms nanos, resulting in successful suppression of the cage population. Overall, these Cas9 promoters hold advantages for homing drives in Drosophila species and may possess valuable homologs in other organisms.
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Affiliation(s)
- Jie Du
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China.
| | - Weizhe Chen
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xihua Jia
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Xuejiao Xu
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Emily Yang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ruizhi Zhou
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Yuqi Zhang
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Matt Metzloff
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, 100871, Beijing, China.
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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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Lawler CD, Nuñez AKP, Hernandes N, Bhide S, Lohrey I, Baxter S, Robin C. The haplolethal gene wupA of Drosophila exhibits potential as a target for an X-poisoning gene drive. G3 (BETHESDA, MD.) 2024; 14:jkae025. [PMID: 38306583 PMCID: PMC10989859 DOI: 10.1093/g3journal/jkae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 06/23/2023] [Accepted: 01/26/2024] [Indexed: 02/04/2024]
Abstract
A synthetic gene drive that targets haplolethal genes on the X chromosome can skew the sex ratio toward males. Like an "X-shredder," it does not involve "homing," and that has advantages including the reduction of gene drive resistance allele formation. We examine this "X-poisoning" strategy by targeting 4 of the 11 known X-linked haplolethal/haplosterile genes of Drosophila melanogaster with CRISPR/Cas9. We find that targeting the wupA gene during spermatogenesis skews the sex ratio so fewer than 14% of progeny are daughters. That is unless we cross the mutagenic males to X^XY female flies that bear attached-X chromosomes, which reverses the inheritance of the poisoned X chromosome so that sons inherit it from their father, in which case only 2% of the progeny are sons. These sex ratio biases suggest that most of the CRISPR/Cas9 mutants we induced in the wupA gene are haplolethal but some are recessive lethal. The males generating wupA mutants do not suffer from reduced fertility; rather, the haplolethal mutants arrest development in the late stages of embryogenesis well after fertilized eggs have been laid. This provides a distinct advantage over genetic manipulation strategies involving sterility which can be countered by the remating of females. We also find that wupA mutants that destroy the nuclear localization signal of shorter isoforms are not haplolethal as long as the open reading frame remains intact. Like D. melanogaster, wupA orthologs of Drosophila suzukii and Anopheles mosquitos are found on X chromosomes making wupA a viable X-poisoning target in multiple species.
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Affiliation(s)
- Clancy D Lawler
- School of BioSciences, The University of Melbourne, Melbourne 3010, Australia
| | | | - Natalia Hernandes
- School of BioSciences, The University of Melbourne, Melbourne 3010, Australia
| | - Soumitra Bhide
- School of BioSciences, The University of Melbourne, Melbourne 3010, Australia
| | - Isabelle Lohrey
- School of BioSciences, The University of Melbourne, Melbourne 3010, Australia
| | - Simon Baxter
- School of BioSciences, The University of Melbourne, Melbourne 3010, Australia
| | - Charles Robin
- School of BioSciences, The University of Melbourne, Melbourne 3010, Australia
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7
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Ma S, Ni X, Chen S, Qiao X, Xu X, Chen W, Champer J, Huang J. A small-molecule approach to restore female sterility phenotype targeted by a homing suppression gene drive in the fruit pest Drosophila suzukii. PLoS Genet 2024; 20:e1011226. [PMID: 38578788 PMCID: PMC11023630 DOI: 10.1371/journal.pgen.1011226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 04/17/2024] [Accepted: 03/15/2024] [Indexed: 04/07/2024] Open
Abstract
CRISPR-based gene drives offer promising prospects for controlling disease-transmitting vectors and agricultural pests. A significant challenge for successful suppression-type drive is the rapid evolution of resistance alleles. One approach to mitigate the development of resistance involves targeting functionally constrained regions using multiple gRNAs. In this study, we constructed a 3-gRNA homing gene drive system targeting the recessive female fertility gene Tyrosine decarboxylase 2 (Tdc2) in Drosophila suzukii, a notorious fruit pest. Our investigation revealed only a low level of homing in the germline, but feeding octopamine restored the egg-laying defects in Tdc2 mutant females, allowing easier line maintenance than for other suppression drive targets. We tested the effectiveness of a similar system in Drosophila melanogaster and constructed additional split drive systems by introducing promoter-Cas9 transgenes to improve homing efficiency. Our findings show that genetic polymorphisms in wild populations may limit the spread of gene drive alleles, and the position effect profoundly influences Cas9 activity. Furthermore, this study highlights the potential of conditionally rescuing the female infertility caused by the gene drive, offering a valuable tool for the industrial-scale production of gene drive transgenic insects.
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Affiliation(s)
- Suhan Ma
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xuyang Ni
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shimin Chen
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | | | - Xuejiao Xu
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
| | - Weizhe Chen
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
- PTN program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
| | - Jia Huang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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8
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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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9
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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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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)
- Jingheng Chen
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xuejiao Xu
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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Li J, Champer J. Harnessing Wolbachia cytoplasmic incompatibility alleles for confined gene drive: A modeling study. PLoS Genet 2023; 19:e1010591. [PMID: 36689491 PMCID: PMC9894560 DOI: 10.1371/journal.pgen.1010591] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/02/2023] [Accepted: 12/21/2022] [Indexed: 01/24/2023] Open
Abstract
Wolbachia are maternally-inherited bacteria, which can spread rapidly in populations by manipulating reproduction. cifA and cifB are genes found in Wolbachia phage that are responsible for cytoplasmic incompatibility, the most common type of Wolbachia reproductive interference. In this phenomenon, no viable offspring are produced when a male with both cifA and cifB (or just cifB in some systems) mates with a female lacking cifA. Utilizing this feature, we propose new types of toxin-antidote gene drives that can be constructed with only these two genes in an insect genome, instead of the whole Wolbachia bacteria. By using both mathematical and simulation models, we found that a drive containing cifA and cifB together creates a confined drive with a moderate to high introduction threshold. When introduced separately, they act as a self-limiting drive. We observed that the performance of these drives is substantially influenced by various ecological parameters and drive characteristics. Extending our models to continuous space, we found that the drive individual release distribution has a critical impact on drive persistence. Our results suggest that these new types of drives based on Wolbachia transgenes are safe and flexible candidates for genetic modification of populations.
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Affiliation(s)
- Jiahe Li
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- * E-mail:
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13
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Raban R, Gendron WAC, Akbari OS. A perspective on the expansion of the genetic technologies to support the control of neglected vector-borne diseases and conservation. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.999273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Genetic-based technologies are emerging as promising tools to support vector population control. Vectors of human malaria and dengue have been the main focus of these development efforts, but in recent years these technologies have become more flexible and adaptable and may therefore have more wide-ranging applications. Culex quinquefasciatus, for example, is the primary vector of avian malaria in Hawaii and other tropical islands. Avian malaria has led to the extinction of numerous native bird species and many native bird species continue to be threatened as climate change is expanding the range of this mosquito. Genetic-based technologies would be ideal to support avian malaria control as they would offer alternatives to interventions that are difficult to implement in natural areas, such as larval source reduction, and limit the need for chemical insecticides, which can harm beneficial species in these natural areas. This mosquito is also an important vector of human diseases, such as West Nile and Saint Louis encephalitis viruses, so genetic-based control efforts for this species could also have a direct impact on human health. This commentary will discuss the current state of development and future needs for genetic-based technologies in lesser studied, but important disease vectors, such as C. quinquefasciatus, and make comparisons to technologies available in more studied vectors. While most current genetic control focuses on human disease, we will address the impact that these technologies could have on both disease and conservation focused vector control efforts and what is needed to prepare these technologies for evaluation in the field. The versatility of genetic-based technologies may result in the development of many important tools to control a variety of vectors that impact human, animal, and ecosystem health.
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Langmüller AM, Champer J, Lapinska S, Xie L, Metzloff M, Champer SE, Liu J, Xu Y, Du J, Clark AG, Messer PW. Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations. eLife 2022; 11:e71809. [PMID: 36135925 PMCID: PMC9545523 DOI: 10.7554/elife.71809] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 provides a highly efficient and flexible genome editing technology with numerous potential applications ranging from gene therapy to population control. Some proposed applications involve the integration of CRISPR/Cas9 endonucleases into an organism's genome, which raises questions about potentially harmful effects to the transgenic individuals. One example for which this is particularly relevant are CRISPR-based gene drives conceived for the genetic alteration of entire populations. The performance of such drives can strongly depend on fitness costs experienced by drive carriers, yet relatively little is known about the magnitude and causes of these costs. Here, we assess the fitness effects of genomic CRISPR/Cas9 expression in Drosophila melanogaster cage populations by tracking allele frequencies of four different transgenic constructs that allow us to disentangle 'direct' fitness costs due to the integration, expression, and target-site activity of Cas9, from fitness costs due to potential off-target cleavage. Using a maximum likelihood framework, we find that a model with no direct fitness costs but moderate costs due to off-target effects fits our cage data best. Consistent with this, we do not observe fitness costs for a construct with Cas9HF1, a high-fidelity version of Cas9. We further demonstrate that using Cas9HF1 instead of standard Cas9 in a homing drive achieves similar drive conversion efficiency. These results suggest that gene drives should be designed with high-fidelity endonucleases and may have implications for other applications that involve genomic integration of CRISPR endonucleases.
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Affiliation(s)
- Anna M Langmüller
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Institut für Populationsgenetik, Vetmeduni ViennaViennaAustria
- Vienna Graduate School of Population Genetics, Vetmeduni ViennaViennaAustria
| | - Jackson Champer
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking UniversityBeijingChina
| | - Sandra Lapinska
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Lin Xie
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Matthew Metzloff
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Samuel E Champer
- Department of Computational Biology, Cornell UniversityIthacaUnited States
| | - Jingxian Liu
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Yineng Xu
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Jie Du
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking UniversityBeijingChina
| | - Andrew G Clark
- Department of Computational Biology, Cornell UniversityIthacaUnited States
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Philipp W Messer
- Department of Computational Biology, Cornell UniversityIthacaUnited States
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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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