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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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2
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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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3
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Kumam Y, Trick HN, Vara Prasad P, Jugulam M. Transformative Approaches for Sustainable Weed Management: The Power of Gene Drive and CRISPR-Cas9. Genes (Basel) 2023; 14:2176. [PMID: 38136999 PMCID: PMC10742955 DOI: 10.3390/genes14122176] [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: 10/27/2023] [Revised: 11/25/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Weeds can negatively impact crop yields and the ecosystem's health. While many weed management strategies have been developed and deployed, there is a greater need for the development of sustainable methods for employing integrated weed management. Gene drive systems can be used as one of the approaches to suppress the aggressive growth and reproductive behavior of weeds, although their efficacy is yet to be tested. Their popularity in insect pest management has increased, however, with the advent of CRISPR-Cas9 technology, which provides specificity and precision in editing the target gene. This review focuses on the different types of gene drive systems, including the use of CRISPR-Cas9-based systems and their success stories in pest management, while also exploring their possible applications in weed species. Factors that govern the success of a gene drive system in weeds, including the mode of reproduction, the availability of weed genome databases, and well-established transformation protocols are also discussed. Importantly, the risks associated with the release of weed populations with gene drive-bearing alleles into wild populations are also examined, along with the importance of addressing ecological consequences and ethical concerns.
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Affiliation(s)
- Yaiphabi Kumam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA;
| | - P.V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
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4
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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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5
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Chen Y, Li H, Yi TC, Shen J, Zhang J. Notch Signaling in Insect Development: A Simple Pathway with Diverse Functions. Int J Mol Sci 2023; 24:14028. [PMID: 37762331 PMCID: PMC10530718 DOI: 10.3390/ijms241814028] [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: 07/31/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Notch signaling is an evolutionarily conserved pathway which functions between adjacent cells to establish their distinct identities. Despite operating in a simple mechanism, Notch signaling plays remarkably diverse roles in development to regulate cell fate determination, organ growth and tissue patterning. While initially discovered and characterized in the model insect Drosophila melanogaster, recent studies across various insect species have revealed the broad involvement of Notch signaling in shaping insect tissues. This review focuses on providing a comprehensive picture regarding the roles of the Notch pathway in insect development. The roles of Notch in the formation and patterning of the insect embryo, wing, leg, ovary and several specific structures, as well as in physiological responses, are summarized. These results are discussed within the developmental context, aiming to deepen our understanding of the diversified functions of the Notch signaling pathway in different insect species.
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Affiliation(s)
- Yao Chen
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Y.C.)
| | - Haomiao Li
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Y.C.)
| | - Tian-Ci Yi
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang 550025, China
| | - Jie Shen
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Y.C.)
| | - Junzheng Zhang
- Department of Plant Biosecurity and MOA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (Y.C.)
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6
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Kim J, Harris KD, Kim IK, Shemesh S, Messer PW, Greenbaum G. Incorporating ecology into gene drive modelling. Ecol Lett 2023; 26 Suppl 1:S62-S80. [PMID: 37840022 DOI: 10.1111/ele.14194] [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: 10/19/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 10/17/2023]
Abstract
Gene drive technology, in which fast-spreading engineered drive alleles are introduced into wild populations, represents a promising new tool in the fight against vector-borne diseases, agricultural pests and invasive species. Due to the risks involved, gene drives have so far only been tested in laboratory settings while their population-level behaviour is mainly studied using mathematical and computational models. The spread of a gene drive is a rapid evolutionary process that occurs over timescales similar to many ecological processes. This can potentially generate strong eco-evolutionary feedback that could profoundly affect the dynamics and outcome of a gene drive release. We, therefore, argue for the importance of incorporating ecological features into gene drive models. We describe the key ecological features that could affect gene drive behaviour, such as population structure, life-history, environmental variation and mode of selection. We review previous gene drive modelling efforts and identify areas where further research is needed. As gene drive technology approaches the level of field experimentation, it is crucial to evaluate gene drive dynamics, potential outcomes, and risks realistically by including ecological processes.
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Affiliation(s)
- Jaehee Kim
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Keith D Harris
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabel K Kim
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Shahar Shemesh
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Gili Greenbaum
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
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7
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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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8
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Melesse Vergara M, Labbé J, Tannous J. Reflection on the Challenges, Accomplishments, and New Frontiers of Gene Drives. BIODESIGN RESEARCH 2022; 2022:9853416. [PMID: 37850135 PMCID: PMC10521683 DOI: 10.34133/2022/9853416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/19/2022] [Indexed: 10/19/2023] Open
Abstract
Ongoing pest and disease outbreaks pose a serious threat to human, crop, and animal lives, emphasizing the need for constant genetic discoveries that could serve as mitigation strategies. Gene drives are genetic engineering approaches discovered decades ago that may allow quick, super-Mendelian dissemination of genetic modifications in wild populations, offering hopes for medicine, agriculture, and ecology in combating diseases. Following its first discovery, several naturally occurring selfish genetic elements were identified and several gene drive mechanisms that could attain relatively high threshold population replacement have been proposed. This review provides a comprehensive overview of the recent advances in gene drive research with a particular emphasis on CRISPR-Cas gene drives, the technology that has revolutionized the process of genome engineering. Herein, we discuss the benefits and caveats of this technology and place it within the context of natural gene drives discovered to date and various synthetic drives engineered. Later, we elaborate on the strategies for designing synthetic drive systems to address resistance issues and prevent them from altering the entire wild populations. Lastly, we highlight the major applications of synthetic CRISPR-based gene drives in different living organisms, including plants, animals, and microorganisms.
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Affiliation(s)
| | - Jesse Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Invaio Sciences, Cambridge, MA 02138USA
| | - Joanna Tannous
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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9
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Asad M, Liu D, Li J, Chen J, Yang G. Development of CRISPR/Cas9-Mediated Gene-Drive Construct Targeting the Phenotypic Gene in Plutella xylostella. Front Physiol 2022; 13:938621. [PMID: 35845988 PMCID: PMC9277308 DOI: 10.3389/fphys.2022.938621] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
The gene-drive system can ensure that desirable traits are transmitted to the progeny more than the normal Mendelian segregation. The clustered regularly interspersed palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated gene-drive system has been demonstrated in dipteran insect species, including Drosophila and Anopheles, not yet in other insect species. Here, we have developed a single CRISPR/Cas9-mediated gene-drive construct for Plutella xylostella, a highly-destructive lepidopteran pest of cruciferous crops. The gene-drive construct was developed containing a Cas9 gene, a marker gene (EGFP) and a gRNA sequence targeting the phenotypic marker gene (Pxyellow) and site-specifically inserted into the P. xylostella genome. This homing-based gene-drive copied ∼12 kb of a fragment containing Cas9 gene, gRNA, and EGFP gene along with their promoters to the target site. Overall, 6.67%–12.59% gene-drive efficiency due to homology-directed repair (HDR), and 80.93%–86.77% resistant-allele formation due to non-homologous-end joining (NHEJ) were observed. Furthermore, the transgenic progeny derived from male parents showed a higher gene-drive efficiency compared with transgenic progeny derived from female parents. This study demonstrates the feasibility of the CRISPR/Cas9-mediated gene-drive construct in P. xylostella that inherits the desired traits to the progeny. The finding of this study provides a foundation to develop an effective CRISPR/Cas9-mediated gene-drive system for pest control.
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Affiliation(s)
- Muhammad Asad
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, 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
| | - Dan Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, 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
| | - Jianwen Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, 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 and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, 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 and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, 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
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Guang Yang,
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10
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Carter L, Mankad A, Hobman EV, Weynberg KD, Kaksonen AH, Cooper C. Three synthetic biology applications and their paths to impact in Australia: Cane toads, bacteriophages and biomining microbes. Biotechnol J 2022; 17:e2200009. [DOI: 10.1002/biot.202200009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/16/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Lucy Carter
- CSIRO Land and Water Brisbane QLD Australia
- CSIRO Synthetic Biology Future Science Platform Australia
| | - Aditi Mankad
- CSIRO Land and Water Brisbane QLD Australia
- CSIRO Synthetic Biology Future Science Platform Australia
| | - Elizabeth V. Hobman
- CSIRO Land and Water Brisbane QLD Australia
- CSIRO Synthetic Biology Future Science Platform Australia
| | - Karen D. Weynberg
- Australian Centre for Ecogenomics School of Chemistry and Molecular Biosciences The University of Queensland St. Lucia QLD Australia
- CSIRO Synthetic Biology Future Science Platform Australia
| | - Anna H. Kaksonen
- CSIRO Land and Water Brisbane QLD Australia
- Land and Water CSIRO Floreat WA Australia
- CSIRO Synthetic Biology Future Science Platform Australia
| | - Caitlin Cooper
- The University of California Davis California United States
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11
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Upadhyay A, Feltman NR, Sychla A, Janzen A, Das SR, Maselko M, Smanski M. Genetically engineered insects with sex-selection and genetic incompatibility enable population suppression. eLife 2022; 11:71230. [PMID: 35108195 PMCID: PMC8860436 DOI: 10.7554/elife.71230] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 01/31/2022] [Indexed: 11/18/2022] Open
Abstract
Engineered Genetic Incompatibility (EGI) is a method to create species-like barriers to sexual reproduction. It has applications in pest control that mimic Sterile Insect Technique when only EGI males are released. This can be facilitated by introducing conditional female-lethality to EGI strains to generate a sex-sorting incompatible male system (SSIMS). Here, we demonstrate a proof of concept by combining tetracycline-controlled female lethality constructs with a pyramus-targeting EGI line in the model insect Drosophila melanogaster. We show that both functions (incompatibility and sex-sorting) are robustly maintained in the SSIMS line and that this approach is effective for population suppression in cage experiments. Further we show that SSIMS males remain competitive with wild-type males for reproduction with wild-type females, including at the level of sperm competition.
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Affiliation(s)
- Ambuj Upadhyay
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Nathan R Feltman
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, United States
| | - Adam Sychla
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, United States
| | - Anna Janzen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, United States
| | - Siba R Das
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, United States
| | | | - Michael Smanski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, United States
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12
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Metchanun N, Borgemeister C, Amzati G, von Braun J, Nikolov M, Selvaraj P, Gerardin J. Modeling impact and cost-effectiveness of driving-Y gene drives for malaria elimination in the Democratic Republic of the Congo. Evol Appl 2022; 15:132-148. [PMID: 35126652 PMCID: PMC8792473 DOI: 10.1111/eva.13331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 11/15/2021] [Accepted: 11/29/2021] [Indexed: 12/17/2022] Open
Abstract
Malaria elimination will be challenging in countries that currently continue to bear high malaria burden. Sex-ratio-distorting gene drives, such as driving-Y, could play a role in an integrated elimination strategy if they can effectively suppress vector populations. Using a spatially explicit, agent-based model of malaria transmission in eight provinces spanning the range of transmission intensities across the Democratic Republic of the Congo, we predict the impact and cost-effectiveness of integrating driving-Y gene drive mosquitoes in malaria elimination strategies that include existing interventions such as insecticide-treated nets and case management of symptomatic malaria. Gene drive mosquitoes could eliminate malaria and were the most cost-effective intervention overall if the drive component was highly effective with at least 95% X-shredder efficiency at relatively low fertility cost, and associated cost of deployment below 7.17 $int per person per year. Suppression gene drive could be a cost-effective supplemental intervention for malaria elimination, but tight constraints on drive effectiveness and cost ceilings may limit its feasibility.
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Affiliation(s)
| | | | - Gaston Amzati
- Université Evangélique en AfriqueBukavuDemocratic Republic of the Congo
| | | | | | | | - Jaline Gerardin
- Institute for Disease ModelingBellevueWashingtonUSA
- Department of Preventive Medicine and Institute for Global HealthNorthwestern UniversityChicagoIllinoisUSA
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13
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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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14
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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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15
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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: 1] [Impact Index Per Article: 0.3] [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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16
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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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Terradas G, Buchman AB, Bennett JB, Shriner I, Marshall JM, Akbari OS, Bier E. Inherently confinable split-drive systems in Drosophila. Nat Commun 2021; 12:1480. [PMID: 33674604 PMCID: PMC7935863 DOI: 10.1038/s41467-021-21771-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
CRISPR-based gene-drive systems, which copy themselves via gene conversion mediated by the homology-directed repair (HDR) pathway, have the potential to revolutionize vector control. However, mutant alleles generated by the competing non-homologous end-joining (NHEJ) pathway, resistant to Cas9 cleavage, can interrupt the spread of gene-drive elements. We hypothesized that drives targeting genes essential for viability or reproduction also carrying recoded sequences that restore endogenous gene functionality should benefit from dominantly-acting maternal clearance of NHEJ alleles combined with recessive Mendelian culling processes. Here, we test split gene-drive (sGD) systems in Drosophila melanogaster that are inserted into essential genes required for viability (rab5, rab11, prosalpha2) or fertility (spo11). In single generation crosses, sGDs copy with variable efficiencies and display sex-biased transmission. In multigenerational cage trials, sGDs follow distinct drive trajectories reflecting their differential tendencies to induce target chromosome damage and/or lethal/sterile mosaic Cas9-dependent phenotypes, leading to inherently confinable drive outcomes. NHEJ alleles and Cas9 remnants after a gene drive introduction are scientific and public concerns. Here, the authors use split drives with recoded rescue elements to target essential genes and minimize the appearance of NHEJ alleles while also leaving no trace of Cas9.
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Affiliation(s)
- Gerard Terradas
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Anna B Buchman
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Jared B Bennett
- Biophysics Graduate Group, Division of Biological Sciences, College of Letters and Science, University of California, Berkeley, CA, USA
| | - Isaiah Shriner
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - John M Marshall
- Divisions of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA.,Innovative Genomics Institute, Berkeley, CA, USA
| | - Omar S Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA. .,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA.
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18
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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: 13] [Impact Index Per Article: 4.3] [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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19
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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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20
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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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21
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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: 26] [Impact Index Per Article: 6.5] [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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22
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Kojin BB, Biedler JK, Tu Z, Adelman ZN. Characterization of a female germline and early zygote promoter from the transcription factor bZip1 in the dengue mosquito Aedes aegypti. Parasit Vectors 2020; 13:353. [PMID: 32680549 PMCID: PMC7367395 DOI: 10.1186/s13071-020-04216-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/06/2020] [Indexed: 11/10/2022] Open
Abstract
Background The wide distribution of Aedes aegypti, the main vector of dengue and yellow fever viruses, currently puts three billion people in the world at risk of infection with these viruses. Continuous transmission of these and other viruses despite aggressive efforts to prevent this emphasizes the need to develop new control strategies. Proposals to control disease transmission based on vector engineering, including both population suppression and population replacement, rely on the development of transgenes under the control of regulatory elements able to drive molecules in a specific tissue, time and strength. Methods Here we report the characterization of a promoter active in both the female germline and early zygote, derived from the transcription factor bZip1 in the mosquito Ae. aegypti, using transposon-based methods and RT-qPCR. Results We generated seven transgenic lines carrying AabZip1-reporter constructs and observed expression in both the ovary and early embryo. RT-qPCR analysis was performed to evaluate transcript expression patterns for each line, confirming that transgenic expression from the AabZip1 promoter largely recapitulated the endogenous expression pattern, albeit the strength of maternal expression appeared to be strongly influenced by chromosomal position. Conclusions This study provides a new regulatory sequence that can be useful for generating transgenic lines that can become a tool in vector control strategies.![]()
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Affiliation(s)
- Bianca B Kojin
- Department of Entomology and Agrilife Research, Texas A&M University, College Station, TX, USA
| | - James K Biedler
- Department of Biochemistry and the Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Zhijian Tu
- Department of Biochemistry and the Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Zach N Adelman
- Department of Entomology and Agrilife Research, Texas A&M University, College Station, TX, USA.
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23
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Oberhofer G, Ivy T, Hay BA. Gene drive and resilience through renewal with next generation Cleave and Rescue selfish genetic elements. Proc Natl Acad Sci U S A 2020; 117:9013-9021. [PMID: 32245808 PMCID: PMC7183144 DOI: 10.1073/pnas.1921698117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Gene drive-based strategies for modifying populations face the problem that genes encoding cargo and the drive mechanism are subject to separation, mutational inactivation, and loss of efficacy. Resilience, an ability to respond to these eventualities in ways that restore population modification with functional genes, is needed for long-term success. Here, we show that resilience can be achieved through cycles of population modification with "Cleave and Rescue" (ClvR) selfish genetic elements. ClvR comprises 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. Cycles of modification can, in principle, be carried out if two ClvR elements targeting different essential genes are located at the same genomic position, and one of them, ClvRn+1, carries a Rescue transgene from an earlier element, ClvRnClvRn+1 should spread within a population of ClvRn, while also bringing about a decrease in its frequency. To test this hypothesis, we first show that multiple ClvRs, each targeting a different essential gene, function when located at a common chromosomal position in Drosophila We then show that when several of these also carry the Rescue from a different ClvR, they spread to transgene fixation in populations fixed for the latter and at its expense. Therefore, genetic modifications of populations can be overwritten with new content, providing an ongoing point of control.
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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;
- St John's College, University of Cambridge, CB2 1TP Cambridge, United Kingdom
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The Developmental Transcriptome of Aedes albopictus, a Major Worldwide Human Disease Vector. G3-GENES GENOMES GENETICS 2020; 10:1051-1062. [PMID: 31964684 PMCID: PMC7056973 DOI: 10.1534/g3.119.401006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aedes albopictus mosquitoes are important vectors for a number of human pathogens including the Zika, dengue, and chikungunya viruses. Capable of displacing Aedes aegypti populations, this mosquito adapts to cooler environments which increases its geographical range and transmission potential. There are limited control strategies for Aedes albopictus mosquitoes which is likely attributed to the lack of comprehensive biological studies on this emerging vector. To fill this void, here using RNAseq we characterized Aedes albopictus mRNA expression profiles at 34 distinct time points throughout development providing the first high-resolution comprehensive view of the developmental transcriptome of this worldwide human disease vector. This enabled us to identify several patterns of shared gene expression among tissues as well as sex-specific expression patterns. To illuminate the similarities and differences with Aedes aegypti, a related human disease vector, we also performed a comparative analysis between the two developmental transcriptomes, identifying life stages where the two species exhibit similar and distinct gene expression patterns. These findings provide insights into the similarities and differences between Aedes albopictus and Aedes aegypti mosquito biology. In summary, the results generated from this study should form the basis for future investigations on the biology of Aedes albopictus and provide a gold mine resource for the development of transgene-based vector control strategies.
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Abstract
Vector-borne diseases, such as dengue, Zika and malaria, are a major cause of morbidity and mortality worldwide. These diseases have proven difficult to control and currently available management tools are insufficient to eliminate them in many regions. Gene drives have the potential to revolutionize vector-borne disease control. This suite of technologies has advanced rapidly in recent years as a result of the availability of new, more efficient gene editing technologies. Gene drives can favorably bias the inheritance of a linked disease-refractory gene, which could possibly be exploited (i) to generate a vector population incapable of transmitting disease or (ii) to disrupt an essential gene for viability or fertility, which could eventually eliminate a population. Importantly, gene drives vary in characteristics such as their transmission efficiency, confinability and reversibility, and their potential to develop resistance to the drive mechanism. Here, we discuss recent advancements in the gene drive field, and contrast the benefits and limitations of a variety of technologies, as well as approaches to overcome these limitations. We also discuss the current state of each gene drive technology and the technical considerations that need to be addressed on the pathway to field implementation. While there are still many obstacles to overcome, recent progress has brought us closer than ever before to genetic-based vector modification as a tool to support vector-borne disease elimination efforts worldwide.
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Affiliation(s)
- Robyn R Raban
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - John M Marshall
- Innovative Genomics Institute, Berkeley, CA 94720, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, USA
| | - Omar S Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
- Division of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
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Kandul NP, Liu J, Buchman A, Gantz VM, Bier E, Akbari OS. Assessment of a Split Homing Based Gene Drive for Efficient Knockout of Multiple Genes. G3 (BETHESDA, MD.) 2020; 10:827-837. [PMID: 31882406 PMCID: PMC7003086 DOI: 10.1534/g3.119.400985] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/19/2019] [Indexed: 01/08/2023]
Abstract
Homing based gene drives (HGD) possess the potential to spread linked cargo genes into natural populations and are poised to revolutionize population control of animals. Given that host encoded genes have been identified that are important for pathogen transmission, targeting these genes using guide RNAs as cargo genes linked to drives may provide a robust method to prevent disease transmission. However, effectiveness of the inclusion of additional guide RNAs that target separate genes has not been thoroughly explored. To test this approach, we generated a split-HGD in Drosophila melanogaster that encoded a drive linked effector consisting of a second gRNA engineered to target a separate host-encoded gene, which we term a gRNA-mediated effector (GME). This design enabled us to assess homing and knockout efficiencies of two target genes simultaneously, and also explore the timing and tissue specificity of Cas9 expression on cleavage/homing rates. We demonstrate that inclusion of a GME can result in high efficiency of disruption of both genes during super-Mendelian propagation of split-HGD. Furthermore, both genes were knocked out one generation earlier than expected indicating the robust somatic expression of Cas9 driven by Drosophila germline-limited promoters. We also assess the efficiency of 'shadow drive' generated by maternally deposited Cas9 protein and accumulation of drive-induced resistance alleles along multiple generations, and discuss design principles of HGD that could mitigate the accumulation of resistance alleles while incorporating a GME.
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Affiliation(s)
| | - Junru Liu
- Section of Cell and Developmental Biology and
| | | | | | - Ethan Bier
- Section of Cell and Developmental Biology and
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093
| | - Omar S Akbari
- Section of Cell and Developmental Biology and
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093
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27
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Cash SA, Robert MA, Lorenzen MD, Gould F. The impact of local population genetic background on the spread of the selfish element Medea-1 in red flour beetles. Ecol Evol 2020; 10:863-874. [PMID: 32015850 PMCID: PMC6988536 DOI: 10.1002/ece3.5946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/24/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022] Open
Abstract
Selfish genetic elements have been found in the genomes of many species, yet our understanding of their evolutionary dynamics is only partially understood. A number of distinct selfish Medea elements are naturally present in many populations of the red flour beetle (Tribolium castaneum). Although these Medea elements are predicted by models to increase in frequency within populations because any offspring of a Medea-bearing mother that do not inherit at least one Medea allele will die, experiments demonstrating an increase in a naturally occurring Medea element are lacking. Our survey of the specific Medea element, M1, in the United States showed that it had a patchy geographic distribution. From the survey, it could not be determined if this distribution was caused by a slow process of M1 colonization of discrete populations or if some populations lacked M1 because they had genetic factors conferring resistance to the Medea mechanism. We show that populations with naturally low to intermediate M1 frequencies likely represent transient states during the process of Medea spread. Furthermore, we find no evidence that genetic factors are excluding M1 from US populations where the element is not presently found. We also show how a known suppressor of Medea can impair the increase of M1 in populations and discuss the implications of our findings for pest-management applications of Medea elements.
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Affiliation(s)
- Sarah A. Cash
- Graduate Program in GeneticsDepartment of Biological SciencesNorth Carolina State UniversityRaleighNorth Carolina
- W. M. Keck Center for Behavioral BiologyNorth Carolina State UniversityRaleighNorth Carolina
| | - Michael A. Robert
- Department of Mathematics, Physics, and StatisticsUniversity of the SciencesPhiladelphiaPennsylvania
| | - Marcé D. Lorenzen
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth Carolina
| | - Fred Gould
- W. M. Keck Center for Behavioral BiologyNorth Carolina State UniversityRaleighNorth Carolina
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth Carolina
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth Carolina
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Cash SA, Lorenzen MD, Gould F. The distribution and spread of naturally occurring Medea selfish genetic elements in the United States. Ecol Evol 2019; 9:14407-14416. [PMID: 31938528 PMCID: PMC6953677 DOI: 10.1002/ece3.5876] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023] Open
Abstract
Selfish genetic elements (SGEs) are DNA sequences that are transmitted to viable offspring in greater than Mendelian frequencies. Medea SGEs occur naturally in some populations of red flour beetle (Tribolium castaneum) and are expected to increase in frequency within populations and spread among populations. The large-scale U.S. distributions of Medea-4 (M4) had been mapped based on samples from 1993 to 1995. We sampled beetles in 2011-2014 and show that the distribution of M4 in the United States is dynamic and has shifted southward. By using a genetic marker of Medea-1 (M1), we found five unique geographic clusters with high and low M1 frequencies in a pattern not predicted by microsatellite-based analysis of population structure. Our results indicate the absence of rigid barriers to Medea spread in the United States, so assessment of what factors have limited its current distribution requires further investigation. There is great interest in using synthetic SGEs, including synthetic Medea, to alter or suppress pest populations, but there is concern about unpredicted spread of these SGEs and potential for populations to become resistant to them. The finding of patchy distributions of Medea elements suggests that released synthetic SGEs cannot always be expected to spread uniformly, especially in target species with limited dispersal.
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Affiliation(s)
- Sarah A. Cash
- Program in GeneticsDepartment of Biological SciencesNorth Carolina State UniversityRaleighNCUSA
| | - Marce D. Lorenzen
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
| | - Fred Gould
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
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Bull JJ, Remien CH, Gomulkiewicz R, Krone SM. Spatial structure undermines parasite suppression by gene drive cargo. PeerJ 2019; 7:e7921. [PMID: 31681512 PMCID: PMC6824332 DOI: 10.7717/peerj.7921] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/18/2019] [Indexed: 12/17/2022] Open
Abstract
Gene drives may be used in two ways to curtail vectored diseases. Both involve engineering the drive to spread in the vector population. One approach uses the drive to directly depress vector numbers, possibly to extinction. The other approach leaves intact the vector population but suppresses the disease agent during its interaction with the vector. This second application may use a drive engineered to carry a genetic cargo that blocks the disease agent. An advantage of the second application is that it is far less likely to select vector resistance to block the drive, but the disease agent may instead evolve resistance to the inhibitory cargo. However, some gene drives are expected to spread so fast and attain such high coverage in the vector population that, if the disease agent can evolve resistance only gradually, disease eradication may be feasible. Here we use simple models to show that spatial structure in the vector population can greatly facilitate persistence and evolution of resistance by the disease agent. We suggest simple approaches to avoid some types of spatial structure, but others may be intrinsic to the populations being challenged and difficult to overcome.
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Affiliation(s)
- James J. Bull
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Christopher H. Remien
- Department of Mathematics, University of Idaho, Moscow, ID, United States of America
| | - Richard Gomulkiewicz
- School of Biological Sciences, Washington State University, Pullman, WA, United States of America
| | - Stephen M. Krone
- Department of Mathematics, University of Idaho, Moscow, ID, United States of America
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Backus GA, Delborne JA. Threshold-Dependent Gene Drives in the Wild: Spread, Controllability, and Ecological Uncertainty. Bioscience 2019. [DOI: 10.1093/biosci/biz098] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AbstractGene drive technology could allow the intentional spread of a desired gene throughout an entire wild population in relatively few generations. However, there are major concerns that gene drives could either fail to spread or spread without restraint beyond the targeted population. One potential solution is to use more localized threshold-dependent drives, which only spread when they are released in a population above a critical frequency. However, under certain conditions, small changes in gene drive fitness could lead to divergent outcomes in spreading behavior. In the face of ecological uncertainty, the inability to estimate gene drive fitness in a real-world context could prove problematic because gene drives designed to be localized could spread to fixation in neighboring populations if ecological conditions unexpectedly favor the gene drive. This perspective offers guidance to developers and managers because navigating gene drive spread and controllability could be risky without detailed knowledge of ecological contexts.
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Dhole S, Lloyd AL, Gould F. Tethered homing gene drives: A new design for spatially restricted population replacement and suppression. Evol Appl 2019; 12:1688-1702. [PMID: 31462923 PMCID: PMC6708424 DOI: 10.1111/eva.12827] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 12/18/2022] Open
Abstract
Optimism regarding potential epidemiological and conservation applications of modern gene drives is tempered by concern about the possibility of unintended spread of engineered organisms beyond the target population. In response, several novel gene drive approaches have been proposed that can, under certain conditions, locally alter characteristics of a population. One challenge for these gene drives is the difficulty of achieving high levels of localized population suppression without very large releases in the face of gene flow. We present a new gene drive system, tethered homing (TH), with improved capacity for both localization and population suppression. The TH drive is based on driving a payload gene using a homing construct that is anchored to a spatially restricted gene drive. We use a proof-of-concept mathematical model to show the dynamics of a TH drive that uses engineered underdominance as an anchor. This system is composed of a split homing drive and a two-locus engineered underdominance drive linked to one part of the split drive (the Cas endonuclease). We use simple population genetic simulations to show that the tethered homing technique can offer improved localized spread of costly transgenic payload genes. Additionally, the TH system offers the ability to gradually adjust the genetic load in a population after the initial alteration, with minimal additional release effort. We discuss potential solutions for improving localization and the feasibility of creating TH drive systems. Further research with models that include additional biological details will be needed to better understand how TH drives would behave in natural populations, but the preliminary results shown here suggest that tethered homing drives can be a useful addition to the repertoire of localized gene drives.
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Affiliation(s)
- Sumit Dhole
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth Carolina
| | - Alun L. Lloyd
- Biomathematics Graduate Program and Department of MathematicsNorth Carolina State UniversityRaleighNorth Carolina
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth Carolina
| | - Fred Gould
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth Carolina
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth Carolina
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Differentially and Co-expressed Genes in Embryo, Germ-Line and Somatic Tissues of Tribolium castaneum. G3-GENES GENOMES GENETICS 2019; 9:2363-2373. [PMID: 31113821 PMCID: PMC6643895 DOI: 10.1534/g3.119.400340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transcriptomic studies of Tribolium castaneum have led to significant advances in our understanding of co-regulation and differential expression of genes in development. However, previously used microarray approaches have covered only a subset of known genes. The aim of this study was to investigate gene expression patterns of beetle embryo, germ-line and somatic tissues. We identified 12,302 expressed genes and determined differentially expressed up and down-regulated genes among all samples. For example, 1624 and 3639 genes were differentially increased in expression greater than or equal to twofold change (FDR < 0.01) in testis vs. ovary (virgin female) and ovary vs. embryo (0-5 hr), respectively. Of these, many developmental, somatic and germ-line differentially expressed genes were identified. Furthermore, many maternally deposited transcripts were identified, whose expression either decreased rapidly or persisted during embryogenesis. Genes with the largest change in expression were predominantly decreased during early embryogenesis as compared to ovary or were increased in testis compared to embryo. We also identify zygotic genes induced after fertilization. The genome wide variation in transcript regulation in maternal and zygotic genes could provide additional information on how the anterior posterior axis formation is established in Tribolium embryos as compared to Drosophila Together, our data will facilitate studies of comparative developmental biology as well as help identify candidate genes for identifying cis-elements to drive transgenic constructs.
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Two-By-One model of cytoplasmic incompatibility: Synthetic recapitulation by transgenic expression of cifA and cifB in Drosophila. PLoS Genet 2019; 15:e1008221. [PMID: 31242186 PMCID: PMC6594578 DOI: 10.1371/journal.pgen.1008221] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/30/2019] [Indexed: 01/22/2023] Open
Abstract
Wolbachia are maternally inherited bacteria that infect arthropod species worldwide and are deployed in vector control to curb arboviral spread using cytoplasmic incompatibility (CI). CI kills embryos when an infected male mates with an uninfected female, but the lethality is rescued if the female and her embryos are likewise infected. Two phage WO genes, cifAwMel and cifBwMel from the wMel Wolbachia deployed in vector control, transgenically recapitulate variably penetrant CI, and one of the same genes, cifAwMel, rescues wild type CI. The proposed Two-by-One genetic model predicts that CI and rescue can be recapitulated by transgenic expression alone and that dual cifAwMeland cifBwMel expression can recapitulate strong CI. Here, we use hatch rate and gene expression analyses in transgenic Drosophila melanogaster to demonstrate that CI and rescue can be synthetically recapitulated in full, and strong, transgenic CI comparable to wild type CI is achievable. These data explicitly validate the Two-by-One model in wMel-infected D. melanogaster, establish a robust system for transgenic studies of CI in a model system, and represent the first case of completely engineering male and female animal reproduction to depend upon bacteriophage gene products. Releases of Wolbachia-infected mosquitos are underway worldwide because Wolbachia block replication of Zika and Dengue viruses and spread themselves maternally through arthropod populations via cytoplasmic incompatibility (CI). The CI drive system depends on a Wolbachia-induced sperm modification that results in embryonic lethality when an infected male mates with an uninfected female, but this lethality is rescued when the female and her embryos are likewise infected. We recently reported that the phage WO genes, cifA and cifB, cause the sperm modification and cifA rescues the embryonic lethality caused by the wMel Wolbachia strain deployed in vector control. These reports motivated proposal of the Two-by-One model of CI whereby two genes cause lethality and one gene rescues it. Here we provide unequivocal support for the model in the Wolbachia strain used in vector control via synthetic methods that recapitulate CI and rescue in the absence of a Wolbachia infections. Our results reveal the set of phage WO genes responsible for this powerful genetic drive system, act as a proof-of-concept that these genes alone can induce gene drive like crossing patterns, and establish methodologies and hypotheses for future studies of CI in Drosophila. We discuss the implications of the Two-by-One model towards functional mechanisms of CI, the emergence of incompatibility between Wolbachia strains, vector control applications, and CI gene nomenclature.
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Bull JJ, Remien CH, Krone SM. Gene-drive-mediated extinction is thwarted by population structure and evolution of sib mating. EVOLUTION MEDICINE AND PUBLIC HEALTH 2019; 2019:66-81. [PMID: 31191905 PMCID: PMC6556056 DOI: 10.1093/emph/eoz014] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/18/2019] [Indexed: 11/12/2022]
Abstract
Background and objectives Genetic engineering combined with CRISPR technology has developed to the point that gene drives can, in theory, be engineered to cause extinction in countless species. Success of extinction programs now rests on the possibility of resistance evolution, which is largely unknown. Depending on the gene-drive technology, resistance may take many forms, from mutations in the nuclease target sequence (e.g. for CRISPR) to specific types of non-random population structures that limit the drive (that may block potentially any gene-drive technology). Methodology We develop mathematical models of various deviations from random mating to consider escapes from extinction-causing gene drives. A main emphasis here is sib mating in the face of recessive-lethal and Y-chromosome drives. Results Sib mating easily evolves in response to both kinds of gene drives and maintains mean fitness above 0, with equilibrium fitness depending on the level of inbreeding depression. Environmental determination of sib mating (as might stem from population density crashes) can also maintain mean fitness above 0. A version of Maynard Smith’s haystack model shows that pre-existing population structure can enable drive-free subpopulations to be maintained against gene drives. Conclusions and implications Translation of mean fitness into population size depends on ecological details, so understanding mean fitness evolution and dynamics is merely the first step in predicting extinction. Nonetheless, these results point to possible escapes from gene-drive-mediated extinctions that lie beyond the control of genome engineering. Lay summary Recent gene drive technologies promise to suppress and even eradicate pests and disease vectors. Simple models of gene-drive evolution in structured populations show that extinction-causing gene drives can be thwarted both through the evolution of sib mating as well as from purely demographic processes that cluster drive-free individuals.
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Affiliation(s)
- James J Bull
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | | | - Stephen M Krone
- Department of Mathematics, University of Idaho, Moscow, ID, USA
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Frieß JL, von Gleich A, Giese B. Gene drives as a new quality in GMO releases-a comparative technology characterization. PeerJ 2019; 7:e6793. [PMID: 31110918 PMCID: PMC6501761 DOI: 10.7717/peerj.6793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/15/2019] [Indexed: 01/10/2023] Open
Abstract
Compared to previous releases of genetically modified organisms (GMOs) which were primarily plants, gene drives represent a paradigm shift in the handling of GMOs: Current regulation of the release of GMOs assumes that for specific periods of time a certain amount of GMOs will be released in a particular region. However, now a type of genetic technology arises whose innermost principle lies in exceeding these limits-the transformation or even eradication of wild populations. The invasive character of gene drives demands a thorough analysis of their functionalities, reliability and potential impact. But such investigations are hindered by the fact that an experimental field test would hardly be reversible. Therefore, an appropriate prospective assessment is of utmost importance for an estimation of the risk potential associated with the application of gene drives. This work is meant to support the inevitable characterization of gene drives by a comparative approach of prospective technology assessment with a focus on potential sources of risk. Therein, the hazard and exposure potential as well as uncertainties with regard to the performance of synthetic gene drives are addressed. Moreover, a quantitative analysis of their invasiveness should enable a differentiated evaluation of their power to transform wild populations.
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Affiliation(s)
- Johannes L Frieß
- Institute for Safety/Security and Risk Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Austria
| | - Arnim von Gleich
- Department of Technology Design and Development, Faculty of Production Engineering, University of Bremen, Germany
| | - Bernd Giese
- Institute for Safety/Security and Risk Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Austria
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36
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Oberhofer G, Ivy T, Hay BA. Cleave and Rescue, a novel selfish genetic element and general strategy for gene drive. Proc Natl Acad Sci U S A 2019; 116:6250-6259. [PMID: 30760597 PMCID: PMC6442612 DOI: 10.1073/pnas.1816928116] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
There is great interest in being able to spread beneficial traits throughout wild populations in ways that are self-sustaining. Here, we describe a chromosomal selfish genetic element, CleaveR [Cleave and Rescue (ClvR)], able to achieve this goal. ClvR comprises two linked chromosomal components. One, germline-expressed Cas9 and guide RNAs (gRNAs)-the Cleaver-cleaves and thereby disrupts endogenous copies of a gene whose product is essential. The other, a recoded version of the essential gene resistant to cleavage and gene conversion with cleaved copies-the Rescue-provides essential gene function. ClvR enhances its transmission, and that of linked genes, by creating conditions in which progeny lacking ClvR die because they have no functional copies of the essential gene. In contrast, those who inherit ClvR survive, resulting in an increase in ClvR frequency. ClvR is predicted to spread to fixation under diverse conditions. To test these predictions, we generated a ClvR element in Drosophila melanogasterClvRtko is located on chromosome 3 and uses Cas9 and four gRNAs to disrupt melanogaster technical knockout (tko), an X-linked essential gene. Rescue activity is provided by tko from Drosophila virilisClvRtko results in germline and maternal carryover-dependent inactivation of melanogaster tko (>99% per generation); lethality caused by this loss is rescued by the virilis transgene; ClvRtko activities are robust to genetic diversity in strains from five continents; and uncleavable but functional melanogaster tko alleles were not observed. Finally, ClvRtko spreads to transgene fixation. The simplicity of ClvR suggests it may be useful for altering populations in diverse species.
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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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37
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Engineered resistance to Zika virus in transgenic Aedes aegypti expressing a polycistronic cluster of synthetic small RNAs. Proc Natl Acad Sci U S A 2019; 116:3656-3661. [PMID: 30723148 PMCID: PMC6397566 DOI: 10.1073/pnas.1810771116] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Here, we describe the generation of Aedes aegypti mosquitoes that are engineered to be resistant to Zika virus (ZIKV) transmission. Our results demonstrate that engineered mosquitoes express a polycistronic cluster of synthetic small RNAs designed to target the ZIKV genome. As a result, homozygous mosquitoes were refractory to ZIKV infection, and therefore could not transmit the virus. Additionally, mosquitoes heterozygous for the transgene showed significantly lower levels of viral infection, dissemination, and transmission compared with wild-type mosquitoes; importantly, these levels were low enough to make such mosquitoes unlikely to transmit ZIKV to a susceptible host. Finally, we discuss how such an engineering approach can be used to combat the major health burden of ZIKV, and potentially other arboviruses, in the future. Recent Zika virus (ZIKV) outbreaks have highlighted the necessity for development of novel vector control strategies to combat arboviral transmission, including genetic versions of the sterile insect technique, artificial infection with Wolbachia to reduce population size and/or vectoring competency, and gene drive-based methods. Here, we describe the development of mosquitoes synthetically engineered to impede vector competence to ZIKV. We demonstrate that a polycistronic cluster of engineered synthetic small RNAs targeting ZIKV is expressed and fully processed in Aedes aegypti, ensuring the formation of mature synthetic small RNAs in the midgut where ZIKV resides in the early stages of infection. Critically, we demonstrate that engineered Ae. aegypti mosquitoes harboring the anti-ZIKV transgene have significantly reduced viral infection, dissemination, and transmission rates of ZIKV. Taken together, these compelling results provide a promising path forward for development of effective genetic-based ZIKV control strategies, which could potentially be extended to curtail other arboviruses.
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38
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Gantz VM, Akbari OS. Gene editing technologies and applications for insects. CURRENT OPINION IN INSECT SCIENCE 2018; 28:66-72. [PMID: 30551769 PMCID: PMC6296244 DOI: 10.1016/j.cois.2018.05.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 05/09/2023]
Abstract
Initially discovered in bacteria, CRISPR-based genome editing endonucleases have proven remarkably amenable for adaptation to insects. To date, these endonucleases have been utilized in a plethora of both model and non-model insects including diverse flies, bees, beetles, butterflies, moths, and grasshoppers, to name a few, thereby revolutionizing functional genomics of insects. In addition to basic genome editing, they have also been invaluable for advanced genome engineering and synthetic biology applications. Here we explore the recent genome editing advancements in insects for generating site-specific genomic mutations, insertions, deletions, as well as more advanced applications such as Homology Assisted Genome Knock-in (HACK), potential to utilize DNA base editing, generating predictable reciprocal chromosomal translocations, and development gene drives to control the fate of wild populations.
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Affiliation(s)
- Valentino M Gantz
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92092, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92092, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, USA.
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39
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Burt A, Deredec A. Self-limiting population genetic control with sex-linked genome editors. Proc Biol Sci 2018; 285:rspb.2018.0776. [PMID: 30051868 PMCID: PMC6083257 DOI: 10.1098/rspb.2018.0776] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
In male heterogametic species the Y chromosome is transmitted solely from fathers to sons, and is selected for based only on its impacts on male fitness. This fact can be exploited to develop efficient pest control strategies that use Y-linked editors to disrupt the fitness of female descendants. With simple population genetic and dynamic models we show that Y-linked editors can be substantially more efficient than other self-limiting strategies and, while not as efficient as gene drive approaches, are expected to have less impact on non-target populations with which there is some gene flow. Efficiency can be further augmented by simultaneously releasing an autosomal X-shredder construct, in either the same or different males. Y-linked editors may be an attractive option to consider when efficient control of a species is desired in some locales but not others.
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Affiliation(s)
- Austin Burt
- Life Sciences, Imperial College, Silwood Park, Ascot SL5 7PY, UK
| | - Anne Deredec
- UMR BIOGER, INRA AgroParisTech, Université Paris-Saclay, Avenue Lucien Bretignières, 78850 Thiverval-Grignon, France
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40
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Noble C, Adlam B, Church GM, Esvelt KM, Nowak MA. Current CRISPR gene drive systems are likely to be highly invasive in wild populations. eLife 2018; 7:33423. [PMID: 29916367 PMCID: PMC6014726 DOI: 10.7554/elife.33423] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/15/2018] [Indexed: 12/25/2022] Open
Abstract
Recent reports have suggested that self-propagating CRISPR-based gene drive systems are unlikely to efficiently invade wild populations due to drive-resistant alleles that prevent cutting. Here we develop mathematical models based on existing empirical data to explicitly test this assumption for population alteration drives. Our models show that although resistance prevents spread to fixation in large populations, even the least effective drive systems reported to date are likely to be highly invasive. Releasing a small number of organisms will often cause invasion of the local population, followed by invasion of additional populations connected by very low rates of gene flow. Hence, initiating contained field trials as tentatively endorsed by the National Academies report on gene drive could potentially result in unintended spread to additional populations. Our mathematical results suggest that self-propagating gene drive is best suited to applications such as malaria prevention that seek to affect all wild populations of the target species.
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Affiliation(s)
- Charleston Noble
- Program for Evolutionary Dynamics, Harvard University, Cambridge, United States.,Department of Genetics, Harvard Medical School, Harvard University, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston MA, United States
| | - Ben Adlam
- Program for Evolutionary Dynamics, Harvard University, Cambridge, United States.,School of Engineering and Applied Science, Harvard University, Cambridge, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Harvard University, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston MA, United States
| | - Kevin M Esvelt
- Massachusetts Institute of Technology Media Lab, Cambridge, United States
| | - Martin A Nowak
- Program for Evolutionary Dynamics, Harvard University, Cambridge, United States.,Department of Mathematics, Harvard University, Cambridge, United States.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
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41
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Buchman AB, Ivy T, Marshall JM, Akbari OS, Hay BA. Engineered Reciprocal Chromosome Translocations Drive High Threshold, Reversible Population Replacement in Drosophila. ACS Synth Biol 2018. [PMID: 29608276 DOI: 10.1101/088393] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Replacement of wild insect populations with transgene-bearing individuals unable to transmit disease or survive under specific environmental conditions using gene drive provides a self-perpetuating method of disease prevention. Mechanisms that require the gene drive element and linked cargo to exceed a high threshold frequency in order for spread to occur are attractive because they offer several points of control: they bring about local, but not global population replacement; and transgenes can be eliminated by reintroducing wildtypes into the population so as to drive the frequency of transgenes below the threshold frequency required for drive. Reciprocal chromosome translocations were proposed as a tool for bringing about high threshold population replacement in 1940 and 1968. However, translocations able to achieve this goal have only been reported once, in the spider mite Tetranychus urticae, a haplo-diploid species in which there is strong selection in haploid males for fit homozygotes. We report the creation of engineered translocation-bearing strains of Drosophila melanogaster, generated through targeted chromosomal breakage and homologous recombination. These strains drive high threshold population replacement in laboratory populations. While it remains to be shown that engineered translocations can bring about population replacement in wild populations, these observations suggest that further exploration of engineered translocations as a tool for controlled population replacement is warranted.
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Affiliation(s)
- Anna B Buchman
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
| | - Tobin Ivy
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - John M Marshall
- School of Public Health , University of California , Berkeley , California 94720 , United States
| | - Omar S Akbari
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
| | - Bruce A Hay
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
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42
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Buchman AB, Ivy T, Marshall JM, Akbari OS, Hay BA. Engineered Reciprocal Chromosome Translocations Drive High Threshold, Reversible Population Replacement in Drosophila. ACS Synth Biol 2018; 7:1359-1370. [PMID: 29608276 DOI: 10.1021/acssynbio.7b00451] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replacement of wild insect populations with transgene-bearing individuals unable to transmit disease or survive under specific environmental conditions using gene drive provides a self-perpetuating method of disease prevention. Mechanisms that require the gene drive element and linked cargo to exceed a high threshold frequency in order for spread to occur are attractive because they offer several points of control: they bring about local, but not global population replacement; and transgenes can be eliminated by reintroducing wildtypes into the population so as to drive the frequency of transgenes below the threshold frequency required for drive. Reciprocal chromosome translocations were proposed as a tool for bringing about high threshold population replacement in 1940 and 1968. However, translocations able to achieve this goal have only been reported once, in the spider mite Tetranychus urticae, a haplo-diploid species in which there is strong selection in haploid males for fit homozygotes. We report the creation of engineered translocation-bearing strains of Drosophila melanogaster, generated through targeted chromosomal breakage and homologous recombination. These strains drive high threshold population replacement in laboratory populations. While it remains to be shown that engineered translocations can bring about population replacement in wild populations, these observations suggest that further exploration of engineered translocations as a tool for controlled population replacement is warranted.
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Affiliation(s)
- Anna B Buchman
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
| | - Tobin Ivy
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - John M Marshall
- School of Public Health , University of California , Berkeley , California 94720 , United States
| | - Omar S Akbari
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
| | - Bruce A Hay
- Division of Biology and Biological Engineering , California Institute of Technology , Pasadena , California 91125 , United States
- Division of Biological Sciences , University of California , San Diego , California 92161 , United States
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Buchman A, Marshall JM, Ostrovski D, Yang T, Akbari OS. Synthetically engineered Medea gene drive system in the worldwide crop pest Drosophila suzukii. Proc Natl Acad Sci U S A 2018. [PMID: 29666236 DOI: 10.1101/162255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Synthetic gene drive systems possess enormous potential to replace, alter, or suppress wild populations of significant disease vectors and crop pests; however, their utility in diverse populations remains to be demonstrated. Here, we report the creation of a synthetic Medea gene drive system in a major worldwide crop pest, Drosophila suzukii We demonstrate that this drive system, based on an engineered maternal "toxin" coupled with a linked embryonic "antidote," is capable of biasing Mendelian inheritance rates with up to 100% efficiency. However, we find that drive resistance, resulting from naturally occurring genetic variation and associated fitness costs, can be selected for and hinder the spread of such a drive. Despite this, our results suggest that this gene drive could maintain itself at high frequencies in a wild population and spread to fixation if either its fitness costs or toxin resistance were reduced, providing a clear path forward for developing future such systems in this pest.
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Affiliation(s)
- Anna Buchman
- Department of Entomology, University of California, Riverside, CA 92521
- Center for Infectious Disease and Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA 94720
| | - Dennis Ostrovski
- Department of Entomology, University of California, Riverside, CA 92521
- Center for Infectious Disease and Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Ting Yang
- Department of Entomology, University of California, Riverside, CA 92521
- Center for Infectious Disease and Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Omar S Akbari
- Department of Entomology, University of California, Riverside, CA 92521;
- Center for Infectious Disease and Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093
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Synthetically engineered Medea gene drive system in the worldwide crop pest Drosophila suzukii. Proc Natl Acad Sci U S A 2018; 115:4725-4730. [PMID: 29666236 PMCID: PMC5939061 DOI: 10.1073/pnas.1713139115] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we describe a fully functional gene drive system constructed in a major worldwide crop pest, Drosophila suzukii. This system is composed of a synthetic Medea drive with a maternal miRNA “toxin” and a zygotic “antidote,” and we demonstrate that it can bias inheritance with 100% efficiency and can persist in a population given high release frequencies. We discuss how such a system may be used to suppress D. suzukii populations or render them harmless to target crops. Synthetic gene drive systems possess enormous potential to replace, alter, or suppress wild populations of significant disease vectors and crop pests; however, their utility in diverse populations remains to be demonstrated. Here, we report the creation of a synthetic Medea gene drive system in a major worldwide crop pest, Drosophila suzukii. We demonstrate that this drive system, based on an engineered maternal “toxin” coupled with a linked embryonic “antidote,” is capable of biasing Mendelian inheritance rates with up to 100% efficiency. However, we find that drive resistance, resulting from naturally occurring genetic variation and associated fitness costs, can be selected for and hinder the spread of such a drive. Despite this, our results suggest that this gene drive could maintain itself at high frequencies in a wild population and spread to fixation if either its fitness costs or toxin resistance were reduced, providing a clear path forward for developing future such systems in this pest.
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45
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Marshall JM, Akbari OS. Can CRISPR-Based Gene Drive Be Confined in the Wild? A Question for Molecular and Population Biology. ACS Chem Biol 2018; 13:424-430. [PMID: 29370514 DOI: 10.1021/acschembio.7b00923] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The recent discovery of CRISPR and its application as a gene editing tool has enabled a range of gene drive systems to be engineered with greater ease. In order for the benefits of this technology to be realized, in some circumstances drive systems should be developed that are capable of both spreading into populations to achieve their desired impact and being recalled in the event of unwanted consequences or public disfavor. We review the performance of three broad categories of drive systems at achieving these goals: threshold-dependent drives, homing-based drive and remediation systems, and temporally self-limiting systems such as daisy-chain drives.
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Affiliation(s)
- John M Marshall
- Divisions of Biostatistics and Epidemiology, School of Public Health, University of California , Berkeley, California 94720, United States
| | - Omar S Akbari
- Section of Cell and Developmental Biology, University of California, San Diego , La Jolla, California 92093, United States of America
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46
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Abstract
Drive is a process of accelerated inheritance from one generation to the next that allows some genes to spread rapidly through populations even if they do not contribute to-or indeed even if they detract from-organismal survival and reproduction. Genetic elements that can spread by drive include gametic and zygotic killers, meiotic drivers, homing endonuclease genes, B chromosomes, and transposable elements. The fact that gene drive can lead to the spread of fitness-reducing traits (including lethality and sterility) makes it an attractive process to consider exploiting to control disease vectors and other pests. There are a number of efforts to develop synthetic gene drive systems, particularly focused on the mosquito-borne diseases that continue to plague us.
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Affiliation(s)
- Austin Burt
- Life Sciences, Imperial College, Silwood Park, Ascot, SL5
7PY, United Kingdom
| | - Andrea Crisanti
- Life Sciences, Imperial College, South Kensington, London, SW7 2AZ, United Kingdom
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Benedict MQ, Burt A, Capurro ML, De Barro P, Handler AM, Hayes KR, Marshall JM, Tabachnick WJ, Adelman ZN. Recommendations for Laboratory Containment and Management of Gene Drive Systems in Arthropods. Vector Borne Zoonotic Dis 2018; 18:2-13. [PMID: 29040058 PMCID: PMC5846571 DOI: 10.1089/vbz.2017.2121] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Versatile molecular tools for creating driving transgenes and other invasive genetic factors present regulatory, ethical, and environmental challenges that should be addressed to ensure their safe use. In this article, we discuss driving transgenes and invasive genetic factors that can potentially spread after their introduction into a small proportion of individuals in a population. The potential of invasive genetic factors to increase their number in natural populations presents challenges that require additional safety measures not provided by previous recommendations regarding accidental release of arthropods. In addition to providing physical containment, invasive genetic factors require greater attention to strain management, including their distribution and identity confirmation. In this study, we focus on insects containing such factors with recommendations for investigators who are creating them, institutional biosafety committees charged with ensuring safety, funding agencies providing support, those managing insectaries handling these materials who are responsible for containment, and other persons who will be receiving insects-transgenic or not-from these facilities. We give specific examples of efforts to modify mosquitoes for mosquito-borne disease control, but similar considerations are relevant to other arthropods that are important to human health, the environment, and agriculture.
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Affiliation(s)
- Mark Q Benedict
- 1 Entomology Branch, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Austin Burt
- 2 Life Sciences, Imperial College London , Ascot, United Kingdom
| | - Margareth L Capurro
- 3 Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo , Sao Paulo, Brazil
- 4 National Institute of Science and Technology in Molecular Entomology , National Council of Scientific and Technological Development (INCT-EM/CNPq), Rio de Janeiro, Brazil
| | | | - Alfred M Handler
- 6 USDA-ARS, Center for Medical, Agricultural, and Veterinary Entomology , Gainesville, Florida
| | | | - John M Marshall
- 8 Divisions of Biostatistics and Epidemiology, School of Public Health, University of California , Berkeley, California
| | - Walter J Tabachnick
- 9 Florida Medical Entomology Laboratory, Department of Entomology and Nematology, University of Florida , Vero Beach, Florida
| | - Zach N Adelman
- 10 Department of Entomology, Texas A&M University , College Station, Texas
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48
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Abstract
Self-propagating gene drive technologies have a number of desirable characteristics that warrant their development for the control of insect pest and vector populations, such as the malaria-transmitting mosquitoes. Theoretically easy to deploy and self-sustaining, these tools may be used to generate cost-effective interventions that benefit society without obvious bias related to wealth, age or education. Their species-specific design offers the potential to reduce environmental risks and aim to be compatible and complementary with other control strategies, potentially expediting the elimination and eradication of malaria. A number of strategies have been proposed for gene-drive based control of the malaria mosquito and recent demonstrations have shown proof-of-principle in the laboratory. Though several technical, ethical and regulatory challenges remain, none appear insurmountable if research continues in a step-wise and open manner.
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Affiliation(s)
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London, UK
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49
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Noble C, Olejarz J, Esvelt KM, Church GM, Nowak MA. Evolutionary dynamics of CRISPR gene drives. SCIENCE ADVANCES 2017; 3:e1601964. [PMID: 28435878 PMCID: PMC5381957 DOI: 10.1126/sciadv.1601964] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/10/2017] [Indexed: 05/28/2023]
Abstract
The alteration of wild populations has been discussed as a solution to a number of humanity's most pressing ecological and public health concerns. Enabled by the recent revolution in genome editing, clustered regularly interspaced short palindromic repeats (CRISPR) gene drives-selfish genetic elements that can spread through populations even if they confer no advantage to their host organism-are rapidly emerging as the most promising approach. However, before real-world applications are considered, it is imperative to develop a clear understanding of the outcomes of drive release in nature. Toward this aim, we mathematically study the evolutionary dynamics of CRISPR gene drives. We demonstrate that the emergence of drive-resistant alleles presents a major challenge to previously reported constructs, and we show that an alternative design that selects against resistant alleles could greatly improve evolutionary stability. We discuss all results in the context of CRISPR technology and provide insights that inform the engineering of practical gene drive systems.
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Affiliation(s)
- Charleston Noble
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School, Cambridge, MA 02138, USA
| | - Jason Olejarz
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
| | - Kevin M. Esvelt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School, Cambridge, MA 02138, USA
| | - Martin A. Nowak
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
- Department of Mathematics, Harvard University, Cambridge, MA 02138, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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50
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Unckless RL, Clark AG, Messer PW. Evolution of Resistance Against CRISPR/Cas9 Gene Drive. Genetics 2017; 205:827-841. [PMID: 27941126 PMCID: PMC5289854 DOI: 10.1534/genetics.116.197285] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/01/2016] [Indexed: 11/18/2022] Open
Abstract
CRISPR/Cas9 gene drive (CGD) promises to be a highly adaptable approach for spreading genetically engineered alleles throughout a species, even if those alleles impair reproductive success. CGD has been shown to be effective in laboratory crosses of insects, yet it remains unclear to what extent potential resistance mechanisms will affect the dynamics of this process in large natural populations. Here we develop a comprehensive population genetic framework for modeling CGD dynamics, which incorporates potential resistance mechanisms as well as random genetic drift. Using this framework, we calculate the probability that resistance against CGD evolves from standing genetic variation, de novo mutation of wild-type alleles, or cleavage repair by nonhomologous end joining (NHEJ)-a likely by-product of CGD itself. We show that resistance to standard CGD approaches should evolve almost inevitably in most natural populations, unless repair of CGD-induced cleavage via NHEJ can be effectively suppressed, or resistance costs are on par with those of the driver. The key factor determining the probability that resistance evolves is the overall rate at which resistance alleles arise at the population level by mutation or NHEJ. By contrast, the conversion efficiency of the driver, its fitness cost, and its introduction frequency have only minor impact. Our results shed light on strategies that could facilitate the engineering of drivers with lower resistance potential, and motivate the possibility to embrace resistance as a possible mechanism for controlling a CGD approach. This study highlights the need for careful modeling of the population dynamics of CGD prior to the actual release of a driver construct into the wild.
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Affiliation(s)
- Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853
| | - Philipp W Messer
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853
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