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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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2
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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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3
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Thevendran R, Maheswaran S. Recognizing CRISPR as the new age disease-modifying drug: Strategies to bioengineer CRISPR/Cas for direct in vivo delivery. Biotechnol J 2023; 18:e2300077. [PMID: 37179485 DOI: 10.1002/biot.202300077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/15/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) have established itself as a frontier technology in genetic engineering. Researchers have successfully used the CRISPR/Cas system as precise gene editing tools and have further expanded their scope beyond both imaging and diagnostic applications. The most prominent utility of CRISPR is its capacity for gene therapy, serving as the contemporary, disease-modifying drug at the genetic level of human medical disorders. Correcting these diseases using CRISPR-based gene editing has developed to the extent of preclinical trials and possible patient treatments. A major impediment in actualizing this is the complications associated with in vivo delivery of the CRISPR/Cas complex. Currently, only the viral vectors (e.g., lentivirus) and non-viral encapsulation (e.g., lipid particles, polymer-based, and gold nanoparticles) techniques have been extensively reviewed, neglecting the efficiency of direct delivery. However, the direct delivery of CRISPR/Cas for in vivo gene editing therapies is an intricate process with numerous drawbacks. Hence, this paper discusses in detail both the need and the strategies that can potentially improve the direct delivery aspects of CRISPR/Cas biomolecules for gene therapy of human diseases. Here, we focus on enhancing the molecular and functional features of the CRISPR/Cas system for targeted in vivo delivery such as on-site localization, internalization, reduced immunogenicity, and better in vivo stability. We additionally emphasize the CRISPR/Cas complex as a multifaceted, biomolecular vehicle for co-delivery with therapeutic agents in targeted disease treatments. The delivery formats of efficient CRISPR/Cas systems for human gene editing are also briefly elaborated.
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Affiliation(s)
- Ramesh Thevendran
- Department of Biotechnology, Faculty of Applied Science, AIMST University, Bedong, Kedah, Malaysia
| | - Solayappan Maheswaran
- Department of Biotechnology, Faculty of Applied Science, AIMST University, Bedong, Kedah, Malaysia
- Centre of Excellence for Nanotechnology and Nanomedicine (CoExNano), AIMST University, Bedong, Kedah, Malaysia
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4
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Combs MA, Golnar AJ, Overcash JM, Lloyd AL, Hayes KR, O'Brochta DA, Pepin KM. Leveraging eco-evolutionary models for gene drive risk assessment. Trends Genet 2023:S0168-9525(23)00090-2. [PMID: 37198063 DOI: 10.1016/j.tig.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023]
Abstract
Engineered gene drives create potential for both widespread benefits and irreversible harms to ecosystems. CRISPR-based systems of allelic conversion have rapidly accelerated gene drive research across diverse taxa, putting field trials and their necessary risk assessments on the horizon. Dynamic process-based models provide flexible quantitative platforms to predict gene drive outcomes in the context of system-specific ecological and evolutionary features. Here, we synthesize gene drive dynamic modeling studies to highlight research trends, knowledge gaps, and emergent principles, organized around their genetic, demographic, spatial, environmental, and implementation features. We identify the phenomena that most significantly influence model predictions, discuss limitations of biological complexity and uncertainty, and provide insights to promote responsible development and model-assisted risk assessment of gene drives.
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Affiliation(s)
- Matthew A Combs
- National Wildlife Research Center, United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, CO, 80521, USA.
| | - Andrew J Golnar
- National Wildlife Research Center, United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, CO, 80521, USA
| | - Justin M Overcash
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Biotechnology Regulatory Services, 20737, USA
| | - Alun L Lloyd
- North Carolina State University, Biomathematics Graduate Program and Department of Mathematics, Raleigh, NC, 27695, USA
| | - Keith R Hayes
- The Commonwealth Scientific and Industrial Research Organisation, Data 61, Hobart, TAS, 7004, Australia
| | - David A O'Brochta
- Foundation for the National Institutes of Health, North Bethesda, MD, 20852, USA
| | - Kim M Pepin
- National Wildlife Research Center, United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, CO, 80521, USA
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5
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Frieß JL, Lalyer CR, Giese B, Simon S, Otto M. Review of gene drive modelling and implications for risk assessment of gene drive organisms. Ecol Modell 2023. [DOI: 10.1016/j.ecolmodel.2023.110285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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R. N. Ferreira JG, A. Americo J, L. A. S. do Amaral D, Sendim F, R. da Cunha Y, Blaxter M, Uliano-Silva M, de F. Rebelo M. A chromosome-level assembly supports genome-wide investigation of the DMRT gene family in the golden mussel (Limnoperna fortunei). Gigascience 2022; 12:giad072. [PMID: 37776366 PMCID: PMC10541798 DOI: 10.1093/gigascience/giad072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/12/2023] [Accepted: 08/21/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND The golden mussel (Limnoperna fortunei) is a highly invasive species that causes environmental and socioeconomic losses in invaded areas. Reference genomes have proven to be a valuable resource for studying the biology of invasive species. While the current golden mussel genome has been useful for identifying new genes, its high fragmentation hinders some applications. FINDINGS In this study, we provide the first chromosome-level reference genome for the golden mussel. The genome was built using PacBio HiFi, 10X, and Hi-C sequencing data. The final assembly contains 99.4% of its total length assembled to the 15 chromosomes of the species and a scaffold N50 of 97.05 Mb. A total of 34,862 protein-coding genes were predicted, of which 84.7% were functionally annotated. A significant (6.48%) proportion of the genome was found to be in a hemizygous state. Using the new genome, we have performed a genome-wide characterization of the Doublesex and Mab-3 related transcription factor gene family, which has been proposed as a target for population control strategies in other species. CONCLUSIONS From the applied research perspective, a higher-quality genome will support genome editing with the aim of developing biotechnology-based solutions to control invasion. From the basic research perspective, the new genome is a high-quality reference for molecular evolutionary studies of Mytilida and other Lophotrochozoa, and it may be used as a reference for future resequencing studies to assess genomic variation among different golden mussel populations, unveiling potential routes of dispersion and helping to establish better control policies.
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Affiliation(s)
- João Gabriel R. N. Ferreira
- Bio Bureau Biotecnologia, Rio de Janeiro 21941-850, Brazil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
| | | | | | - Fábio Sendim
- Bio Bureau Biotecnologia, Rio de Janeiro 21941-850, Brazil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
| | - Yasmin R. da Cunha
- Bio Bureau Biotecnologia, Rio de Janeiro 21941-850, Brazil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
| | | | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Hinxton CB10 1RQ, UK
| | | | - Mauro de F. Rebelo
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
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Asad M, Liu D, Chen J, Yang G. Applications of gene drive systems for population suppression of insect pests. BULLETIN OF ENTOMOLOGICAL RESEARCH 2022; 112:724-733. [PMID: 36043456 DOI: 10.1017/s0007485322000268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Population suppression is an effective way for controlling insect pests and disease vectors, which cause significant damage to crop and spread contagious diseases to plants, animals and humans. Gene drive systems provide innovative opportunities for the insect pests population suppression by driving genes that impart fitness costs on populations of pests or disease vectors. Different gene-drive systems have been developed in insects and applied for their population suppression. Here, different categories of gene drives such as meiotic drive (MD), under-dominance (UD), homing endonuclease-based gene drive (HEGD) and especially the CRISPR/Cas9-based gene drive (CCGD) were reviewed, including the history, types, process and mechanisms. Furthermore, the advantages and limitations of applying different gene-drive systems to suppress the insect population were also summarized. This review provides a foundation for developing a specific gene-drive system for insect population suppression.
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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 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou 350002, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou 350002, 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 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou 350002, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou 350002, 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 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou 350002, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou 350002, 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 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou 350002, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Karmakar S, Das P, Panda D, Xie K, Baig MJ, Molla KA. A detailed landscape of CRISPR-Cas-mediated plant disease and pest management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111376. [PMID: 35835393 DOI: 10.1016/j.plantsci.2022.111376] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.
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Affiliation(s)
| | - Priya Das
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mirza J Baig
- ICAR-National Rice Research Institute, Cuttack 753006, India.
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9
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Pacheco ID, Walling LL, Atkinson PW. Gene Editing and Genetic Control of Hemipteran Pests: Progress, Challenges and Perspectives. Front Bioeng Biotechnol 2022; 10:900785. [PMID: 35747496 PMCID: PMC9209771 DOI: 10.3389/fbioe.2022.900785] [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: 03/21/2022] [Accepted: 05/09/2022] [Indexed: 12/16/2022] Open
Abstract
The origin of the order Hemiptera can be traced to the late Permian Period more than 230 MYA, well before the origin of flowering plants 100 MY later in during the Cretaceous period. Hemipteran species consume their liquid diets using a sucking proboscis; for phytophagous hemipterans their mouthparts (stylets) are elegant structures that enable voracious feeding from plant xylem or phloem. This adaptation has resulted in some hemipteran species becoming globally significant pests of agriculture resulting in significant annual crop losses. Due to the reliance on chemical insecticides for the control of insect pests in agricultural settings, many hemipteran pests have evolved resistance to insecticides resulting in an urgent need to develop new, species-specific and environmentally friendly methods of pest control. The rapid advances in CRISPR/Cas9 technologies in model insects such as Drosophila melanogaster, Tribolium castaneum, Bombyx mori, and Aedes aegypti has spurred a new round of innovative genetic control strategies in the Diptera and Lepidoptera and an increased interest in assessing genetic control technologies for the Hemiptera. Genetic control approaches in the Hemiptera have, to date, been largely overlooked due to the problems of introducing genetic material into the germline of these insects. The high frequency of CRISPR-mediated mutagenesis in model insect species suggest that, if the delivery problem for Hemiptera could be solved, then gene editing in the Hemiptera might be quickly achieved. Significant advances in CRISPR/Cas9 editing have been realized in nine species of Hemiptera over the past 4 years. Here we review progress in the Hemiptera and discuss the challenges and opportunities for extending contemporary genetic control strategies into species in this agriculturally important insect orderr.
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Affiliation(s)
- Inaiara D. Pacheco
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| | - Linda L. Walling
- Department of Botany & Plant Sciences, University of California, Riverside, Riverside, CA, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Peter W. Atkinson
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Peter W. Atkinson,
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10
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Beaghton PJ, Burt A. Gene drives and population persistence vs elimination: The impact of spatial structure and inbreeding at low density. Theor Popul Biol 2022; 145:109-125. [PMID: 35247370 DOI: 10.1016/j.tpb.2022.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 11/26/2022]
Abstract
Synthetic gene drive constructs are being developed to control disease vectors, invasive species, and other pest species. In a well-mixed random mating population a sufficiently strong gene drive is expected to eliminate a target population, but it is not clear whether the same is true when spatial processes play a role. In species with an appropriate biology it is possible that drive-induced reductions in density might lead to increased inbreeding, reducing the efficacy of drive, eventually leading to suppression rather than elimination, regardless of how strong the drive is. To investigate this question we analyse a series of explicitly solvable stochastic models considering a range of scenarios for the relative timing of mating, reproduction, and dispersal and analyse the impact of two different types of gene drive, a Driving Y chromosome and a homing construct targeting an essential gene. We find in all cases a sufficiently strong Driving Y will go to fixation and the population will be eliminated, except in the one life history scenario (reproduction and mating in patches followed by dispersal) where low density leads to increased inbreeding, in which case the population persists indefinitely, tending to either a stable equilibrium or a limit cycle. These dynamics arise because Driving Y males have reduced mating success, particularly at low densities, due to having fewer sisters to mate with. Increased inbreeding at low densities can also prevent a homing construct from eliminating a population. For both types of drive, if there is strong inbreeding depression, then the population cannot be rescued by inbreeding and it is eliminated. These results highlight the potentially critical role that low-density-induced inbreeding and inbreeding depression (and, by extension, other sources of Allee effects) can have on the eventual impact of a gene drive on a target population.
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Affiliation(s)
- P J Beaghton
- Institute for Security Science and Technology, South Kensington Campus, Imperial College London, London, UK; Department of Computing, South Kensington Campus, Imperial College London, London, UK.
| | - Austin Burt
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
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11
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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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12
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López Hernández JF, Helston RM, Lange JJ, Billmyre RB, Schaffner SH, Eickbush MT, McCroskey S, Zanders SE. Diverse mating phenotypes impact the spread of wtf meiotic drivers in Schizosaccharomyces pombe. eLife 2021; 10:e70812. [PMID: 34895466 PMCID: PMC8789285 DOI: 10.7554/elife.70812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022] Open
Abstract
Meiotic drivers are genetic elements that break Mendel's law of segregation to be transmitted into more than half of the offspring produced by a heterozygote. The success of a driver relies on outcrossing (mating between individuals from distinct lineages) because drivers gain their advantage in heterozygotes. It is, therefore, curious that Schizosaccharomyces pombe, a species reported to rarely outcross, harbors many meiotic drivers. To address this paradox, we measured mating phenotypes in S. pombe natural isolates. We found that the propensity for cells from distinct clonal lineages to mate varies between natural isolates and can be affected both by cell density and by the available sexual partners. Additionally, we found that the observed levels of preferential mating between cells from the same clonal lineage can slow, but not prevent, the spread of a wtf meiotic driver in the absence of additional fitness costs linked to the driver. These analyses reveal parameters critical to understanding the evolution of S. pombe and help explain the success of meiotic drivers in this species.
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Affiliation(s)
| | | | - Jeffrey J Lange
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | - Samantha H Schaffner
- Stowers Institute for Medical ResearchKansas CityUnited States
- Kenyon CollegeGambierUnited States
| | | | - Scott McCroskey
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Sarah E Zanders
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Molecular and Integrative Physiology, University of Kansas Medical CenterKansas CityUnited States
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13
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Lalyer CR, Sigsgaard L, Giese B. Ecological vulnerability analysis for suppression of Drosophila suzukii by gene drives. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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14
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Lewald KM, Abrieux A, Wilson DA, Lee Y, Conner WR, Andreazza F, Beers EH, Burrack HJ, Daane KM, Diepenbrock L, Drummond FA, Fanning PD, Gaffney MT, Hesler SP, Ioriatti C, Isaacs R, Little BA, Loeb GM, Miller B, Nava DE, Rendon D, Sial AA, da Silva CSB, Stockton DG, Van Timmeren S, Wallingford A, Walton VM, Wang X, Zhao B, Zalom FG, Chiu JC. Population genomics of Drosophila suzukii reveal longitudinal population structure and signals of migrations in and out of the continental United States. G3-GENES GENOMES GENETICS 2021; 11:6380432. [PMID: 34599814 PMCID: PMC8664444 DOI: 10.1093/g3journal/jkab343] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/10/2021] [Indexed: 11/14/2022]
Abstract
Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. In this study, we sequenced whole genomes of 237 individual flies collected across the continental United States, as well as several sites in Europe, Brazil, and Asia, to identify and analyze hundreds of thousands of genetic markers. We observed strong population structure between Western and Eastern US populations, but no evidence of any population structure between different latitudes within the continental United States, suggesting that there are no broad-scale adaptations occurring in response to differences in winter climates. We detect admixture from Hawaii to the Western United States and from the Eastern United States to Europe, in agreement with previously identified introduction routes inferred from microsatellite analysis. We also detect potential signals of admixture from the Western United States back to Asia, which could have important implications for shipping and quarantine policies for exported agriculture. We anticipate this large genomic dataset will spur future research into the genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.
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Affiliation(s)
- Kyle M Lewald
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Antoine Abrieux
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Derek A Wilson
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Yoosook Lee
- Florida Medical Entomology Laboratory, University of Florida Institute of Food and Agricultural Sciences, Vero Beach, FL 32603, USA
| | - William R Conner
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Felipe Andreazza
- Laboratory of Entomology, Embrapa Clima Temperado, BR 392 Km 78, Caixa Postal 403, Pelotas, RS 96010-971, Brazil
| | - Elizabeth H Beers
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA 99164, USA
| | - Hannah J Burrack
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27601, USA
| | - Kent M Daane
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Lauren Diepenbrock
- UF IFAS Citrus Research and Education Center, University of Florida, Lake Alfred, FL 32603, USA
| | - Francis A Drummond
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Philip D Fanning
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Michael T Gaffney
- Horticultural Development Department, Teagasc, Ashtown, Dublin 15, Ireland
| | - Stephen P Hesler
- Department of Entomology, Cornell AgriTech, Cornell University, Geneva, NY 14850, USA
| | - Claudio Ioriatti
- Technology Transfer Centre, Fondazione Edmund Mach, Via E. Mach, 1, 38010 San Michele all'Adige (TN), Italy
| | - Rufus Isaacs
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Brian A Little
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Gregory M Loeb
- Department of Entomology, Cornell AgriTech, Cornell University, Geneva, NY 14850, USA
| | - Betsey Miller
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Dori E Nava
- Laboratory of Entomology, Embrapa Clima Temperado, BR 392 Km 78, Caixa Postal 403, Pelotas, RS 96010-971, Brazil
| | - Dalila Rendon
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Ashfaq A Sial
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | | | - Dara G Stockton
- Department of Entomology, Cornell AgriTech, Cornell University, Geneva, NY 14850, USA.,USDA-ARS, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA
| | - Steven Van Timmeren
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Anna Wallingford
- Department of Entomology, Cornell AgriTech, Cornell University, Geneva, NY 14850, USA.,Department of Agriculture, Nutrition & Food Systems, University of New Hampshire, Durham, NH 03824, USA
| | - Vaughn M Walton
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Xingeng Wang
- USDA Agricultural Research Service, Beneficial Insects Introduction Research Unit, Newark, DE 19713, USA
| | - Bo Zhao
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27601, USA
| | - Frank G Zalom
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616, USA
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15
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Reid WR, Olson KE, Franz AWE. Current Effector and Gene-Drive Developments to Engineer Arbovirus-Resistant Aedes aegypti (Diptera: Culicidae) for a Sustainable Population Replacement Strategy in the Field. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1987-1996. [PMID: 33704462 PMCID: PMC8421695 DOI: 10.1093/jme/tjab030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 05/13/2023]
Abstract
Arthropod-borne viruses (arboviruses) such as dengue, Zika, and chikungunya viruses cause morbidity and mortality among human populations living in the tropical regions of the world. Conventional mosquito control efforts based on insecticide treatments and/or the use of bednets and window curtains are currently insufficient to reduce arbovirus prevalence in affected regions. Novel, genetic strategies that are being developed involve the genetic manipulation of mosquitoes for population reduction and population replacement purposes. Population replacement aims at replacing arbovirus-susceptible wild-type mosquitoes in a target region with those that carry a laboratory-engineered antiviral effector to interrupt arboviral transmission in the field. The strategy has been primarily developed for Aedes aegypti (L.), the most important urban arbovirus vector. Antiviral effectors based on long dsRNAs, miRNAs, or ribozymes destroy viral RNA genomes and need to be linked to a robust gene drive to ensure their fixation in the target population. Synthetic gene-drive concepts are based on toxin/antidote, genetic incompatibility, and selfish genetic element principles. The CRISPR/Cas9 gene editing system can be configurated as a homing endonuclease gene (HEG) and HEG-based drives became the preferred choice for mosquitoes. HEGs are highly allele and nucleotide sequence-specific and therefore sensitive to single-nucleotide polymorphisms/resistant allele formation. Current research efforts test new HEG-based gene-drive designs that promise to be less sensitive to resistant allele formation. Safety aspects in conjunction with gene drives are being addressed by developing procedures that would allow a recall or overwriting of gene-drive transgenes once they have been released.
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Affiliation(s)
- William R Reid
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Ken E Olson
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Alexander W E Franz
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
- Corresponding author, e-mail:
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16
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El-Sappah AH, Yan K, Huang Q, Islam MM, Li Q, Wang Y, Khan MS, Zhao X, Mir RR, Li J, El-Tarabily KA, Abbas M. Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2021; 12:705249. [PMID: 34589097 PMCID: PMC8475493 DOI: 10.3389/fpls.2021.705249] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/10/2021] [Indexed: 05/19/2023]
Abstract
Gene silencing is a negative feedback mechanism that regulates gene expression to define cell fate and also regulates metabolism and gene expression throughout the life of an organism. In plants, gene silencing occurs via transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). TGS obscures transcription via the methylation of 5' untranslated region (5'UTR), whereas PTGS causes the methylation of a coding region to result in transcript degradation. In this review, we summarized the history and molecular mechanisms of gene silencing and underlined its specific role in plant growth and crop production.
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Affiliation(s)
- Ahmed H. El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Qiulan Huang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
- College of Tea Science, Yibin University, Yibin, China
| | | | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Wang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Muhammad Sarwar Khan
- Center of Agriculture Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Xianming Zhao
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST–K), Sopore, India
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Khaled A. El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
- Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
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17
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Feng X, Kambic L, Nishimoto JH, Reed FA, Denton JA, Sutton JT, Gantz VM. Evaluation of Gene Knockouts by CRISPR as Potential Targets for the Genetic Engineering of the Mosquito Culex quinquefasciatus. CRISPR J 2021; 4:595-608. [PMID: 34280034 PMCID: PMC8392076 DOI: 10.1089/crispr.2021.0028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Culex quinquefasciatus mosquitoes are a globally widespread vector of several human and animal pathogens. Their biology and behavior allow them to thrive in proximity to urban areas, rendering them a constant public health threat. Their mixed bird/mammal feeding behavior further offers a vehicle for zoonotic pathogens transmission to people and, separately, poses a threat to the conservation of insular birds. The advent of CRISPR has led to the development of novel technologies for the genetic engineering of wild mosquito populations. Yet, research into Cx. quinquefasciatus has been lagging compared to other disease vectors. Here, we use this tool to disrupt a set of five pigmentation genes in Cx. quinquefasciatus that, when altered, lead to visible, homozygous-viable phenotypes. We further validate this approach in separate laboratories and in two distinct strains of Cx. quinquefasciatus that are relevant to potential future public health and bird conservation applications. We generate a double-mutant line, demonstrating the possibility of sequentially combining multiple such mutations in a single individual. Lastly, we target two loci, doublesex in the sex-determination pathway and proboscipedia, a hox gene, demonstrating the flexibility of these methods applied to novel targets. Our work provides a platform of seven validated loci that could be used for targeted mutagenesis in Cx. quinquefasciatus and the future development of genetic suppression strategies for this species. Furthermore, the mutant lines generated here could have widespread utility to the research community using this model organism, as they could be used as targets for transgene delivery, where a copy of the disrupted gene could be included as an easily scored transgenesis marker.
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Affiliation(s)
- Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
| | - Lukas Kambic
- Department of Biology, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, USA
| | | | - Floyd A. Reed
- School of Life Sciences, University of Hawaiʻi at Mānoa, Honolulu, Hawai‘i, USA
| | - Jai A. Denton
- Institute of Vector-borne Disease, University of Monash, Clayton, Australia
| | - Jolene T. Sutton
- Department of Biology, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, USA
| | - Valentino M. Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
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18
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Targeting Conserved Sequences Circumvents the Evolution of Resistance in a Viral Gene Drive against Human Cytomegalovirus. J Virol 2021; 95:e0080221. [PMID: 34011551 DOI: 10.1128/jvi.00802-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gene drives are genetic systems designed to efficiently spread a modification through a population. They have been designed almost exclusively in eukaryotic species, especially in insects. We recently developed a CRISPR-based gene drive system in herpesviruses that relies on similar mechanisms and could efficiently spread into a population of wild-type viruses. A common consequence of gene drives in insects is the appearance and selection of drive-resistant sequences that are no longer recognized by CRISPR-Cas9. In this study, we analyzed in cell culture experiments the evolution of resistance in a viral gene drive against human cytomegalovirus. We report that after an initial invasion of the wild-type population, a drive-resistant population is positively selected over time and outcompetes gene drive viruses. However, we show that targeting evolutionarily conserved sequences ensures that drive-resistant viruses acquire long-lasting mutations and are durably attenuated. As a consequence, and even though engineered viruses do not stably persist in the viral population, remaining viruses have a replication defect, leading to a long-term reduction of viral levels. This marks an important step toward developing effective gene drives in herpesviruses, especially for therapeutic applications. IMPORTANCE The use of defective viruses that interfere with the replication of their infectious parent after coinfecting the same cells-a therapeutic strategy known as viral interference-has recently generated a lot of interest. The CRISPR-based system that we recently reported for herpesviruses represents a novel interfering strategy that causes the conversion of wild-type viruses into new recombinant viruses and drives the native viral population to extinction. In this study, we analyzed how targeted viruses evolved resistance against the technology. Through numerical simulations and cell culture experiments with human cytomegalovirus, we showed that after the initial propagation, a resistant viral population is positively selected and outcompetes engineered viruses over time. We show, however, that targeting evolutionarily conserved sequences ensures that resistant viruses are mutated and attenuated, which leads to a long-term reduction of viral levels. This marks an important step toward the development of novel therapeutic strategies against herpesviruses.
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19
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Lanzaro GC, Sánchez C HM, Collier TC, Marshall JM, James AA. Population modification strategies for malaria vector control are uniquely resilient to observed levels of gene drive resistance alleles. Bioessays 2021; 43:e2000282. [PMID: 34151435 DOI: 10.1002/bies.202000282] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 05/13/2021] [Accepted: 05/31/2021] [Indexed: 11/09/2022]
Abstract
Cas9/guide RNA (gRNA)-based gene drive systems are expected to play a transformative role in malaria elimination efforts., whether through population modification, in which the drive system contains parasite-refractory genes, or population suppression, in which the drive system induces a severe fitness load resulting in population decline or extinction. DNA sequence polymorphisms representing alternate alleles at gRNA target sites may confer a drive-resistant phenotype in individuals carrying them. Modeling predicts that, for observed levels of SGV at potential target sites and observed rates of de novo DRA formation, population modification strategies are uniquely resilient to DRAs. We conclude that gene drives can succeed when fitness costs incurred by drive-carrying mosquitoes are low enough to prevent strong positive selection for DRAs produced de novo or as part of the SGV and that population modification strategies are less prone to failure due to drive resistance.
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Affiliation(s)
- Gregory C Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Hector M Sánchez C
- Divisions of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, California, USA
| | - Travis C Collier
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - John M Marshall
- Divisions of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, California, USA
| | - Anthony A James
- Department of Microbiology & Molecular Genetics, University of California, Irvine, California, USA.,Department of Molecular Biology & Biochemistry, University of California, Irvine, California, USA
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20
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Orr TJ, Hayssen V. The Female Snark Is Still a Boojum: Looking toward the Future of Studying Female Reproductive Biology. Integr Comp Biol 2021; 60:782-795. [PMID: 32702114 DOI: 10.1093/icb/icaa091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Philosophical truths are hidden in Lewis Carroll's nonsense poems, such as "The hunting of the snark." When the poem is used as a scientific allegory, a snark stands for the pursuit of scientific truth, while a boojum is a spurious discovery. In the study of female biology, boojums have been the result of the use of cultural stereotypes to frame hypotheses and methodologies. Although female reproduction is key for the continuation of sexually reproducing species, not only have females been understudied in many regards, but also data have commonly been interpreted in the context of now-outdated social mores. Spurious discoveries, boojums, are the result. In this article, we highlight specific gaps in our knowledge of female reproductive biology and provide a jumping-off point for future research. We discuss the promise of emerging methodologies (e.g., micro-CT scanning, high-throughput sequencing, proteomics, big-data analysis, CRISPR-Cas9, and viral vector technology) that can yield insights into previously cryptic processes and features. For example, in mice, deoxyribonucleic acid sequencing via chromatin immunoprecipitation followed by sequencing is already unveiling how epigenetics lead to sex differences in brain development. Similarly, new explorations, including microbiome research, are rapidly debunking dogmas such as the notion of the "sterile womb." Finally, we highlight how understanding female reproductive biology is well suited to the National Science Foundation's big idea, "Predicting Rules of Life." Studies of female reproductive biology will enable scholars to (1) traverse levels of biological organization from reproductive proteins at the molecular level, through anatomical details of the ovum and female reproductive tract, into physiological aspects of whole-organism performance, leading to behaviors associated with mating and maternal care, and eventually reaching population structure and ecology; (2) discover generalizable rules such as the co-evolution of maternal-offspring phenotypes in gestation and lactation; and (3) predict the impacts of changes to reproductive timing when the reliability of environmental cues becomes unpredictable. Studies in these key areas relative to female reproduction are sure to further our understanding across a range of diverse taxa.
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Affiliation(s)
- Teri J Orr
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Virginia Hayssen
- Department of Biological Sciences, Smith College, Northampton, MA, USA
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21
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Greenbaum G, Feldman MW, Rosenberg NA, Kim J. Designing gene drives to limit spillover to non-target populations. PLoS Genet 2021; 17:e1009278. [PMID: 33630838 PMCID: PMC7943199 DOI: 10.1371/journal.pgen.1009278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 03/09/2021] [Accepted: 11/14/2020] [Indexed: 12/12/2022] Open
Abstract
The prospect of utilizing CRISPR-based gene-drive technology for controlling populations has generated much excitement. However, the potential for spillovers of gene-drive alleles from the target population to non-target populations has raised concerns. Here, using mathematical models, we investigate the possibility of limiting spillovers to non-target populations by designing differential-targeting gene drives, in which the expected equilibrium gene-drive allele frequencies are high in the target population but low in the non-target population. We find that achieving differential targeting is possible with certain configurations of gene-drive parameters, but, in most cases, only under relatively low migration rates between populations. Under high migration, differential targeting is possible only in a narrow region of the parameter space. Because fixation of the gene drive in the non-target population could severely disrupt ecosystems, we outline possible ways to avoid this outcome. We apply our model to two potential applications of gene drives—field trials for malaria-vector gene drives and control of invasive species on islands. We discuss theoretical predictions of key requirements for differential targeting and their practical implications. CRISPR-based gene drive is an emerging genetic engineering technology that enables engineered genetic variants, which are usually designed to be harmful to the organism carrying them, to be spread rapidly in populations. Although this technology is promising for controlling disease vectors and invasive species, there is a considerable risk that a gene drive could unintentionally spillover from the target population, where it was deployed, to non-target populations. We develop mathematical models of gene-drive dynamics that incorporate migration between target and non-target populations to investigate the possibility of effectively applying a gene drive in the target population while limiting its spillover to non-target populations (‘differential targeting’). We observe that the feasibility of differential targeting depends on the gene-drive design specification, as well as on the migration rates between the populations. Even when differential targeting is possible, as migration increases, the possibility for differential targeting disappears. We find that differential targeting can be effective for low migration rates, and that it is sensitive to the design of the gene drive under high migration rates. We suggest that differential targeting could be used, in combination with other mitigation measures, as an additional safeguard to limit gene drive spillovers.
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Affiliation(s)
- Gili Greenbaum
- Department of Ecology, Evolution, and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
| | - Marcus W. Feldman
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Noah A. Rosenberg
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Jaehee Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
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22
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Abstract
Gene drives offer the possibility of altering and even suppressing wild populations of countless plant and animal species, and CRISPR technology now provides the technical feasibility of engineering them. However, population-suppression gene drives are prone to select resistance, should it arise. Here, we develop mathematical and computational models to identify conditions under which suppression drives will evade resistance, even if resistance is present initially. Previous models assumed resistance is allelic to the drive. We relax this assumption and show that linkage between the resistance and drive loci is critical to the evolution of resistance and that evolution of resistance requires (negative) linkage disequilibrium between the two loci. When the two loci are unlinked or only partially so, a suppression drive that causes limited inviability can evolve to fixation while causing only a minor increase in resistance frequency. Once fixed, the drive allele no longer selects resistance. Our analyses suggest that among gene drives that cause moderate suppression, toxin-antidote systems are less apt to select for resistance than homing drives. Single drives of moderate effect might cause only moderate population suppression, but multiple drives (perhaps delivered sequentially) would allow arbitrary levels of suppression. The most favorable case for evolution of resistance appears to be with suppression homing drives in which resistance is dominant and fully suppresses transmission distortion; partial suppression by resistance heterozygotes or recessive resistance are less prone to resistance evolution. Given that it is now possible to engineer CRISPR-based gene drives capable of circumventing allelic resistance, this design may allow for the engineering of suppression gene drives that are effectively resistance-proof.
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Affiliation(s)
- Richard Gomulkiewicz
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Micki L Thies
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - James J Bull
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
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23
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Noble LM, Yuen J, Stevens L, Moya N, Persaud R, Moscatelli M, Jackson JL, Zhang G, Chitrakar R, Baugh LR, Braendle C, Andersen EC, Seidel HS, Rockman MV. Selfing is the safest sex for Caenorhabditis tropicalis. eLife 2021; 10:e62587. [PMID: 33427200 PMCID: PMC7853720 DOI: 10.7554/elife.62587] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 01/08/2021] [Indexed: 12/30/2022] Open
Abstract
Mating systems have profound effects on genetic diversity and compatibility. The convergent evolution of self-fertilization in three Caenorhabditis species provides a powerful lens to examine causes and consequences of mating system transitions. Among the selfers, Caenorhabditis tropicalis is the least genetically diverse and most afflicted by outbreeding depression. We generated a chromosomal-scale genome for C. tropicalis and surveyed global diversity. Population structure is very strong, and islands of extreme divergence punctuate a genomic background that is highly homogeneous around the globe. Outbreeding depression in the laboratory is caused largely by multiple Medea-like elements, genetically consistent with maternal toxin/zygotic antidote systems. Loci with Medea activity harbor novel and duplicated genes, and their activity is modified by mito-nuclear background. Segregating Medea elements dramatically reduce fitness, and simulations show that selfing limits their spread. Frequent selfing in C. tropicalis may therefore be a strategy to avoid Medea-mediated outbreeding depression.
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Affiliation(s)
- Luke M Noble
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
- Institute de Biologie, École Normale Supérieure, CNRS, InsermParisFrance
| | - John Yuen
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Nicolas Moya
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Riaad Persaud
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
| | - Marc Moscatelli
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
| | - Jacqueline L Jackson
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | | | - L Ryan Baugh
- Department of Biology, Duke UniversityDurhamUnited States
| | - Christian Braendle
- Institut de Biologie Valrose, Université Côte d’Azur, CNRS, InsermNiceFrance
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Hannah S Seidel
- Department of Biology, Eastern Michigan UniversityYpsilantiUnited States
| | - Matthew V Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York UniversityNew YorkUnited States
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24
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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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25
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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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26
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Xu XRS, Bulger EA, Gantz VM, Klanseck C, Heimler SR, Auradkar A, Bennett JB, Miller LA, Leahy S, Juste SS, Buchman A, Akbari OS, Marshall JM, Bier E. Active Genetic Neutralizing Elements for Halting or Deleting Gene Drives. Mol Cell 2020; 80:246-262.e4. [PMID: 32949493 PMCID: PMC10962758 DOI: 10.1016/j.molcel.2020.09.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 05/03/2020] [Accepted: 09/01/2020] [Indexed: 01/02/2023]
Abstract
CRISPR-Cas9-based gene drive systems possess the inherent capacity to spread progressively throughout target populations. Here we describe two self-copying (or active) guide RNA-only genetic elements, called e-CHACRs and ERACRs. These elements use Cas9 produced in trans by a gene drive either to inactivate the cas9 transgene (e-CHACRs) or to delete and replace the gene drive (ERACRs). e-CHACRs can be inserted at various genomic locations and carry two or more gRNAs, the first copying the e-CHACR and the second mutating and inactivating the cas9 transgene. Alternatively, ERACRs are inserted at the same genomic location as a gene drive, carrying two gRNAs that cut on either side of the gene drive to excise it. e-CHACRs efficiently inactivate Cas9 and can drive to completion in cage experiments. Similarly, ERACRs, particularly those carrying a recoded cDNA-restoring endogenous gene activity, can drive reliably to fully replace a gene drive. We compare the strengths of these two systems.
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Affiliation(s)
- Xiang-Ru Shannon Xu
- 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
| | - Emily A Bulger
- 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; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, and Gladstone Institutes, San Francisco, CA, USA
| | - Valentino M Gantz
- 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
| | - Carissa Klanseck
- 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
| | - Stephanie R Heimler
- 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
| | - Ankush Auradkar
- 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
| | - Jared B Bennett
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lauren Ashley Miller
- 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
| | - Sarah Leahy
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Sara Sanz Juste
- 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 Buchman
- 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
| | - Omar S Akbari
- 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
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, Berkeley, 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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Li J, Aidlin Harari O, Doss A, Walling LL, Atkinson PW, Morin S, Tabashnik BE. Can CRISPR gene drive work in pest and beneficial haplodiploid species? Evol Appl 2020; 13:2392-2403. [PMID: 33005229 PMCID: PMC7513724 DOI: 10.1111/eva.13032] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 02/06/2023] Open
Abstract
Gene drives based on CRISPR/Cas9 have the potential to reduce the enormous harm inflicted by crop pests and insect vectors of human disease, as well as to bolster valued species. In contrast with extensive empirical and theoretical studies in diploid organisms, little is known about CRISPR gene drive in haplodiploids, despite their immense global impacts as pollinators, pests, natural enemies of pests, and invasive species in native habitats. Here, we analyze mathematical models demonstrating that, in principle, CRISPR homing gene drive can work in haplodiploids, as well as at sex-linked loci in diploids. However, relative to diploids, conditions favoring the spread of alleles deleterious to haplodiploid pests by CRISPR gene drive are narrower, the spread is slower, and resistance to the drive evolves faster. By contrast, the spread of alleles that impose little fitness cost or boost fitness was not greatly hindered in haplodiploids relative to diploids. Therefore, altering traits to minimize damage caused by harmful haplodiploids, such as interfering with transmission of plant pathogens, may be more likely to succeed than control efforts based on introducing traits that reduce pest fitness. Enhancing fitness of beneficial haplodiploids with CRISPR gene drive is also promising.
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Affiliation(s)
- Jun Li
- Department of StatisticsUniversity of CaliforniaRiversideCAUSA
| | | | | | - Linda L. Walling
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCAUSA
| | | | - Shai Morin
- Department of EntomologyHebrew University of JerusalemRehovotIsrael
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Abstract
Gene drives are genetic modifications designed to propagate in a population with high efficiency. Current gene drive strategies rely on sexual reproduction and are thought to be restricted to sexual organisms. Here, we report on a gene drive system that allows the spread of an engineered trait in populations of DNA viruses and, in particular, herpesviruses. We describe the successful transmission of a gene drive sequence between distinct strains of human cytomegalovirus (human herpesvirus 5) and show that gene drive viruses can efficiently target and replace wildtype populations in cell culture experiments. Moreover, by targeting sequences necessary for viral replication, our results indicate that a viral gene drive can be used as a strategy to suppress a viral infection. Taken together, this work offers a proof of principle for the design of a gene drive in viruses. Current gene drive strategies are restricted to sexually reproducing species. Here the authors develop a gene drive in herpesviruses that allows the spread of an engineered trait through a viral population.
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Affiliation(s)
- Marius Walter
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
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29
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Rode NO, Courtier-Orgogozo V, Débarre F. Can a Population Targeted by a CRISPR-Based Homing Gene Drive Be Rescued? G3 (BETHESDA, MD.) 2020; 10:3403-3415. [PMID: 32727921 PMCID: PMC7466991 DOI: 10.1534/g3.120.401484] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022]
Abstract
CRISPR-based homing gene drive is a genetic control technique aiming to modify or eradicate natural populations. This technique is based on the release of individuals carrying an engineered piece of DNA that can be preferentially inherited by the progeny. The development of countermeasures is important to control the spread of gene drives, should they result in unanticipated damages. One proposed countermeasure is the introduction of individuals carrying a brake construct that targets and inactivates the drive allele but leaves the wild-type allele unaffected. Here we develop models to investigate the efficiency of such brakes. We consider a variable population size and use a combination of analytical and numerical methods to determine the conditions where a brake can prevent the extinction of a population targeted by an eradication drive. We find that a brake is not guaranteed to prevent eradication and that characteristics of both the brake and the drive affect the likelihood of recovering the wild-type population. In particular, brakes that restore fitness are more efficient than brakes that do not. Our model also indicates that threshold-dependent drives (drives that can spread only when introduced above a threshold) are more amenable to control with a brake than drives that can spread from an arbitrary low introduction frequency (threshold-independent drives). Based on our results, we provide practical recommendations and discuss safety issues.
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Affiliation(s)
- Nicolas O Rode
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - Florence Débarre
- Sorbonne Université, CNRS, IRD, INRA, Institute of Ecology and Environmental Sciences-Paris (IEES Paris), place Jussieu, 75005, France
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30
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Next-generation gene drive for population modification of the malaria vector mosquito, Anopheles gambiae. Proc Natl Acad Sci U S A 2020; 117:22805-22814. [PMID: 32839345 PMCID: PMC7502704 DOI: 10.1073/pnas.2010214117] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Genetic systems for controlling transmission of vector-borne diseases are moving from discovery-stage demonstrations of proofs-of-principle to the next phases of development. A successful transition requires meeting safety and efficacy criteria defined in target product profiles. We show here that the Cas9/guide RNA-based gene-drive components of a genetically-engineered malaria mosquito vector, Anopheles gambiae, achieve key target product profile requirements for efficacy and performance. This system is designed to achieve mosquito population modification when coupled with genes encoding antiparasite effector molecules and result in stable and sustainable blocking of malaria parasite transmission. A Cas9/guide RNA-based gene drive strain, AgNosCd-1, was developed to deliver antiparasite effector molecules to the malaria vector mosquito, Anopheles gambiae. The drive system targets the cardinal gene ortholog producing a red-eye phenotype. Drive can achieve 98 to 100% in both sexes and full introduction was observed in small cage trials within 6 to 10 generations following a single release of gene-drive males. No genetic load resulting from the integrated transgenes impaired drive performance in the trials. Potential drive-resistant target-site alleles arise at a frequency <0.1, and five of the most prevalent polymorphisms in the guide RNA target site in collections of colonized and wild-derived African mosquitoes do not prevent cleavage in vitro by the Cas9/guide RNA complex. Only one predicted off-target site is cleavable in vitro, with negligible deletions observed in vivo. AgNosCd-1 meets key performance criteria of a target product profile and can be a valuable component of a field-ready strain for mosquito population modification to control malaria transmission.
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31
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Lester PJ, Bulgarella M, Baty JW, Dearden PK, Guhlin J, Kean JM. The potential for a CRISPR gene drive to eradicate or suppress globally invasive social wasps. Sci Rep 2020; 10:12398. [PMID: 32709966 PMCID: PMC7382497 DOI: 10.1038/s41598-020-69259-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022] Open
Abstract
CRISPR gene drives have potential for widespread and cost-efficient pest control, but are highly controversial. We examined a potential gene drive targeting spermatogenesis to control the invasive common wasp (Vespula vulgaris) in New Zealand. Vespula wasps are haplodiploid. Their life cycle makes gene drive production challenging, as nests are initiated by single fertilized queens in spring followed by several cohorts of sterile female workers and the production of reproductives in autumn. We show that different spermatogenesis genes have different levels of variation between introduced and native ranges, enabling a potential 'precision drive' that could target the reduced genetic diversity and genotypes within the invaded range. In vitro testing showed guide-RNA target specificity and efficacy that was dependent on the gene target within Vespula, but no cross-reactivity in other Hymenoptera. Mathematical modelling incorporating the genetic and life history traits of Vespula wasps identified characteristics for a male sterility drive to achieve population control. There was a trade-off between drive infiltration and impact: a drive causing complete male sterility would not spread, while partial sterility could be effective in limiting population size if the homing rate is high. Our results indicate that gene drives may offer viable suppression for wasps and other haplodiploid pests.
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Affiliation(s)
- Philip J Lester
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand.
| | - Mariana Bulgarella
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - James W Baty
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Peter K Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Joseph Guhlin
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - John M Kean
- AgResearch Limited, Hamilton, 3240, New Zealand
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32
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Schmidt H, Collier TC, Hanemaaijer MJ, Houston PD, Lee Y, Lanzaro GC. Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes. Nat Commun 2020; 11:1425. [PMID: 32188851 PMCID: PMC7080748 DOI: 10.1038/s41467-020-15204-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/21/2020] [Indexed: 12/19/2022] Open
Abstract
A number of recent papers report that standing genetic variation in natural populations includes ubiquitous polymorphisms within target sites for Cas9-based gene drive (CGD) and that these "drive resistant alleles" (DRA) preclude the successful application of CGD for managing these populations. Here we report the results of a survey of 1280 genomes of the mosquitoes Anopheles gambiae, An. coluzzii, and Aedes aegypti in which we determine that ~90% of all protein-encoding CGD target genes in natural populations include at least one target site with no DRAs at a frequency of ≥1.0%. We conclude that the abundance of conserved target sites in mosquito genomes and the inherent flexibility in CGD design obviates the concern that DRAs present in the standing genetic variation of mosquito populations will be detrimental to the deployment of this technology for population modification strategies.
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Affiliation(s)
- Hanno Schmidt
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Travis C Collier
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Mark J Hanemaaijer
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
- Winclove Probiotics, Hulstweg 11, 1032 LB, Amesterdam, Netherlands
| | - Parker D Houston
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Yoosook Lee
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Gregory C Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
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Famakinde DO. Public health concerns over gene-drive mosquitoes: will future use of gene-drive snails for schistosomiasis control gain increased level of community acceptance? Pathog Glob Health 2020; 114:55-63. [PMID: 32100643 DOI: 10.1080/20477724.2020.1731667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
With the advent of CRISPR (clustered regularly interspaced short palindromic repeat)-based gene drive, present genetic research in schistosomiasis vector control envisages the breeding and release of transgenic schistosome-resistant (TSR) snail vectors to curb the spread of the disease. Although this approach is still in its infancy, studies focussing on production of genetically modified (GM) mosquitoes (including gene-drive mosquitoes) are well advanced and set the pace for other transgenic vector research. Unfortunately, as with other GM mosquitoes, open field release of gene-drive mosquitoes is currently challenged in part by some concerns such as gene drive failure and increased transmission potential for other mosquito-borne diseases among others, which might have adverse effects on human well-being. Therefore, not only should we learn from the GM mosquito protocols, frameworks and guidelines but also appraise the applicability of its current hurdles to other transgenic vector systems, such as the TSR snail approach. Placing these issues in a coherent comparative perspective, I argue that although the use of TSR snails may face similar technical, democratic and diplomatic challenges, some of the concerns over gene-drive mosquitoes may not apply to gene-drive snails, proposing a theory that community consent will be no harder and possibly easier to obtain for TSR snails than the experience with GM mosquitoes. In the future, these observations may help public health practitioners and policy makers in effective communication with communities on issues regarding the use of TSR snails to interrupt schistosomiasis transmission, especially in sub-Saharan Africa.
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Affiliation(s)
- Damilare O Famakinde
- Department of Medical Microbiology and Parasitology, University of Lagos, Lagos, Nigeria
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34
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López Del Amo V, Bishop AL, Sánchez C HM, Bennett JB, Feng X, Marshall JM, Bier E, Gantz VM. A transcomplementing gene drive provides a flexible platform for laboratory investigation and potential field deployment. Nat Commun 2020; 11:352. [PMID: 31953404 PMCID: PMC6969112 DOI: 10.1038/s41467-019-13977-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
CRISPR-based gene drives can spread through wild populations by biasing their own transmission above the 50% value predicted by Mendelian inheritance. These technologies offer population-engineering solutions for combating vector-borne diseases, managing crop pests, and supporting ecosystem conservation efforts. Current technologies raise safety concerns for unintended gene propagation. Herein, we address such concerns by splitting the drive components, Cas9 and gRNAs, into separate alleles to form a trans-complementing split-gene-drive (tGD) and demonstrate its ability to promote super-Mendelian inheritance of the separate transgenes. This dual-component configuration allows for combinatorial transgene optimization and increases safety by restricting escape concerns to experimentation windows. We employ the tGD and a small-molecule-controlled version to investigate the biology of component inheritance and resistant allele formation, and to study the effects of maternal inheritance and impaired homology on efficiency. Lastly, mathematical modeling of tGD spread within populations reveals potential advantages for improving current gene-drive technologies for field population modification.
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Affiliation(s)
- Víctor López Del Amo
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alena L Bishop
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Héctor M Sánchez C
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Jared B Bennett
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720, USA
| | - Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0349, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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Antiviral Effectors and Gene Drive Strategies for Mosquito Population Suppression or Replacement to Mitigate Arbovirus Transmission by Aedes aegypti. INSECTS 2020; 11:insects11010052. [PMID: 31940960 PMCID: PMC7023000 DOI: 10.3390/insects11010052] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/11/2022]
Abstract
The mosquito vector Aedes aegypti transmits arthropod-borne viruses (arboviruses) of medical importance, including Zika, dengue, and yellow fever viruses. Controlling mosquito populations remains the method of choice to prevent disease transmission. Novel mosquito control strategies based on genetically manipulating mosquitoes are being developed as additional tools to combat arbovirus transmission. Genetic control of mosquitoes includes two basic strategies: population suppression and population replacement. The former aims to eliminate mosquito populations while the latter aims to replace wild populations with engineered, pathogen-resistant mosquitoes. In this review, we outline suppression strategies being applied in the field, as well as current antiviral effector genes that have been characterized and expressed in transgenic Ae. aegypti for population replacement. We discuss cutting-edge gene drive technologies that can be used to enhance the inheritance of effector genes, while highlighting the challenges and opportunities associated with gene drives. Finally, we present currently available models that can estimate mosquito release numbers and time to transgene fixation for several gene drive systems. Based on the recent advances in genetic engineering, we anticipate that antiviral transgenic Ae. aegypti exhibiting gene drive will soon emerge; however, close monitoring in simulated field conditions will be required to demonstrate the efficacy and utility of such transgenic mosquitoes.
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Perotti VE, Larran AS, Palmieri VE, Martinatto AK, Permingeat HR. Herbicide resistant weeds: A call to integrate conventional agricultural practices, molecular biology knowledge and new technologies. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110255. [PMID: 31779903 DOI: 10.1016/j.plantsci.2019.110255] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 05/16/2023]
Abstract
Herbicide resistant (HR) weeds are of major concern in modern agriculture. This situation is exacerbated by the massive adoption of herbicide-based technologies along with the overuse of a few active ingredients to control weeds over vast areas year after year. Also, many other anthropological, biological, and environmental factors have defined a higher rate of herbicide resistance evolution in numerous weed species around the world. This review focuses on two central points: 1) how these factors have affected the resistance evolution process; and 2) which cultural practices and new approaches would help to achieve an effective integrated weed management. We claim that global climate change is an unnoticed factor that may be acting on the selection of HR weeds, especially those evolving into non-target-site resistance mechanisms. And we present several new tools -such as Gene Drive and RNAi technologies- that may be adopted to cope with herbicide resistance spread, as well as discuss their potential application at field level. This is the first review that integrates agronomic and molecular knowledge of herbicide resistance. It covers not only the genetic basis of the most relevant resistance mechanisms but also the strengths and weaknesses of traditional and forthcoming agricultural practices.
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Affiliation(s)
- Valeria E Perotti
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Alvaro S Larran
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina; Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Valeria E Palmieri
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Andrea K Martinatto
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina
| | - Hugo R Permingeat
- Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina; Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, S2125ZAA, Zavalla, Argentina.
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37
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Abstract
Evolution can potentially rescue populations from being driven extinct by biological invasions, but predictions for this occurrence are generally lacking. Here I derive theoretical predictions for evolutionary rescue of a resident population experiencing invasion from an introduced competitor that spreads over its introduced range as a traveling spatial wave that displaces residents. I compare the likelihood of evolutionary rescue from invasion for two modes of competition: exploitation and interference competition. I find that, all else equal, evolutionary rescue is less effective at preventing extinction caused by interference-driven invasions than by exploitation-driven invasions. Rescue from interference-driven invasions is, surprisingly, independent of invader dispersal rate or the speed of invasion and is more weakly dependent on range size than in the exploitation-driven case. In contrast, rescue from exploitation-driven invasions strongly depends on range size and is less likely during fast invasions. The results presented here have potential applications for conserving endemic species from nonnative invaders and for ensuring extinction of pests using intentionally introduced biocontrol agents.
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38
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Maier T, Wheeler NJ, Namigai EKO, Tycko J, Grewelle RE, Woldeamanuel Y, Klohe K, Perez-Saez J, Sokolow SH, De Leo GA, Yoshino TP, Zamanian M, Reinhard-Rupp J. Gene drives for schistosomiasis transmission control. PLoS Negl Trop Dis 2019; 13:e0007833. [PMID: 31856157 PMCID: PMC6922350 DOI: 10.1371/journal.pntd.0007833] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Schistosomiasis is one of the most important and widespread neglected tropical diseases (NTD), with over 200 million people infected in more than 70 countries; the disease has nearly 800 million people at risk in endemic areas. Although mass drug administration is a cost-effective approach to reduce occurrence, extent, and severity of the disease, it does not provide protection to subsequent reinfection. Interventions that target the parasites’ intermediate snail hosts are a crucial part of the integrated strategy required to move toward disease elimination. The recent revolution in gene drive technology naturally leads to questions about whether gene drives could be used to efficiently spread schistosome resistance traits in a population of snails and whether gene drives have the potential to contribute to reduced disease transmission in the long run. Responsible implementation of gene drives will require solutions to complex challenges spanning multiple disciplines, from biology to policy. This Review Article presents collected perspectives from practitioners of global health, genome engineering, epidemiology, and snail/schistosome biology and outlines strategies for responsible gene drive technology development, impact measurements of gene drives for schistosomiasis control, and gene drive governance. Success in this arena is a function of many factors, including gene-editing specificity and efficiency, the level of resistance conferred by the gene drive, how fast gene drives may spread in a metapopulation over a complex landscape, ecological sustainability, social equity, and, ultimately, the reduction of infection prevalence in humans. With combined efforts from across the broad global health community, gene drives for schistosomiasis control could fortify our defenses against this devastating disease in the future.
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Affiliation(s)
- Theresa Maier
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Nicolas James Wheeler
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Global Health Institute of Merck (KGaA), Eysins, Switzerland
| | | | - Josh Tycko
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Richard Ernest Grewelle
- Hopkins Marine Station, School of Humanities and Sciences, Stanford University, Pacific Grove, California, United States of America
| | - Yimtubezinash Woldeamanuel
- Department of Microbiology, Immunology & Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Javier Perez-Saez
- Laboratory of Ecohydrology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Susanne H. Sokolow
- Woods Institute for the Environment, Stanford University, Stanford, California, United States of America
- Marine Science Institute, University of California, Santa Barbara, California, United States of America
| | - Giulio A. De Leo
- Hopkins Marine Station, School of Humanities and Sciences, Stanford University, Pacific Grove, California, United States of America
| | - Timothy P. Yoshino
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mostafa Zamanian
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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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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Taxiarchi C, Kranjc N, Kriezis A, Kyrou K, Bernardini F, Russell S, Nolan T, Crisanti A, Galizi R. High-resolution transcriptional profiling of Anopheles gambiae spermatogenesis reveals mechanisms of sex chromosome regulation. Sci Rep 2019; 9:14841. [PMID: 31619757 PMCID: PMC6795909 DOI: 10.1038/s41598-019-51181-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/25/2019] [Indexed: 12/20/2022] Open
Abstract
Although of high priority for the development of genetic tools to control malaria-transmitting mosquitoes, only a few germline-specific regulatory regions have been characterised to date and the presence of global regulatory mechanisms, such as dosage compensation and meiotic sex chromosome inactivation (MSCI), are mostly assumed from transcriptomic analyses of reproductive tissues or whole gonads. In such studies, samples include a significant portion of somatic tissues inevitably complicating the reconstruction of a defined transcriptional map of gametogenesis. By exploiting recent advances in transgenic technologies and gene editing tools, combined with fluorescence-activated cell sorting and RNA sequencing, we have separated four distinct cell lineages from the Anopheles gambiae male gonads: premeiotic, meiotic (primary and secondary spermatocytes) and postmeiotic. By comparing the overall expression levels of X-linked and autosomal genes across the four populations, we revealed a striking transcriptional repression of the X chromosome coincident with the meiotic phase, classifiable as MSCI, and highlighted genes that may evade silencing. In addition, chromosome-wide median expression ratios of the premeiotic population confirmed the absence of dosage compensation in the male germline. Applying differential expression analysis, we highlighted genes and transcript isoforms enriched at specific timepoints and reconstructed the expression dynamics of the main biological processes regulating the key stages of sperm development and maturation. We generated the first transcriptomic atlas of A. gambiae spermatogenesis that will expand the available toolbox for the genetic engineering of vector control technologies. We also describe an innovative and multidimensional approach to isolate specific cell lineages that can be used for the targeted analysis of other A. gambiae organs or transferred to other medically relevant species and model organisms.
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Affiliation(s)
- Chrysanthi Taxiarchi
- Department of Life Sciences, Imperial College London, London, UK
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, London, UK
| | - Antonios Kriezis
- Department of Life Sciences, Imperial College London, London, UK
| | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, London, UK
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, UK
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London, UK.
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Abstract
Synthetic gene drives may soon be used to suppress or eliminate populations of disease vectors, pathogens, invasive species, and agricultural pests. Recent proposals have focused on using Z-linked gene drives to control species with ZW sex determination, which include Lepidopteran pests, parasitic trematodes, and cane toads. These proposals include Z-linked 'W-shredders', which would suppress populations by cleaving the W chromosome and causing females to produce only sons, as well as Z-linked female-sterilizing gene drives. Here, I use eco-evolutionary simulations to evaluate the potential of some proposed Z-linked gene drives, and to produce recommendations regarding their design and use. The simulations show that W-shredders are likely to be highly effective at eradicating populations provided that resistance to W-shredding cannot evolve. However, W-shredder alleles can invade populations from very low frequencies, making it difficult to eliminate specific populations while leaving nearby populations untouched; this issue may restrict their possible uses.
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Affiliation(s)
- Luke Holman
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
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Barrett LG, Legros M, Kumaran N, Glassop D, Raghu S, Gardiner DM. Gene drives in plants: opportunities and challenges for weed control and engineered resilience. Proc Biol Sci 2019; 286:20191515. [PMID: 31551052 PMCID: PMC6784734 DOI: 10.1098/rspb.2019.1515] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023] Open
Abstract
Plant species, populations and communities are under threat from climate change, invasive pathogens, weeds and habitat fragmentation. Despite considerable research effort invested in genome engineering for crop improvement, the development of genetic tools for the management of wild plant populations has rarely been given detailed consideration. Gene drive systems that allow direct genetic management of plant populations via the spread of fitness-altering genetic modifications could be of great utility. However, despite the rapid development of synthetic tools and their enormous promise, little explicit consideration has been given to their application in plants and, to date, they remain untested. This article considers the potential utility of gene drives for the management of wild plant populations, and examines the factors that might influence the design, spread and efficacy of synthetic drives. To gain insight into optimal ways to design and deploy synthetic drive systems, we investigate the diversity of mechanisms underlying natural gene drives and their dynamics within plant populations and species. We also review potential approaches for engineering gene drives and discuss their potential application to plant genomes. We highlight the importance of considering the impact of plant life-history and genetic architecture on the dynamics of drive, investigate the potential for different types of resistance evolution, and touch on the ethical, regulatory and social challenges ahead.
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Affiliation(s)
- Luke G. Barrett
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - Mathieu Legros
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, Australian Capital Territory, Australia
| | | | - Donna Glassop
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - S. Raghu
- CSIRO Health and Biosecurity, Brisbane, Queensland, Australia
| | - Donald M. Gardiner
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
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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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Manser A, Cornell SJ, Sutter A, Blondel DV, Serr M, Godwin J, Price TAR. Controlling invasive rodents via synthetic gene drive and the role of polyandry. Proc Biol Sci 2019; 286:20190852. [PMID: 31431159 PMCID: PMC6732378 DOI: 10.1098/rspb.2019.0852] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/25/2019] [Indexed: 12/25/2022] Open
Abstract
House mice are a major ecosystem pest, particularly threatening island ecosystems as a non-native invasive species. Rapid advances in synthetic biology offer new avenues to control pest species for biodiversity conservation. Recently, a synthetic sperm-killing gene drive construct called t-Sry has been proposed as a means to eradicate target mouse populations owing to a lack of females. A factor that has received little attention in the discussion surrounding such drive applications is polyandry. Previous research has demonstrated that sperm-killing drivers are extremely damaging to a male's sperm competitive ability. Here, we examine the importance of this effect on the t-Sry system using a theoretical model. We find that polyandry substantially hampers the spread of t-Sry such that release efforts have to be increased three- to sixfold for successful eradication. We discuss the implications of our finding for potential pest control programmes, the risk of drive spread beyond the target population, and the emergence of drive resistance. Our work highlights that a solid understanding of the forces that determine drive dynamics in a natural setting is key for successful drive application, and that exploring the natural diversity of gene drives may inform effective gene drive design.
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Affiliation(s)
- Andri Manser
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK
| | - Stephen J. Cornell
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK
| | - Andreas Sutter
- Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich, UK
| | - Dimitri V. Blondel
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA
| | - Megan Serr
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA
| | - John Godwin
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA
| | - Tom A. R. Price
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK
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Breed MF, Harrison PA, Blyth C, Byrne M, Gaget V, Gellie NJC, Groom SVC, Hodgson R, Mills JG, Prowse TAA, Steane DA, Mohr JJ. The potential of genomics for restoring ecosystems and biodiversity. Nat Rev Genet 2019; 20:615-628. [PMID: 31300751 DOI: 10.1038/s41576-019-0152-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2019] [Indexed: 01/12/2023]
Abstract
Billions of hectares of natural ecosystems have been degraded through human actions. The global community has agreed on targets to halt and reverse these declines, and the restoration sector faces the important but arduous task of implementing programmes to meet these objectives. Existing and emerging genomics tools offer the potential to improve the odds of achieving these targets. These tools include population genomics that can improve seed sourcing, meta-omics that can improve assessment and monitoring of restoration outcomes, and genome editing that can generate novel genotypes for restoring challenging environments. We identify barriers to adopting these tools in a restoration context and emphasize that regulatory and ethical frameworks are required to guide their use.
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Affiliation(s)
- Martin F Breed
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia.
| | - Peter A Harrison
- School of Natural Sciences, Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Colette Blyth
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Western Australia, Australia
| | - Virginie Gaget
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Nicholas J C Gellie
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Scott V C Groom
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia, Australia
| | - Riley Hodgson
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Jacob G Mills
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Thomas A A Prowse
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia.,School of Mathematical Sciences, University of Adelaide, North Terrace, South Australia, Australia
| | - Dorothy A Steane
- School of Natural Sciences, Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Jakki J Mohr
- College of Business, Institute on Ecosystems, University of Montana, Missoula, MT, USA
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VARSCOT: variant-aware detection and scoring enables sensitive and personalized off-target detection for CRISPR-Cas9. BMC Biotechnol 2019; 19:40. [PMID: 31248401 PMCID: PMC6598273 DOI: 10.1186/s12896-019-0535-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 06/17/2019] [Indexed: 12/26/2022] Open
Abstract
Background Natural variations in a genome can drastically alter the CRISPR-Cas9 off-target landscape by creating or removing sites. Despite the resulting potential side-effects from such unaccounted for sites, current off-target detection pipelines are not equipped to include variant information. To address this, we developed VARiant-aware detection and SCoring of Off-Targets (VARSCOT). Results VARSCOT identifies only 0.6% of off-targets to be common between 4 individual genomes and the reference, with an average of 82% of off-targets unique to an individual. VARSCOT is the most sensitive detection method for off-targets, finding 40 to 70% more experimentally verified off-targets compared to other popular software tools and its machine learning model allows for CRISPR-Cas9 concentration aware off-target activity scoring. Conclusions VARSCOT allows researchers to take genomic variation into account when designing individual or population-wide targeting strategies. VARSCOT is available from https://github.com/BauerLab/VARSCOT. Electronic supplementary material The online version of this article (10.1186/s12896-019-0535-5) contains supplementary material, which is available to authorized users.
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48
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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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49
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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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Rode NO, Estoup A, Bourguet D, Courtier-Orgogozo V, Débarre F. Population management using gene drive: molecular design, models of spread dynamics and assessment of ecological risks. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01165-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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