1
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Apte RA, Smidler AL, Pai JJ, Chow ML, Chen S, Mondal A, Sánchez C. HM, Antoshechkin I, Marshall JM, Akbari OS. Eliminating malaria vectors with precision-guided sterile males. Proc Natl Acad Sci U S A 2024; 121:e2312456121. [PMID: 38917000 PMCID: PMC11228498 DOI: 10.1073/pnas.2312456121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 05/03/2024] [Indexed: 06/27/2024] Open
Abstract
Controlling the principal African malaria vector, the mosquito Anopheles gambiae, is considered essential to curtail malaria transmission. However, existing vector control technologies rely on insecticides, which are becoming increasingly ineffective. Sterile insect technique (SIT) is a powerful suppression approach that has successfully eradicated a number of insect pests, yet the A. gambiae toolkit lacks the requisite technologies for its implementation. SIT relies on iterative mass releases of nonbiting, nondriving, sterile males which seek out and mate with monandrous wild females. Once mated, females are permanently sterilized due to mating-induced refractoriness, which results in population suppression of the subsequent generation. However, sterilization by traditional methods renders males unfit, making the creation of precise genetic sterilization methods imperative. Here, we introduce a vector control technology termed precision-guided sterile insect technique (pgSIT), in A. gambiae for inducible, programmed male sterilization and female elimination for wide-scale use in SIT campaigns. Using a binary CRISPR strategy, we cross separate engineered Cas9 and gRNA strains to disrupt male-fertility and female-essential genes, yielding >99.5% male sterility and >99.9% female lethality in hybrid progeny. We demonstrate that these genetically sterilized males have good longevity, are able to induce sustained population suppression in cage trials, and are predicted to eliminate wild A. gambiae populations using mathematical models, making them ideal candidates for release. This work provides a valuable addition to the malaria genetic biocontrol toolkit, enabling scalable SIT-like confinable, species-specific, and safe suppression in the species.
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Affiliation(s)
- Reema A. Apte
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
| | - Andrea L. Smidler
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
| | - James J. Pai
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
| | - Martha L. Chow
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
| | - Sanle Chen
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
| | - Agastya Mondal
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA94720
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA94720
| | - Héctor M. Sánchez C.
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA94720
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA94720
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
| | - John M. Marshall
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA94720
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA94720
- Innovative Genomics Institute, University of California, Berkeley, CA94720
| | - Omar S. Akbari
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA92093
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2
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Li M, Kandul NP, Sun R, Yang T, Benetta ED, Brogan DJ, Antoshechkin I, Sánchez C HM, Zhan Y, DeBeaubien NA, Loh YM, Su MP, Montell C, Marshall JM, Akbari OS. Targeting sex determination to suppress mosquito populations. eLife 2024; 12:RP90199. [PMID: 38289340 PMCID: PMC10945564 DOI: 10.7554/elife.90199] [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: 02/01/2024] Open
Abstract
Each year, hundreds of millions of people are infected with arboviruses such as dengue, yellow fever, chikungunya, and Zika, which are all primarily spread by the notorious mosquito Aedes aegypti. Traditional control measures have proven insufficient, necessitating innovations. In response, here we generate a next-generation CRISPR-based precision-guided sterile insect technique (pgSIT) for Ae. aegypti that disrupts genes essential for sex determination and fertility, producing predominantly sterile males that can be deployed at any life stage. Using mathematical models and empirical testing, we demonstrate that released pgSIT males can effectively compete with, suppress, and eliminate caged mosquito populations. This versatile species-specific platform has the potential for field deployment to effectively control wild populations of disease vectors.
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Affiliation(s)
- Ming Li
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, BerkeleyBerkeleyUnited States
| | - Nikolay P Kandul
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, BerkeleyBerkeleyUnited States
| | - Ruichen Sun
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, BerkeleyBerkeleyUnited States
| | - Ting Yang
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, BerkeleyBerkeleyUnited States
| | - Elena D Benetta
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, BerkeleyBerkeleyUnited States
| | - Daniel J Brogan
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, BerkeleyBerkeleyUnited States
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering (BBE), California Institute of TechnologyPasadenaUnited States
| | - Héctor M Sánchez C
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, BerkeleyBerkeleyUnited States
| | - Yinpeng Zhan
- Department of Molecular, Cellular, and Developmental Biology and the Neuroscience Research, Institute, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Nicolas A DeBeaubien
- Department of Molecular, Cellular, and Developmental Biology and the Neuroscience Research, Institute, University of California, Santa BarbaraSanta BarbaraUnited States
| | - YuMin M Loh
- Graduate School of Science, Nagoya UniversityNagoyaJapan
| | - Matthew P Su
- Graduate School of Science, Nagoya UniversityNagoyaJapan
- Institute for Advanced Research, Nagoya UniversityNagoyaJapan
| | - Craig Montell
- Department of Molecular, Cellular, and Developmental Biology and the Neuroscience Research, Institute, University of California, Santa BarbaraSanta BarbaraUnited States
| | - John M Marshall
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, BerkeleyBerkeleyUnited States
- Innovative Genomics InstituteBerkeleyUnited States
| | - Omar S Akbari
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, BerkeleyBerkeleyUnited States
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3
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Anderson MAE, Gonzalez E, Edgington MP, Ang JXD, Purusothaman DK, Shackleford L, Nevard K, Verkuijl SAN, Harvey-Samuel T, Leftwich PT, Esvelt K, Alphey L. A multiplexed, confinable CRISPR/Cas9 gene drive can propagate in caged Aedes aegypti populations. Nat Commun 2024; 15:729. [PMID: 38272895 PMCID: PMC10810878 DOI: 10.1038/s41467-024-44956-2] [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: 08/09/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Aedes aegypti is the main vector of several major pathogens including dengue, Zika and chikungunya viruses. Classical mosquito control strategies utilizing insecticides are threatened by rising resistance. This has stimulated interest in new genetic systems such as gene drivesHere, we test the regulatory sequences from the Ae. aegypti benign gonial cell neoplasm (bgcn) homolog to express Cas9 and a separate multiplexing sgRNA-expressing cassette inserted into the Ae. aegypti kynurenine 3-monooxygenase (kmo) gene. When combined, these two elements provide highly effective germline cutting at the kmo locus and act as a gene drive. Our target genetic element drives through a cage trial population such that carrier frequency of the element increases from 50% to up to 89% of the population despite significant fitness costs to kmo insertions. Deep sequencing suggests that the multiplexing design could mitigate resistance allele formation in our gene drive system.
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Affiliation(s)
- Michelle A E Anderson
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Estela Gonzalez
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Matthew P Edgington
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Joshua X D Ang
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Deepak-Kumar Purusothaman
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- MRC-University of Glasgow Centre for Virus Research, Henry Wellcome Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Lewis Shackleford
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Katherine Nevard
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
| | - Sebald A N Verkuijl
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | | | - Philip T Leftwich
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Kevin Esvelt
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK.
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
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4
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Raban R, Marshall JM, Hay BA, Akbari OS. Manipulating the Destiny of Wild Populations Using CRISPR. Annu Rev Genet 2023; 57:361-390. [PMID: 37722684 PMCID: PMC11064769 DOI: 10.1146/annurev-genet-031623-105059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Genetic biocontrol aims to suppress or modify populations of species to protect public health, agriculture, and biodiversity. Advancements in genome engineering technologies have fueled a surge in research in this field, with one gene editing technology, CRISPR, leading the charge. This review focuses on the current state of CRISPR technologies for genetic biocontrol of pests and highlights the progress and ongoing challenges of using these approaches.
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Affiliation(s)
- Robyn Raban
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
| | - John M Marshall
- Divisions of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, California, USA
| | - Bruce A Hay
- Division of Biology and Biological Engineering (BBE), California Institute of Technology, Pasadena, California, USA
| | - Omar S Akbari
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
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5
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Li M, Kandul NP, Sun R, Yang T, Benetta ED, Brogan DJ, Antoshechkin I, Sánchez C. HM, Zhan Y, DeBeaubien NA, Loh YM, Su MP, Montell C, Marshall JM, Akbari OS. Targeting Sex Determination to Suppress Mosquito Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537404. [PMID: 37131747 PMCID: PMC10153225 DOI: 10.1101/2023.04.18.537404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Each year, hundreds of millions of people are infected with arboviruses such as dengue, yellow fever, chikungunya, and Zika, which are all primarily spread by the notorious mosquito Aedes aegypti. Traditional control measures have proven insufficient, necessitating innovations. In response, here we generate a next generation CRISPR-based precision-guided sterile insect technique (pgSIT) for Aedes aegypti that disrupts genes essential for sex determination and fertility, producing predominantly sterile males that can be deployed at any life stage. Using mathematical models and empirical testing, we demonstrate that released pgSIT males can effectively compete with, suppress, and eliminate caged mosquito populations. This versatile species-specific platform has the potential for field deployment to effectively control wild populations of disease vectors.
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Affiliation(s)
- Ming Li
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nikolay P. Kandul
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ruichen Sun
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ting Yang
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elena D. Benetta
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel J. Brogan
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering (BBE), California Institute of Technology, Pasadena, CA 91125, USA
| | - Héctor M. Sánchez C.
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Yinpeng Zhan
- Department of Molecular, Cellular, and Developmental Biology and the Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Nicolas A. DeBeaubien
- Department of Molecular, Cellular, and Developmental Biology and the Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - YuMin M. Loh
- Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Matthew P. Su
- Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
- Institute for Advanced Research, Nagoya University, Nagoya, Aichi, Japan
| | - Craig Montell
- Department of Molecular, Cellular, and Developmental Biology and the Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - John M. Marshall
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94720, USA
| | - Omar S. Akbari
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
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6
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Smidler AL, Apte RA, Pai JJ, Chow ML, Chen S, Mondal A, Sánchez C. HM, Antoshechkin I, Marshall JM, Akbari OS. Eliminating Malaria Vectors with Precision Guided Sterile Males. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.20.549947. [PMID: 37503146 PMCID: PMC10370176 DOI: 10.1101/2023.07.20.549947] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Controlling the principal African malaria vector, the mosquito Anopheles gambiae, is considered essential to curtail malaria transmission. However existing vector control technologies rely on insecticides, which are becoming increasingly ineffective. Sterile insect technique (SIT) is a powerful suppression approach that has successfully eradicated a number of insect pests, yet the A. gambiae toolkit lacks the requisite technologies for its implementation. SIT relies on iterative mass-releases of non-biting, non-driving, sterile males which seek out and mate with monandrous wild females. Once mated, females are permanently sterilized due to mating-induced refractoriness, which results in population suppression of the subsequent generation. However, sterilization by traditional methods renders males unfit, making the creation of precise genetic sterilization methods imperative. Here we develop precision guided Sterile Insect Technique (pgSIT) in the mosquito A. gambiae for inducible, programmed male-sterilization and female-elimination for wide scale use in SIT campaigns. Using a binary CRISPR strategy, we cross separate engineered Cas9 and gRNA strains to disrupt male-fertility and female-essential genes, yielding >99.5% male-sterility and >99.9% female-lethality in hybrid progeny. We demonstrate that these genetically sterilized males have good longevity, are able to induce population suppression in cage trials, and are predicted to eliminate wild A. gambiae populations using mathematical models, making them ideal candidates for release. This work provides a valuable addition to the malaria genetic biocontrol toolkit, for the first time enabling scalable SIT-like confinable suppression in the species.
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Affiliation(s)
- Andrea L. Smidler
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Reema A. Apte
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - James J. Pai
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Martha L. Chow
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Sanle Chen
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Agastya Mondal
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Héctor M. Sánchez C.
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering (BBE), California Institute of Technology, Pasadena, CA91125, USA
| | - John M. Marshall
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Omar S. Akbari
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
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7
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Anderson MAE, Gonzalez E, Ang JXD, Shackleford L, Nevard K, Verkuijl SAN, Edgington MP, Harvey-Samuel T, Alphey L. Closing the gap to effective gene drive in Aedes aegypti by exploiting germline regulatory elements. Nat Commun 2023; 14:338. [PMID: 36670107 PMCID: PMC9860013 DOI: 10.1038/s41467-023-36029-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/13/2023] [Indexed: 01/22/2023] Open
Abstract
CRISPR/Cas9-based homing gene drives have emerged as a potential new approach to mosquito control. While attempts have been made to develop such systems in Aedes aegypti, none have been able to match the high drive efficiency observed in Anopheles species. Here we generate Ae. aegypti transgenic lines expressing Cas9 using germline-specific regulatory elements and assess their ability to bias inheritance of an sgRNA-expressing element (kmosgRNAs). Four shu-Cas9 and one sds3-Cas9 isolines can significantly bias the inheritance of kmosgRNAs, with sds3G1-Cas9 causing the highest average inheritance of ~86% and ~94% from males and females carrying both elements outcrossed to wild-type, respectively. Our mathematical model demonstrates that sds3G1-Cas9 could enable the spread of the kmosgRNAs element to either reach a higher (by ~15 percentage point) maximum carrier frequency or to achieve similar maximum carrier frequency faster (by 12 generations) when compared to two other established split drive systems.
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Affiliation(s)
- Michelle A E Anderson
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Estela Gonzalez
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Joshua X D Ang
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Lewis Shackleford
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Katherine Nevard
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Sebald A N Verkuijl
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- Mathematical Ecology Research Group, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX13SZ, UK
| | - Matthew P Edgington
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Tim Harvey-Samuel
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
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8
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Terradas G, Bennett JB, Li Z, Marshall JM, Bier E. Genetic conversion of a split-drive into a full-drive element. Nat Commun 2023; 14:191. [PMID: 36635291 PMCID: PMC9837192 DOI: 10.1038/s41467-022-35044-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/16/2022] [Indexed: 01/13/2023] Open
Abstract
The core components of CRISPR-based gene drives, Cas9 and guide RNA (gRNA), either can be linked within a self-contained single cassette (full gene-drive, fGD) or be provided in two separate elements (split gene-drive, sGD), the latter offering greater control options. We previously engineered split systems that could be converted genetically into autonomous full drives. Here, we examine such dual systems inserted at the spo11 locus that are recoded to restore gene function and thus organismic fertility. Despite minimal differences in transmission efficiency of the sGD or fGD drive elements in single generation crosses, the reconstituted spo11 fGD cassette surprisingly exhibits slower initial drive kinetics than the unlinked sGD element in multigenerational cage studies, but then eventually catches up to achieve a similar level of final introduction. These unexpected kinetic behaviors most likely reflect differing transient fitness costs associated with individuals co-inheriting Cas9 and gRNA transgenes during the drive process.
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Affiliation(s)
- Gerard Terradas
- Department 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, La Jolla, CA, 92093, USA.,Department of Entomology, The Center for Infectious Disease Dynamics, and the Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jared B Bennett
- Biophysics Graduate Group, Division of Biological Sciences, College of Letters and Science, University of California, Berkeley, CA, 94720, USA
| | - Zhiqian Li
- Department 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, La Jolla, CA, 92093, USA
| | - John M Marshall
- Divisions of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Ethan Bier
- Department 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, La Jolla, CA, 92093, USA.
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9
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Brown EA, Eikenbary SR, Landis WG. Bayesian network-based risk assessment of synthetic biology: Simulating CRISPR-Cas9 gene drive dynamics in invasive rodent management. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2022; 42:2835-2846. [PMID: 35568962 DOI: 10.1111/risa.13948] [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
Gene drive technology has been proposed to control invasive rodent populations as an alternative to rodenticides. However, this approach has not undergone risk assessment that meets criteria established by Gene Drives on the Horizon, a 2016 report by the National Academies of Sciences, Engineering, and Medicine. To conduct a risk assessment of gene drives, we employed the Bayesian network-relative risk model to calculate the risk of mouse eradication on Southeast Farallon Island using a CRISPR-Cas9 homing gene drive construct. We modified and implemented the R-based model "MGDrivE" to simulate and compare 60 management strategies for gene drive rodent management. These scenarios spanned four gene drive mouse release schemes, three gene drive homing rates, three levels of supplemental rodenticide dose, and two timings of rodenticide application relative to gene drive release. Simulation results showed that applying a supplemental rodenticide simultaneously with gene drive mouse deployment resulted in faster eradication of the island mouse population. Gene drive homing rate had the highest influence on the overall probability of successful eradication, as increased gene drive accuracy reduces the likelihood of mice developing resistance to the CRISPR-Cas9 homing mechanism.
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Affiliation(s)
- Ethan A Brown
- Institute of Environmental Toxicology and Chemistry, College of the Environment, Western Washington University, Bellingham, Washington, USA
| | - Steven R Eikenbary
- Institute of Environmental Toxicology and Chemistry, College of the Environment, Western Washington University, Bellingham, Washington, USA
| | - Wayne G Landis
- Institute of Environmental Toxicology and Chemistry, College of the Environment, Western Washington University, Bellingham, Washington, USA
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10
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Verkuijl SAN, Gonzalez E, Li M, Ang JXD, Kandul NP, Anderson MAE, Akbari OS, Bonsall MB, Alphey L. A CRISPR endonuclease gene drive reveals distinct mechanisms of inheritance bias. Nat Commun 2022; 13:7145. [PMID: 36414618 PMCID: PMC9681865 DOI: 10.1038/s41467-022-34739-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR/Cas gene drives can bias transgene inheritance through different mechanisms. Homing drives are designed to replace a wild-type allele with a copy of a drive element on the homologous chromosome. In Aedes aegypti, the sex-determining locus is closely linked to the white gene, which was previously used as a target for a homing drive element (wGDe). Here, through an analysis using this linkage we show that in males inheritance bias of wGDe did not occur by homing, rather through increased propagation of the donor drive element. We test the same wGDe drive element with transgenes expressing Cas9 with germline regulatory elements sds3, bgcn, and nup50. We only find inheritance bias through homing, even with the identical nup50-Cas9 transgene. We propose that DNA repair outcomes may be more context dependent than anticipated and that other previously reported homing drives may, in fact, bias their inheritance through other mechanisms.
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Affiliation(s)
- Sebald A N Verkuijl
- Mathematical Ecology Research Group, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Estela Gonzalez
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ming Li
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Joshua X D Ang
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Nikolay P Kandul
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michelle A E Anderson
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Omar S Akbari
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michael B Bonsall
- Mathematical Ecology Research Group, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
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11
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Raban R, Gendron WAC, Akbari OS. A perspective on the expansion of the genetic technologies to support the control of neglected vector-borne diseases and conservation. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.999273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Genetic-based technologies are emerging as promising tools to support vector population control. Vectors of human malaria and dengue have been the main focus of these development efforts, but in recent years these technologies have become more flexible and adaptable and may therefore have more wide-ranging applications. Culex quinquefasciatus, for example, is the primary vector of avian malaria in Hawaii and other tropical islands. Avian malaria has led to the extinction of numerous native bird species and many native bird species continue to be threatened as climate change is expanding the range of this mosquito. Genetic-based technologies would be ideal to support avian malaria control as they would offer alternatives to interventions that are difficult to implement in natural areas, such as larval source reduction, and limit the need for chemical insecticides, which can harm beneficial species in these natural areas. This mosquito is also an important vector of human diseases, such as West Nile and Saint Louis encephalitis viruses, so genetic-based control efforts for this species could also have a direct impact on human health. This commentary will discuss the current state of development and future needs for genetic-based technologies in lesser studied, but important disease vectors, such as C. quinquefasciatus, and make comparisons to technologies available in more studied vectors. While most current genetic control focuses on human disease, we will address the impact that these technologies could have on both disease and conservation focused vector control efforts and what is needed to prepare these technologies for evaluation in the field. The versatility of genetic-based technologies may result in the development of many important tools to control a variety of vectors that impact human, animal, and ecosystem health.
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12
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Melesse Vergara M, Labbé J, Tannous J. Reflection on the Challenges, Accomplishments, and New Frontiers of Gene Drives. BIODESIGN RESEARCH 2022; 2022:9853416. [PMID: 37850135 PMCID: PMC10521683 DOI: 10.34133/2022/9853416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/19/2022] [Indexed: 10/19/2023] Open
Abstract
Ongoing pest and disease outbreaks pose a serious threat to human, crop, and animal lives, emphasizing the need for constant genetic discoveries that could serve as mitigation strategies. Gene drives are genetic engineering approaches discovered decades ago that may allow quick, super-Mendelian dissemination of genetic modifications in wild populations, offering hopes for medicine, agriculture, and ecology in combating diseases. Following its first discovery, several naturally occurring selfish genetic elements were identified and several gene drive mechanisms that could attain relatively high threshold population replacement have been proposed. This review provides a comprehensive overview of the recent advances in gene drive research with a particular emphasis on CRISPR-Cas gene drives, the technology that has revolutionized the process of genome engineering. Herein, we discuss the benefits and caveats of this technology and place it within the context of natural gene drives discovered to date and various synthetic drives engineered. Later, we elaborate on the strategies for designing synthetic drive systems to address resistance issues and prevent them from altering the entire wild populations. Lastly, we highlight the major applications of synthetic CRISPR-based gene drives in different living organisms, including plants, animals, and microorganisms.
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Affiliation(s)
| | - Jesse Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Invaio Sciences, Cambridge, MA 02138USA
| | - Joanna Tannous
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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13
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Gantz VM, Bier E. Active genetics comes alive: Exploring the broad applications of CRISPR-based selfish genetic elements (or gene-drives): Exploring the broad applications of CRISPR-based selfish genetic elements (or gene-drives). Bioessays 2022; 44:e2100279. [PMID: 35686327 PMCID: PMC9397133 DOI: 10.1002/bies.202100279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/11/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based "active genetic" elements developed in 2015 bypassed the fundamental rules of traditional genetics. Inherited in a super-Mendelian fashion, such selfish genetic entities offered a variety of potential applications including: gene-drives to disseminate gene cassettes carrying desired traits throughout insect populations to control disease vectors or pest species, allelic drives biasing inheritance of preferred allelic variants, neutralizing genetic elements to delete and replace or to halt the spread of gene-drives, split-drives with the core constituent Cas9 endonuclease and guide RNA (gRNA) components inserted at separate genomic locations to accelerate assembly of complex arrays of genetic traits or to gain genetic entry into novel organisms (vertebrates, plants, bacteria), and interhomolog based copying systems in somatic cells to develop tools for treating inherited or infectious diseases. Here, we summarize the substantial advances that have been made on all of these fronts and look forward to the next phase of this rapidly expanding and impactful field.
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Affiliation(s)
- Valentino M Gantz
- Department of Cell and Developmental Biology, University of California, La Jolla, California, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, La Jolla, California, USA
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14
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Asad M, Liu D, Li J, Chen J, Yang G. Development of CRISPR/Cas9-Mediated Gene-Drive Construct Targeting the Phenotypic Gene in Plutella xylostella. Front Physiol 2022; 13:938621. [PMID: 35845988 PMCID: PMC9277308 DOI: 10.3389/fphys.2022.938621] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
The gene-drive system can ensure that desirable traits are transmitted to the progeny more than the normal Mendelian segregation. The clustered regularly interspersed palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated gene-drive system has been demonstrated in dipteran insect species, including Drosophila and Anopheles, not yet in other insect species. Here, we have developed a single CRISPR/Cas9-mediated gene-drive construct for Plutella xylostella, a highly-destructive lepidopteran pest of cruciferous crops. The gene-drive construct was developed containing a Cas9 gene, a marker gene (EGFP) and a gRNA sequence targeting the phenotypic marker gene (Pxyellow) and site-specifically inserted into the P. xylostella genome. This homing-based gene-drive copied ∼12 kb of a fragment containing Cas9 gene, gRNA, and EGFP gene along with their promoters to the target site. Overall, 6.67%–12.59% gene-drive efficiency due to homology-directed repair (HDR), and 80.93%–86.77% resistant-allele formation due to non-homologous-end joining (NHEJ) were observed. Furthermore, the transgenic progeny derived from male parents showed a higher gene-drive efficiency compared with transgenic progeny derived from female parents. This study demonstrates the feasibility of the CRISPR/Cas9-mediated gene-drive construct in P. xylostella that inherits the desired traits to the progeny. The finding of this study provides a foundation to develop an effective CRISPR/Cas9-mediated gene-drive system for pest control.
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Affiliation(s)
- Muhammad Asad
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Dan Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Jianwen Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Jing Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control, Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Guang Yang,
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15
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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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16
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Yang E, Metzloff M, Langmüller AM, Xu X, Clark AG, Messer PW, Champer J. A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance alleles. G3 (BETHESDA, MD.) 2022; 12:jkac081. [PMID: 35394026 PMCID: PMC9157102 DOI: 10.1093/g3journal/jkac081] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/30/2022] [Indexed: 11/14/2022]
Abstract
Gene drives are engineered alleles that can bias inheritance in their favor, allowing them to spread throughout a population. They could potentially be used to modify or suppress pest populations, such as mosquitoes that spread diseases. CRISPR/Cas9 homing drives, which copy themselves by homology-directed repair in drive/wild-type heterozygotes, are a powerful form of gene drive, but they are vulnerable to resistance alleles that preserve the function of their target gene. Such resistance alleles can prevent successful population suppression. Here, we constructed a homing suppression drive in Drosophila melanogaster that utilized multiplexed gRNAs to inhibit the formation of functional resistance alleles in its female fertility target gene. The selected gRNA target sites were close together, preventing reduction in drive conversion efficiency. The construct reached a moderate equilibrium frequency in cage populations without apparent formation of resistance alleles. However, a moderate fitness cost prevented elimination of the cage population, showing the importance of using highly efficient drives in a suppression strategy, even if resistance can be addressed. Nevertheless, our results experimentally demonstrate the viability of the multiplexed gRNAs strategy in homing suppression gene drives.
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Affiliation(s)
- Emily Yang
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Matthew Metzloff
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Anna M Langmüller
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
- Vienna Graduate School of Population Genetics, 1210 Wien, Austria
| | - Xuejiao Xu
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jackson Champer
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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17
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Metzloff M, Yang E, Dhole S, Clark AG, Messer PW, Champer J. Experimental demonstration of tethered gene drive systems for confined population modification or suppression. BMC Biol 2022; 20:119. [PMID: 35606745 PMCID: PMC9128227 DOI: 10.1186/s12915-022-01292-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Homing gene drives hold great promise for the genetic control of natural populations. However, current homing systems are capable of spreading uncontrollably between populations connected by even marginal levels of migration. This could represent a substantial sociopolitical barrier to the testing or deployment of such drives and may generally be undesirable when the objective is only local population control, such as suppression of an invasive species outside of its native range. Tethered drive systems, in which a locally confined gene drive provides the CRISPR nuclease needed for a homing drive, could provide a solution to this problem, offering the power of a homing drive and confinement of the supporting drive. RESULTS Here, we demonstrate the engineering of a tethered drive system in Drosophila, using a regionally confined CRISPR Toxin-Antidote Recessive Embryo (TARE) drive to support modification and suppression homing drives. Each drive was able to bias inheritance in its favor, and the TARE drive was shown to spread only when released above a threshold frequency in experimental cage populations. After the TARE drive had established in the population, it facilitated the spread of a subsequently released split homing modification drive (to all individuals in the cage) and of a homing suppression drive (to its equilibrium frequency). CONCLUSIONS Our results show that the tethered drive strategy is a viable and easily engineered option for providing confinement of homing drives to target populations.
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Affiliation(s)
- Matthew Metzloff
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Emily Yang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Sumit Dhole
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jackson Champer
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
- Present Address: Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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18
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Nash A, Capriotti P, Hoermann A, Papathanos PA, Windbichler N. Intronic gRNAs for the Construction of Minimal Gene Drive Systems. Front Bioeng Biotechnol 2022; 10:857460. [PMID: 35646834 PMCID: PMC9133698 DOI: 10.3389/fbioe.2022.857460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Gene drives are promising tools for the genetic control of insect vector or pest populations. CRISPR-based gene drives are generally highly complex synthetic constructs consisting of multiple transgenes and their respective regulatory elements. This complicates the generation of new gene drives and the testing of the behavior of their constituent functional modules. Here, we explored the minimal genetic components needed to constitute autonomous gene drives in Drosophila melanogaster. We first designed intronic gRNAs that can be located directly within coding transgene sequences and tested their functions in cell lines. We then integrated a Cas9 open reading frame hosting such an intronic gRNA within the Drosophila rcd-1r locus that drives the expression in the male and female germlines. We showed that upon removal of the fluorescent transformation marker, the rcd-1rd allele supports efficient gene drive. We assessed the propensity of this driver, designed to be neutral with regards to fitness and host gene function, to propagate in caged fly populations. Because of their simplicity, such integral gene drives could enable the modularization of drive and effector functions. We also discussed the possible biosafety implications of minimal and possibly recoded gene drives.
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Affiliation(s)
- Alexander Nash
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Paolo Capriotti
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Astrid Hoermann
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Phillipos Aris Papathanos
- Department of Entomology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, London, United Kingdom
- *Correspondence: Nikolai Windbichler,
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19
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Verkuijl SAN, Ang JXD, Alphey L, Bonsall MB, Anderson MAE. The Challenges in Developing Efficient and Robust Synthetic Homing Endonuclease Gene Drives. Front Bioeng Biotechnol 2022; 10:856981. [PMID: 35419354 PMCID: PMC8996256 DOI: 10.3389/fbioe.2022.856981] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Making discrete and precise genetic changes to wild populations has been proposed as a means of addressing some of the world's most pressing ecological and public health challenges caused by insect pests. Technologies that would allow this, such as synthetic gene drives, have been under development for many decades. Recently, a new generation of programmable nucleases has dramatically accelerated technological development. CRISPR-Cas9 has improved the efficiency of genetic engineering and has been used as the principal effector nuclease in different gene drive inheritance biasing mechanisms. Of these nuclease-based gene drives, homing endonuclease gene drives have been the subject of the bulk of research efforts (particularly in insects), with many different iterations having been developed upon similar core designs. We chart the history of homing gene drive development, highlighting the emergence of challenges such as unintended repair outcomes, "leaky" expression, and parental deposition. We conclude by discussing the progress made in developing strategies to increase the efficiency of homing endonuclease gene drives and mitigate or prevent unintended outcomes.
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Affiliation(s)
- Sebald A. N. Verkuijl
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Joshua X. D. Ang
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
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20
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Bunting MD, Pfitzner C, Gierus L, White M, Piltz S, Thomas PQ. Generation of Gene Drive Mice for Invasive Pest Population Suppression. Methods Mol Biol 2022; 2495:203-230. [PMID: 35696035 DOI: 10.1007/978-1-0716-2301-5_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Gene drives are genetic elements that are transmitted to greater than 50% of offspring and have potential for population modification or suppression. While gene drives are known to occur naturally, the recent emergence of CRISPR-Cas9 genome-editing technology has enabled generation of synthetic gene drives in a range of organisms including mosquitos, flies, and yeast. For example, studies in Anopheles mosquitos have demonstrated >95% transmission of CRISPR-engineered gene drive constructs, providing a possible strategy for malaria control. Recently published studies have also indicated that it may be possible to develop gene drive technology in invasive rodents such as mice. Here, we discuss the prospects for gene drive development in mice, including synthetic "homing drive" and X-shredder strategies as well as modifications of the naturally occurring t haplotype. We also provide detailed protocols for generation of gene drive mice through incorporation of plasmid-based transgenes in a targeted and non-targeted manner. Importantly, these protocols can be used for generating transgenic mice for any project that requires insertion of kilobase-scale transgenes such as knock-in of fluorescent reporters, gene swaps, overexpression/ectopic expression studies, and conditional "floxed" alleles.
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Affiliation(s)
- Mark D Bunting
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Chandran Pfitzner
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Luke Gierus
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Melissa White
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia
- South Australian Genome Editing Facility, North Terrace, Adelaide, SA, Australia
| | - Sandra Piltz
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia
- South Australian Genome Editing Facility, North Terrace, Adelaide, SA, Australia
| | - Paul Q Thomas
- School of Medicine, University of Adelaide, North Terrace, Adelaide, SA, Australia.
- South Australian Genome Editing Facility, North Terrace, Adelaide, SA, Australia.
- South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.
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21
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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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22
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Abstract
Gene drives are an emerging technology with tremendous potential to impact public health, agriculture, and conservation. While gene drives can be described simply as selfish genetic elements (natural or engineered) that are inherited at non-Mendelian rates, upon closer inspection, engineered gene drive technology is a complex class of biotechnology that uses a diverse number of genetic features to bias rates of inheritance. As a complex technology, gene drives can be difficult to comprehend, not only for the public and stakeholders, but also to risk assessors, risk managers, and decisionmakers not familiar with gene drive literature. To address this difficulty, we describe a gene drive classification system based on 5 functional characteristics. These characteristics include a gene drive's objective, mechanism, release threshold, range, and persistence. The aggregate of the gene drive's characteristics can be described as the gene drive's architecture. Establishing a classification system to define different gene drive technologies should make them more comprehensible to the public and provide a framework to guide regulatory evaluation and decisionmaking.
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Affiliation(s)
- Justin Overcash
- Justin Overcash, PhD, is an Animal and Plant Health Inspection Service (APHIS) Science Fellow, Biotechnology Regulatory Services, Riverdale, MD
| | - Andrew Golnar
- Andrew Golnar, PhD, is an APHIS Science Fellow, Wildlife Services, Fort Collins, CO
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23
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Gamez S, Chaverra-Rodriguez D, Buchman A, Kandul NP, Mendez-Sanchez SC, Bennett JB, Sánchez C HM, Yang T, Antoshechkin I, Duque JE, Papathanos PA, Marshall JM, Akbari OS. Exploiting a Y chromosome-linked Cas9 for sex selection and gene drive. Nat Commun 2021; 12:7202. [PMID: 34893590 PMCID: PMC8664916 DOI: 10.1038/s41467-021-27333-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023] Open
Abstract
CRISPR-based genetic engineering tools aimed to bias sex ratios, or drive effector genes into animal populations, often integrate the transgenes into autosomal chromosomes. However, in species with heterogametic sex chromsomes (e.g. XY, ZW), sex linkage of endonucleases could be beneficial to drive the expression in a sex-specific manner to produce genetic sexing systems, sex ratio distorters, or even sex-specific gene drives, for example. To explore this possibility, here we develop a transgenic line of Drosophila melanogaster expressing Cas9 from the Y chromosome. We functionally characterize the utility of this strain for both sex selection and gene drive finding it to be quite effective. To explore its utility for population control, we built mathematical models illustrating its dynamics as compared to other state-of-the-art systems designed for both population modification and suppression. Taken together, our results contribute to the development of current CRISPR genetic control tools and demonstrate the utility of using sex-linked Cas9 strains for genetic control of animals.
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Affiliation(s)
- Stephanie Gamez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Agragene Inc., San Diego, CA, 92121, USA
| | - Duverney Chaverra-Rodriguez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anna Buchman
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Verily Life Sciences, South San Francisco, CA, 94080, USA
| | - Nikolay P Kandul
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stelia C Mendez-Sanchez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Group for Research in Biochemistry and Microbiology (Grupo de Investigación en Bioquímica Y Microbiología-GIBIM), School of Chemistry, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Jared B Bennett
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720, USA
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Héctor M Sánchez C
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Ting Yang
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering (BBE), California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jonny E Duque
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Centro de Investigaciones en Enfermedades Tropicales - CINTROP, Facultad de Salud, Escuela de Medicina, Departamento de Ciencias Básicas, Universidad Industrial de Santander, Piedecuesta, Santander, Colombia
| | - Philippos A Papathanos
- Department of Entomology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - John M Marshall
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.
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24
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Abstract
Releases of sterile males are the gold standard for many insect population control programs, and precise sex sorting to remove females prior to male releases is essential to the success of these operations. To advance traditional methods for scaling the generation of sterile males, we previously described a CRISPR-mediated precision-guided sterile insect technique (pgSIT), in which Cas9 and gRNA strains are genetically crossed to generate sterile males for mass release. While effective at generating F1 sterile males, pgSIT requires a genetic cross between the two parental strains, which requires maintenance and sexing of two strains in a factory. Therefore, to advance pgSIT further by removing this crossing step, here we describe a next-generation temperature-inducible pgSIT (TI-pgSIT) technology and demonstrate its proof-of-concept in Drosophila melanogaster. Importantly, we were able to develop a true breeding strain for TI-pgSIT that eliminates the requirement for sex sorting-a feature that may help further automate production at scale.
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Affiliation(s)
- Nikolay P. Kandul
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA
| | - Omar S. Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA
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25
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Kandul NP, Belikoff EJ, Liu J, Buchman A, Li F, Yamamoto A, Yang T, Shriner I, Scott MJ, Akbari OS. Genetically Encoded CRISPR Components Yield Efficient Gene Editing in the Invasive Pest Drosophila suzukii. CRISPR J 2021; 4:739-751. [PMID: 34661429 DOI: 10.1089/crispr.2021.0032] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Originally from Asia, Drosophila suzukii Matsumura is a global pest of economically important soft-skinned fruits. Also commonly known as spotted wing drosophila, it is largely controlled through repeated applications of broad-spectrum insecticides by which resistance has been observed in the field. There is a pressing need for a better understanding of D. suzukii biology and for developing alternative environmentally friendly methods of control. The RNA-guided Cas9 nuclease has revolutionized functional genomics and is an integral component of several recently developed genetic strategies for population control of insects. Here, we describe genetically modified strains that encode three different terminators and four different promoters to express Cas9 robustly in both the soma and/or germline of D. suzukii. The Cas9 strains were rigorously evaluated through genetic crossing to transgenic strains that encode single-guide RNAs targeting the conserved X-linked yellow body and white eye genes. We find that several Cas9/gRNA strains display remarkably high editing capacity. Going forward, these tools will be instrumental for evaluating gene function in D. suzukii and may even provide tools useful for the development of new genetic strategies for control of this invasive species.
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Affiliation(s)
- Nikolay P Kandul
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
| | - Esther J Belikoff
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
| | - Anna Buchman
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
| | - Fang Li
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Akihiko Yamamoto
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Ting Yang
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
| | - Isaiah Shriner
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
| | - Maxwell J Scott
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
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26
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Fuchs S, Garrood WT, Beber A, Hammond A, Galizi R, Gribble M, Morselli G, Hui TYJ, Willis K, Kranjc N, Burt A, Crisanti A, Nolan T. Resistance to a CRISPR-based gene drive at an evolutionarily conserved site is revealed by mimicking genotype fixation. PLoS Genet 2021; 17:e1009740. [PMID: 34610011 PMCID: PMC8519452 DOI: 10.1371/journal.pgen.1009740] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/15/2021] [Accepted: 09/24/2021] [Indexed: 01/06/2023] Open
Abstract
CRISPR-based homing gene drives can be designed to disrupt essential genes whilst biasing their own inheritance, leading to suppression of mosquito populations in the laboratory. This class of gene drives relies on CRISPR-Cas9 cleavage of a target sequence and copying ('homing') therein of the gene drive element from the homologous chromosome. However, target site mutations that are resistant to cleavage yet maintain the function of the essential gene are expected to be strongly selected for. Targeting functionally constrained regions where mutations are not easily tolerated should lower the probability of resistance. Evolutionary conservation at the sequence level is often a reliable indicator of functional constraint, though the actual level of underlying constraint between one conserved sequence and another can vary widely. Here we generated a novel adult lethal gene drive (ALGD) in the malaria vector Anopheles gambiae, targeting an ultra-conserved target site in a haplosufficient essential gene (AGAP029113) required during mosquito development, which fulfils many of the criteria for the target of a population suppression gene drive. We then designed a selection regime to experimentally assess the likelihood of generation and subsequent selection of gene drive resistant mutations at its target site. We simulated, in a caged population, a scenario where the gene drive was approaching fixation, where selection for resistance is expected to be strongest. Continuous sampling of the target locus revealed that a single, restorative, in-frame nucleotide substitution was selected. Our findings show that ultra-conservation alone need not be predictive of a site that is refractory to target site resistance. Our strategy to evaluate resistance in vivo could help to validate candidate gene drive targets for their resilience to resistance and help to improve predictions of the invasion dynamics of gene drives in field populations.
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Affiliation(s)
- Silke Fuchs
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - William T. Garrood
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Anna Beber
- Department of Biology, University of Padua, Padua, Italy
| | - Andrew Hammond
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, United States of America
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Matthew Gribble
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Giulia Morselli
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tin-Yu J. Hui
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Katie Willis
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Molecular Medicine, University of Padua, Padua, Italy
- * E-mail: (AC); (TN)
| | - Tony Nolan
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail: (AC); (TN)
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27
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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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28
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Quinn C, Anthousi A, Wondji C, Nolan T. CRISPR-mediated knock-in of transgenes into the malaria vector Anopheles funestus. G3 (BETHESDA, MD.) 2021; 11:6303614. [PMID: 34849822 PMCID: PMC8496255 DOI: 10.1093/g3journal/jkab201] [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] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/17/2021] [Indexed: 01/15/2023]
Abstract
The ability to introduce mutations, or transgenes, of choice to precise genomic locations has revolutionized our ability to understand how genes and organisms work. In many mosquito species that are vectors of various human diseases, the advent of CRISPR genome editing tools has shed light on basic aspects of their biology that are relevant to their efficiency as disease vectors. This allows a better understanding of how current control tools work and opens up the possibility of novel genetic control approaches, such as gene drives, that deliberately introduce genetic traits into populations. Yet for the Anopheles funestus mosquito, a significant vector of malaria in sub-Saharan Africa and indeed the dominant vector species in many countries, transgenesis has yet to be achieved. We describe herein an optimized transformation system based on the germline delivery of CRISPR components that allows efficient cleavage of a previously validated genomic site and preferential repair of these cut sites via homology-directed repair (HDR), which allows the introduction of exogenous template sequence, rather than end-joining repair. The rates of transformation achieved are sufficiently high that it should be able to introduce alleles of choice to a target locus, and recover these, without the need to include additional dominant marker genes. Moreover, the high rates of HDR observed suggest that gene drives, which employ an HDR-type mechanism to ensure their proliferation in the genome, may be well suited to work in A. funestus.
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Affiliation(s)
| | - Amalia Anthousi
- Department of Biology, University of Crete, Heraklion 700 13, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 700 13, Greece
| | - Charles Wondji
- Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
- Department of Medical Entomology, Centre for Research in Infectious Diseases (CRID), Yaoundé 5, Cameroon
| | - Tony Nolan
- Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
- Corresponding author:
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29
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Bier E, Nizet V. Driving to Safety: CRISPR-Based Genetic Approaches to Reducing Antibiotic Resistance. Trends Genet 2021; 37:745-757. [PMID: 33745750 DOI: 10.1016/j.tig.2021.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Bacterial resistance to antibiotics has reached critical levels, skyrocketing in hospitals and the environment and posing a major threat to global public health. The complex and challenging problem of reducing antibiotic resistance (AR) requires a network of both societal and science-based solutions to preserve the most lifesaving pharmaceutical intervention known to medicine. In addition to developing new classes of antibiotics, it is essential to safeguard the clinical efficacy of existing drugs. In this review, we examine the potential application of novel CRISPR-based genetic approaches to reducing AR in both environmental and clinical settings and prolonging the utility of vital antibiotics.
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Affiliation(s)
- Ethan Bier
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA.
| | - Victor Nizet
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Collaborative to Halt Antibiotic-Resistant Microbes, Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA; Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA
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30
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Wang GH, Gamez S, Raban RR, Marshall JM, Alphey L, Li M, Rasgon JL, Akbari OS. Combating mosquito-borne diseases using genetic control technologies. Nat Commun 2021; 12:4388. [PMID: 34282149 PMCID: PMC8290041 DOI: 10.1038/s41467-021-24654-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/30/2021] [Indexed: 01/03/2023] Open
Abstract
Mosquito-borne diseases, such as dengue and malaria, pose significant global health burdens. Unfortunately, current control methods based on insecticides and environmental maintenance have fallen short of eliminating the disease burden. Scalable, deployable, genetic-based solutions are sought to reduce the transmission risk of these diseases. Pathogen-blocking Wolbachia bacteria, or genome engineering-based mosquito control strategies including gene drives have been developed to address these problems, both requiring the release of modified mosquitoes into the environment. Here, we review the latest developments, notable similarities, and critical distinctions between these promising technologies and discuss their future applications for mosquito-borne disease control.
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Affiliation(s)
- Guan-Hong Wang
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Stephanie Gamez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA
| | - Robyn R Raban
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Pirbright, UK
| | - Ming Li
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA
| | - Jason L Rasgon
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
- The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA.
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31
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Terradas G, Buchman AB, Bennett JB, Shriner I, Marshall JM, Akbari OS, Bier E. Inherently confinable split-drive systems in Drosophila. Nat Commun 2021; 12:1480. [PMID: 33674604 PMCID: PMC7935863 DOI: 10.1038/s41467-021-21771-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
CRISPR-based gene-drive systems, which copy themselves via gene conversion mediated by the homology-directed repair (HDR) pathway, have the potential to revolutionize vector control. However, mutant alleles generated by the competing non-homologous end-joining (NHEJ) pathway, resistant to Cas9 cleavage, can interrupt the spread of gene-drive elements. We hypothesized that drives targeting genes essential for viability or reproduction also carrying recoded sequences that restore endogenous gene functionality should benefit from dominantly-acting maternal clearance of NHEJ alleles combined with recessive Mendelian culling processes. Here, we test split gene-drive (sGD) systems in Drosophila melanogaster that are inserted into essential genes required for viability (rab5, rab11, prosalpha2) or fertility (spo11). In single generation crosses, sGDs copy with variable efficiencies and display sex-biased transmission. In multigenerational cage trials, sGDs follow distinct drive trajectories reflecting their differential tendencies to induce target chromosome damage and/or lethal/sterile mosaic Cas9-dependent phenotypes, leading to inherently confinable drive outcomes. NHEJ alleles and Cas9 remnants after a gene drive introduction are scientific and public concerns. Here, the authors use split drives with recoded rescue elements to target essential genes and minimize the appearance of NHEJ alleles while also leaving no trace of Cas9.
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Affiliation(s)
- Gerard Terradas
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Anna B Buchman
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Jared B Bennett
- Biophysics Graduate Group, Division of Biological Sciences, College of Letters and Science, University of California, Berkeley, CA, USA
| | - Isaiah Shriner
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - John M Marshall
- Divisions of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA.,Innovative Genomics Institute, Berkeley, CA, USA
| | - Omar S Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA. .,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA.
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32
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Kandul NP, Liu J, Bennett JB, Marshall JM, Akbari OS. A confinable home-and-rescue gene drive for population modification. eLife 2021; 10:e65939. [PMID: 33666174 PMCID: PMC7968924 DOI: 10.7554/elife.65939] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Homing-based gene drives, engineered using CRISPR/Cas9, have been proposed to spread desirable genes throughout populations. However, invasion of such drives can be hindered by the accumulation of resistant alleles. To limit this obstacle, we engineer a confinable population modification home-and-rescue (HomeR) drive in Drosophila targeting an essential gene. In our experiments, resistant alleles that disrupt the target gene function were recessive lethal and therefore disadvantaged. We demonstrate that HomeR can achieve an increase in frequency in population cage experiments, but that fitness costs due to the Cas9 insertion limit drive efficacy. Finally, we conduct mathematical modeling comparing HomeR to contemporary gene drive architectures for population modification over wide ranges of fitness costs, transmission rates, and release regimens. HomeR could potentially be adapted to other species, as a means for safe, confinable, modification of wild populations.
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Affiliation(s)
- Nikolay P Kandul
- Section of Cell and Developmental Biology, University of California, San DiegoSan DiegoUnited States
| | - Junru Liu
- Section of Cell and Developmental Biology, University of California, San DiegoSan DiegoUnited States
| | - Jared B Bennett
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, BerkeleyBerkeleyUnited States
| | - Omar S Akbari
- Section of Cell and Developmental Biology, University of California, San DiegoSan DiegoUnited States
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33
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Trivedi D. Using CRISPR-Cas9-based genome engineering tools in Drosophila melanogaster. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:85-121. [PMID: 33934839 DOI: 10.1016/bs.pmbts.2021.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drosophila melanogaster has been used as a model organism for over a century. Mutant-based analyses have been used extensively to understand the genetic basis of different cellular processes, including development, neuronal function and diseases. Most of the earlier genetic mutants and specific tools were generated by random insertions and deletion strategies and then mapped to specific genomic loci. Since all genomic regions are not equally accessible to random mutations and insertions, many genes still remain uncharacterized. Low efficiency of targeted genomic manipulation approaches that rely on homologous recombination, and difficulty in generating resources for sequence-specific endonucleases, such as ZFNs (Zinc Finger Nucleases) and TALENs (Transcription Activator-Like Effector Nucleases), could not make these gene targeting techniques very popular. However, recently RNA directed DNA endonucleases, such as CRISPR-Cas, have transformed genome engineering owing to their comparative ease, versatility, and low expense. With the added advantage of preexisting genetic tools, CRISPR-Cas-based manipulations are being extensively used in Drosophila melanogaster and simultaneously being fine-tuned for specific experimental requirements. In this chapter, I will discuss various uses of CRISPR-Cas-based genetic engineering and specific design methods in Drosophila melanogaster. I will summarize various already available tools that are being utilized in conjunction with CRISPR-Cas technology to generate specific genetic manipulation and are being optimized to address specific questions. Finally, I will discuss the future directions of Drosophila genetics research and how CRISPR-Cas can be utilized to target specific questions, addressing which has not been possible thus far.
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Affiliation(s)
- Deepti Trivedi
- National Centre for Biological Sciences-TIFR, Bengaluru, India.
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Nolan T. Control of malaria-transmitting mosquitoes using gene drives. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190803. [PMID: 33357060 PMCID: PMC7776936 DOI: 10.1098/rstb.2019.0803] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2020] [Indexed: 01/13/2023] Open
Abstract
Gene drives are selfish genetic elements that can be re-designed to invade a population and they hold tremendous potential for the control of mosquitoes that transmit disease. Much progress has been made recently in demonstrating proof of principle for gene drives able to suppress populations of malarial mosquitoes, or to make them refractory to the Plasmodium parasites they transmit. This has been achieved using CRISPR-based gene drives. In this article, I will discuss the relative merits of this type of gene drive, as well as barriers to its technical development and to its deployment in the field as malaria control. This article is part of the theme issue 'Novel control strategies for mosquito-borne diseases'.
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Affiliation(s)
- Tony Nolan
- Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
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Oberhofer G, Ivy T, Hay BA. Split versions of Cleave and Rescue selfish genetic elements for measured self limiting gene drive. PLoS Genet 2021; 17:e1009385. [PMID: 33600432 PMCID: PMC7951863 DOI: 10.1371/journal.pgen.1009385] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 03/11/2021] [Accepted: 01/28/2021] [Indexed: 12/26/2022] Open
Abstract
Gene drive elements promote the spread of linked traits, providing methods for changing the composition or fate of wild populations. Drive mechanisms that are self-limiting are attractive because they allow control over the duration and extent of trait spread in time and space, and are reversible through natural selection as drive wanes. Self-sustaining Cleave and Rescue (ClvR) elements include a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene, a tightly linked recoded version of the essential gene resistant to cleavage (the Rescue), and a Cargo. ClvR spreads by creating loss-of-function (LOF) conditions in which those without ClvR die because they lack functional copies of the essential gene. We use modeling to show that when the Rescue-Cargo and one or both components required for LOF allele creation (Cas9 and gRNA) reside at different locations (split ClvR), drive of Rescue-Cargo is self-limiting due to a progressive decrease in Cas9 frequency, and thus opportunities for creation of LOF alleles, as spread occurs. Importantly, drive strength and duration can be extended in a measured manner-which is still self-limiting-by moving the two components close enough to each other that they experience some degree of linkage. With linkage, Cas9 transiently experiences drive by hitchhiking with Rescue-Cargo until linkage disequilibrium between the two disappears, a function of recombination frequency and number of generations, creating a novel point of control. We implement split ClvR in Drosophila, with key elements on different chromosomes. Cargo/Rescue/gRNAs spreads to high frequency in a Cas9-dependent manner, while the frequency of Cas9 decreases. These observations show that measured, transient drive, coupled with a loss of future drive potential, can be achieved using the simple toolkit that make up ClvR elements-Cas9 and gRNAs and a Rescue/Cargo.
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Affiliation(s)
- Georg Oberhofer
- California Institute of Technology, Pasadena, California, United States of America
| | - Tobin Ivy
- California Institute of Technology, Pasadena, California, United States of America
| | - Bruce A. Hay
- California Institute of Technology, Pasadena, California, United States of America
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Hammond A, Karlsson X, Morianou I, Kyrou K, Beaghton A, Gribble M, Kranjc N, Galizi R, Burt A, Crisanti A, Nolan T. Regulating the expression of gene drives is key to increasing their invasive potential and the mitigation of resistance. PLoS Genet 2021; 17:e1009321. [PMID: 33513149 PMCID: PMC7886172 DOI: 10.1371/journal.pgen.1009321] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 02/16/2021] [Accepted: 12/22/2020] [Indexed: 12/27/2022] Open
Abstract
Homing-based gene drives use a germline source of nuclease to copy themselves at specific target sites in a genome and bias their inheritance. Such gene drives can be designed to spread and deliberately suppress populations of malaria mosquitoes by impairing female fertility. However, strong unintended fitness costs of the drive and a propensity to generate resistant mutations can limit a gene drive’s potential to spread. Alternative germline regulatory sequences in the drive element confer improved fecundity of carrier individuals and reduced propensity for target site resistance. This is explained by reduced rates of end-joining repair of DNA breaks from parentally deposited nuclease in the embryo, which can produce heritable mutations that reduce gene drive penetrance. We tracked the generation and selection of resistant mutations over the course of a gene drive invasion of a population. Improved gene drives show faster invasion dynamics, increased suppressive effect and later onset of target site resistance. Our results show that regulation of nuclease expression is as important as the choice of target site when developing a robust homing-based gene drive for population suppression. Gene drives are selfish genetic elements that are able to drastically bias their own inheritance. They can rapidly invade populations, even starting from a very low frequency. Recent advances have allowed the engineering of gene drives deliberately designed to spread genetic traits of choice into populations of malaria-transmitting mosquito species–for example traits that impair a mosquito’s ability to reproduce or its ability to transmit parasites. The class of gene drive in question uses a very precise cutting and copying mechanism, termed ‘homing’, that allows it to increase its numbers in the cells that go on to form sperm or eggs, thereby increasing the chances that a copy of the gene drive is transmitted to offspring. However, while this type of gene drive can rapidly invade a mosquito population, mosquitoes can also eventually become resistant to the gene drive in some cases. Here we show that restricting the cutting activity of the gene drive to the germline tissue is crucial to maintaining its potency and we illustrate how failure to restrict this activity can lead to the generation of mutations that can make mosquitoes resistant to the gene drive.
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Affiliation(s)
- Andrew Hammond
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Xenia Karlsson
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Ioanna Morianou
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Andrea Beaghton
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Matthew Gribble
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, United Kingdom
- University of Padova, Padova, Italy
- * E-mail: (AC); (TN)
| | - Tony Nolan
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail: (AC); (TN)
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Kranjc N, Crisanti A, Nolan T, Bernardini F. Anopheles gambiae Genome Conservation as a Resource for Rational Gene Drive Target Site Selection. INSECTS 2021; 12:97. [PMID: 33498790 PMCID: PMC7911984 DOI: 10.3390/insects12020097] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022]
Abstract
The increase in molecular tools for the genetic engineering of insect pests and disease vectors, such as Anopheles mosquitoes that transmit malaria, has led to an unprecedented investigation of the genomic landscape of these organisms. The understanding of genome variability in wild mosquito populations is of primary importance for vector control strategies. This is particularly the case for gene drive systems, which look to introduce genetic traits into a population by targeting specific genomic regions. Gene drive targets with functional or structural constraints are highly desirable as they are less likely to tolerate mutations that prevent targeting by the gene drive and consequent failure of the technology. In this study we describe a bioinformatic pipeline that allows the analysis of whole genome data for the identification of highly conserved regions that can point at potential functional or structural constraints. The analysis was conducted across the genomes of 22 insect species separated by more than hundred million years of evolution and includes the observed genomic variation within field caught samples of Anopheles gambiae and Anopheles coluzzii, the two most dominant malaria vectors. This study offers insight into the level of conservation at a genome-wide scale as well as at per base-pair resolution. The results of this analysis are gathered in a data storage system that allows for flexible extraction and bioinformatic manipulation. Furthermore, it represents a valuable resource that could provide insight into population structure and dynamics of the species in the complex and benefit the development and implementation of genetic strategies to tackle malaria.
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Affiliation(s)
- Nace Kranjc
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK; (N.K.); (A.C.)
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK; (N.K.); (A.C.)
| | - Tony Nolan
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Federica Bernardini
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK; (N.K.); (A.C.)
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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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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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Rocha EM, Katak RDM, Campos de Oliveira J, Araujo MDS, Carlos BC, Galizi R, Tripet F, Marinotti O, Souza-Neto JA. Vector-Focused Approaches to Curb Malaria Transmission in the Brazilian Amazon: An Overview of Current and Future Challenges and Strategies. Trop Med Infect Dis 2020; 5:E161. [PMID: 33092228 PMCID: PMC7709627 DOI: 10.3390/tropicalmed5040161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 01/05/2023] Open
Abstract
In Brazil, malaria transmission is mostly confined to the Amazon, where substantial progress has been made towards disease control in the past decade. Vector control has been historically considered a fundamental part of the main malaria control programs implemented in Brazil. However, the conventional vector-control tools have been insufficient to control or eliminate local vector populations due to the complexity of the Amazonian rainforest environment and ecological features of malaria vector species in the Amazon, especially Anopheles darlingi. Malaria elimination in Brazil and worldwide eradication will require a combination of conventional and new approaches that takes into account the regional specificities of vector populations and malaria transmission dynamics. Here we present an overview on both conventional and novel promising vector-focused tools to curb malaria transmission in the Brazilian Amazon. If well designed and employed, vector-based approaches may improve the implementation of malaria-control programs, particularly in remote or difficult-to-access areas and in regions where existing interventions have been unable to eliminate disease transmission. However, much effort still has to be put into research expanding the knowledge of neotropical malaria vectors to set the steppingstones for the optimization of conventional and development of innovative vector-control tools.
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Affiliation(s)
- Elerson Matos Rocha
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Amazonas—PPGBIOTEC/UFAM, Manaus 69067-005, Brazil; (E.M.R.); (R.d.M.K.); (J.C.d.O.)
| | - Ricardo de Melo Katak
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Amazonas—PPGBIOTEC/UFAM, Manaus 69067-005, Brazil; (E.M.R.); (R.d.M.K.); (J.C.d.O.)
| | - Juan Campos de Oliveira
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Amazonas—PPGBIOTEC/UFAM, Manaus 69067-005, Brazil; (E.M.R.); (R.d.M.K.); (J.C.d.O.)
| | - Maisa da Silva Araujo
- Laboratory of Medical Entomology, Oswaldo Cruz Foundation, FIOCRUZ RONDONIA, Porto Velho, RO 76812-245, Brazil;
| | - Bianca Cechetto Carlos
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil;
- Central Multiuser Laboratory, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
| | - Roberto Galizi
- Centre of Applied Entomology and Parasitology, School of Life Sciences, Keele University, Staffordshire ST5 5GB, UK; (R.G.); (F.T.)
| | - Frederic Tripet
- Centre of Applied Entomology and Parasitology, School of Life Sciences, Keele University, Staffordshire ST5 5GB, UK; (R.G.); (F.T.)
| | | | - Jayme A. Souza-Neto
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil;
- Central Multiuser Laboratory, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
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Gamez S, Srivastav S, Akbari OS, Lau NC. Diverse Defenses: A Perspective Comparing Dipteran Piwi-piRNA Pathways. Cells 2020; 9:E2180. [PMID: 32992598 PMCID: PMC7601171 DOI: 10.3390/cells9102180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
Animals face the dual threat of virus infections hijacking cellular function and transposons proliferating in germline genomes. For insects, the deeply conserved RNA interference (RNAi) pathways and other chromatin regulators provide an important line of defense against both viruses and transposons. For example, this innate immune system displays adaptiveness to new invasions by generating cognate small RNAs for targeting gene silencing measures against the viral and genomic intruders. However, within the Dipteran clade of insects, Drosophilid fruit flies and Culicids mosquitoes have evolved several unique mechanistic aspects of their RNAi defenses to combat invading transposons and viruses, with the Piwi-piRNA arm of the RNAi pathways showing the greatest degree of novel evolution. Whereas central features of Piwi-piRNA pathways are conserved between Drosophilids and Culicids, multiple lineage-specific innovations have arisen that may reflect distinct genome composition differences and specific ecological and physiological features dividing these two branches of Dipterans. This perspective review focuses on the most recent findings illuminating the Piwi/piRNA pathway distinctions between fruit flies and mosquitoes, and raises open questions that need to be addressed in order to ameliorate human diseases caused by pathogenic viruses that mosquitoes transmit as vectors.
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Affiliation(s)
- Stephanie Gamez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA 92093, USA; (S.G.); (O.S.A.)
| | - Satyam Srivastav
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA;
| | - Omar S. Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA 92093, USA; (S.G.); (O.S.A.)
| | - Nelson C. Lau
- Department of Biochemistry and Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA
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A day in the life of a mosquito insectary team: pushing for solutions to mosquito-borne diseases. Lab Anim (NY) 2020; 49:241-243. [PMID: 32807984 DOI: 10.1038/s41684-020-0617-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Quinn CM, Nolan T. Nuclease-based gene drives, an innovative tool for insect vector control: advantages and challenges of the technology. CURRENT OPINION IN INSECT SCIENCE 2020; 39:77-83. [PMID: 32339930 DOI: 10.1016/j.cois.2020.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/09/2020] [Accepted: 03/19/2020] [Indexed: 06/11/2023]
Abstract
Genetic control of insects involves the release of modified insects that contain altered genetic traits and are competent to mate with target populations to introduce the traits therein. Since it relies on mating, this type of control is species-specific, non-toxic, and has the advantage that the released insects can do the difficult task of reaching remote and otherwise inaccessible insect niches. Gene drives are capable of drastically biasing their own transmission and are being developed as a new type of genetic control, one that would be self-sustaining, requiring low numbers in the initial release in order to spread and persist within a population. In this review, the advantages and challenges of building and deploying this technology will be discussed, using mosquito control as an example.
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Affiliation(s)
| | - Tony Nolan
- Liverpool School of Tropical Medicine, United Kingdom.
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The Developmental Transcriptome of Aedes albopictus, a Major Worldwide Human Disease Vector. G3-GENES GENOMES GENETICS 2020; 10:1051-1062. [PMID: 31964684 PMCID: PMC7056973 DOI: 10.1534/g3.119.401006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aedes albopictus mosquitoes are important vectors for a number of human pathogens including the Zika, dengue, and chikungunya viruses. Capable of displacing Aedes aegypti populations, this mosquito adapts to cooler environments which increases its geographical range and transmission potential. There are limited control strategies for Aedes albopictus mosquitoes which is likely attributed to the lack of comprehensive biological studies on this emerging vector. To fill this void, here using RNAseq we characterized Aedes albopictus mRNA expression profiles at 34 distinct time points throughout development providing the first high-resolution comprehensive view of the developmental transcriptome of this worldwide human disease vector. This enabled us to identify several patterns of shared gene expression among tissues as well as sex-specific expression patterns. To illuminate the similarities and differences with Aedes aegypti, a related human disease vector, we also performed a comparative analysis between the two developmental transcriptomes, identifying life stages where the two species exhibit similar and distinct gene expression patterns. These findings provide insights into the similarities and differences between Aedes albopictus and Aedes aegypti mosquito biology. In summary, the results generated from this study should form the basis for future investigations on the biology of Aedes albopictus and provide a gold mine resource for the development of transgene-based vector control strategies.
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Abstract
Vector-borne diseases, such as dengue, Zika and malaria, are a major cause of morbidity and mortality worldwide. These diseases have proven difficult to control and currently available management tools are insufficient to eliminate them in many regions. Gene drives have the potential to revolutionize vector-borne disease control. This suite of technologies has advanced rapidly in recent years as a result of the availability of new, more efficient gene editing technologies. Gene drives can favorably bias the inheritance of a linked disease-refractory gene, which could possibly be exploited (i) to generate a vector population incapable of transmitting disease or (ii) to disrupt an essential gene for viability or fertility, which could eventually eliminate a population. Importantly, gene drives vary in characteristics such as their transmission efficiency, confinability and reversibility, and their potential to develop resistance to the drive mechanism. Here, we discuss recent advancements in the gene drive field, and contrast the benefits and limitations of a variety of technologies, as well as approaches to overcome these limitations. We also discuss the current state of each gene drive technology and the technical considerations that need to be addressed on the pathway to field implementation. While there are still many obstacles to overcome, recent progress has brought us closer than ever before to genetic-based vector modification as a tool to support vector-borne disease elimination efforts worldwide.
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Affiliation(s)
- Robyn R Raban
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - John M Marshall
- Innovative Genomics Institute, Berkeley, CA 94720, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, USA
| | - Omar S Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
- Division of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
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Li M, Yang T, Kandul NP, Bui M, Gamez S, Raban R, Bennett J, Sánchez C HM, Lanzaro GC, Schmidt H, Lee Y, Marshall JM, Akbari OS. Development of a confinable gene drive system in the human disease vector Aedes aegypti. eLife 2020; 9:e51701. [PMID: 31960794 PMCID: PMC6974361 DOI: 10.7554/elife.51701] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022] Open
Abstract
Aedes aegypti is the principal mosquito vector for many arboviruses that increasingly infect millions of people every year. With an escalating burden of infections and the relative failure of traditional control methods, the development of innovative control measures has become of paramount importance. The use of gene drives has sparked significant enthusiasm for genetic control of mosquitoes; however, no such system has been developed in Ae. aegypti. To fill this void, here we develop several CRISPR-based split gene drives for use in this vector. With cleavage rates up to 100% and transmission rates as high as 94%, mathematical models predict that these systems could spread anti-pathogen effector genes into wild populations in a safe, confinable and reversible manner appropriate for field trials and effective for controlling disease. These findings could expedite the development of effector-linked gene drives that could safely control wild populations of Ae. aegypti to combat local pathogen transmission.
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Affiliation(s)
- Ming Li
- Section of Cell and Developmental BiologyUniversity of California, San DiegoSan DiegoUnited States
| | - Ting Yang
- Section of Cell and Developmental BiologyUniversity of California, San DiegoSan DiegoUnited States
| | - Nikolay P Kandul
- Section of Cell and Developmental BiologyUniversity of California, San DiegoSan DiegoUnited States
| | - Michelle Bui
- Section of Cell and Developmental BiologyUniversity of California, San DiegoSan DiegoUnited States
| | - Stephanie Gamez
- Section of Cell and Developmental BiologyUniversity of California, San DiegoSan DiegoUnited States
| | - Robyn Raban
- Section of Cell and Developmental BiologyUniversity of California, San DiegoSan DiegoUnited States
| | - Jared Bennett
- Department of BiophysicsUniversity of California, BerkeleyBerkeleyUnited States
| | - Héctor M Sánchez C
- Division of Epidemiology and Biostatistics, School of Public HealthUniversity of California, BerkeleyBerkeleyUnited States
| | - Gregory C Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, School of Veterinary MedicineUniversity of California, DavisDavisUnited States
| | - Hanno Schmidt
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, School of Veterinary MedicineUniversity of California, DavisDavisUnited States
| | - Yoosook Lee
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, School of Veterinary MedicineUniversity of California, DavisDavisUnited States
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public HealthUniversity of California, BerkeleyBerkeleyUnited States
- Innovative Genomics InstituteBerkeleyUnited States
| | - Omar S Akbari
- Section of Cell and Developmental BiologyUniversity of California, San DiegoSan DiegoUnited States
- Tata Institute for Genetics and SocietyUniversity of California, San DiegoLa JollaUnited States
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Buchman A, Gamez S, Li M, Antoshechkin I, Li HH, Wang HW, Chen CH, Klein MJ, Duchemin JB, Crowe JE, Paradkar PN, Akbari OS. Broad dengue neutralization in mosquitoes expressing an engineered antibody. PLoS Pathog 2020; 16:e1008103. [PMID: 31945137 PMCID: PMC6964813 DOI: 10.1371/journal.ppat.1008103] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022] Open
Abstract
With dengue virus (DENV) becoming endemic in tropical and subtropical regions worldwide, there is a pressing global demand for effective strategies to control the mosquitoes that spread this disease. Recent advances in genetic engineering technologies have made it possible to create mosquitoes with reduced vector competence, limiting their ability to acquire and transmit pathogens. Here we describe the development of Aedes aegypti mosquitoes synthetically engineered to impede vector competence to DENV. These mosquitoes express a gene encoding an engineered single-chain variable fragment derived from a broadly neutralizing DENV human monoclonal antibody and have significantly reduced viral infection, dissemination, and transmission rates for all four major antigenically distinct DENV serotypes. Importantly, this is the first engineered approach that targets all DENV serotypes, which is crucial for effective disease suppression. These results provide a compelling route for developing effective genetic-based DENV control strategies, which could be extended to curtail other arboviruses.
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Affiliation(s)
- Anna Buchman
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Stephanie Gamez
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Ming Li
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Hsing-Han Li
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Hsin-Wei Wang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Chun-Hong Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Melissa J. Klein
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - Jean-Bernard Duchemin
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Departments of Pediatrics, Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Prasad N. Paradkar
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - Omar S. Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, United States of America
- Tata Institute for Genetics and Society-UCSD, La Jolla, California, United States of America
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