1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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. bioRxiv 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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Davydova S, Liu J, Kandul NP, Braswell WE, Akbari OS, Meccariello A. Next-generation genetic sexing strain establishment in the agricultural pest Ceratitis capitata. Sci Rep 2023; 13:19866. [PMID: 37964160 PMCID: PMC10646097 DOI: 10.1038/s41598-023-47276-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/11/2023] [Indexed: 11/16/2023] Open
Abstract
Tephritid fruit fly pests pose an increasing threat to the agricultural industry due to their global dispersion and a highly invasive nature. Here we showcase the feasibility of an early-detection SEPARATOR sex sorting approach through using the non-model Tephritid pest, Ceratitis capitata. This system relies on female-only fluorescent marker expression, accomplished through the use of a sex-specific intron of the highly-conserved transformer gene from C. capitata and Anastrepha ludens. The herein characterized strains have 100% desired phenotype outcomes, allowing accurate male-female separation during early development. Overall, we describe an antibiotic and temperature-independent sex-sorting system in C. capitata, which, moving forward, may be implemented in other non-model Tephritid pest species. This strategy can facilitate the establishment of genetic sexing systems with endogenous elements exclusively, which, on a wider scale, can improve pest population control strategies like sterile insect technique.
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Affiliation(s)
- Serafima Davydova
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Junru Liu
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Nikolay P Kandul
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - W Evan Braswell
- USDA APHIS PPQ Science and Technology Insect Management and Molecular Diagnostic Laboratory, 22675 North Moorefield Road, Edinburg, TX, 78541, USA
| | - Omar S Akbari
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Angela Meccariello
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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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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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Li M, Yang T, Bui M, Gamez S, Wise T, Kandul NP, Liu J, Alcantara L, Lee H, Edula JR, Raban R, Zhan Y, Wang Y, DeBeaubien N, Chen J, Sánchez C HM, Bennett JB, Antoshechkin I, Montell C, Marshall JM, Akbari OS. Suppressing mosquito populations with precision guided sterile males. Nat Commun 2021; 12:5374. [PMID: 34508072 PMCID: PMC8433431 DOI: 10.1038/s41467-021-25421-w] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/23/2021] [Indexed: 01/06/2023] Open
Abstract
The mosquito Aedes aegypti is the principal vector for arboviruses including dengue/yellow fever, chikungunya, and Zika virus, infecting hundreds of millions of people annually. Unfortunately, traditional control methodologies are insufficient, so innovative control methods are needed. To complement existing measures, here we develop a molecular genetic control system termed precision-guided sterile insect technique (pgSIT) in Aedes aegypti. PgSIT uses a simple CRISPR-based approach to generate flightless females and sterile males that are deployable at any life stage. Supported by mathematical models, we empirically demonstrate that released pgSIT males can compete, suppress, and even eliminate mosquito populations. This platform technology could be used in the field, and adapted to many vectors, for controlling wild populations to curtail disease in a safe, confinable, and reversible manner. A. aegypti is the principal vector for arboviruses that impact on human health and wellbeing. Here the authors use precision guided sterile insect technique—pgSIT—to suppress or eliminate mosquito populations in multigeneration cage experiments.
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Affiliation(s)
- Ming Li
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Ting Yang
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Michelle Bui
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Stephanie Gamez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Tyler Wise
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Nikolay P Kandul
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Lenissa Alcantara
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Haena Lee
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Jyotheeswara R Edula
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA.,Tata Institute for Genetics and Society, La Jolla, CA, USA.,Tata Institute for Genetics and Society (TIGS), TIGS Center at inStem, GKVK Campus, Bangalore, Karnataka, India
| | - Robyn Raban
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Yinpeng Zhan
- Department of Molecular, Cellular, and Developmental Biology and the Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Yijin Wang
- Department of Molecular, Cellular, and Developmental Biology and the Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Nick DeBeaubien
- Department of Molecular, Cellular, and Developmental Biology and the Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Jieyan Chen
- Department of Molecular, Cellular, and Developmental Biology and the Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Héctor M Sánchez C
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | - Jared B Bennett
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, USA.,Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering (BBE), California Institute of Technology, Pasadena, CA, USA
| | - Craig Montell
- Department of Molecular, Cellular, and Developmental Biology and the Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - John M Marshall
- Divisions of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA. .,Tata Institute for Genetics and Society, La Jolla, CA, USA.
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9
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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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10
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Abstract
Here, we describe a drug-inducible genetic system for insect sex-separation that demonstrates proof-of-principle for positive sex selection in D. melanogaster. The system exploits the toxicity of commonly used broad-spectrum antibiotics geneticin and puromycin to kill the non-rescued sex. Sex-specific rescue is achieved by inserting sex-specific introns into the coding sequences of antibiotic-resistance genes. When raised on geneticin-supplemented food, the sex-sorter line establishes 100% positive selection for female progeny, while the food supplemented with puromycin positively selects 100% male progeny. Since the described system exploits conserved sex-specific splicing mechanisms and reagents, it has the potential to be adaptable to other insect species of medical and agricultural importance.
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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, CA, 92092, USA
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92092, USA
| | - Alexander D Hsu
- Division of Biology and Biological Engineering, MC 156-29, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Bruce A Hay
- Division of Biology and Biological Engineering, MC 156-29, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92092, USA.
- Division of Biology and Biological Engineering, MC 156-29, California Institute of Technology, Pasadena, CA, 91125, USA.
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA, USA.
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11
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Kandul NP, Liu J, Buchman A, Gantz VM, Bier E, Akbari OS. Assessment of a Split Homing Based Gene Drive for Efficient Knockout of Multiple Genes. G3 (Bethesda) 2020; 10:827-837. [PMID: 31882406 PMCID: PMC7003086 DOI: 10.1534/g3.119.400985] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/19/2019] [Indexed: 01/08/2023]
Abstract
Homing based gene drives (HGD) possess the potential to spread linked cargo genes into natural populations and are poised to revolutionize population control of animals. Given that host encoded genes have been identified that are important for pathogen transmission, targeting these genes using guide RNAs as cargo genes linked to drives may provide a robust method to prevent disease transmission. However, effectiveness of the inclusion of additional guide RNAs that target separate genes has not been thoroughly explored. To test this approach, we generated a split-HGD in Drosophila melanogaster that encoded a drive linked effector consisting of a second gRNA engineered to target a separate host-encoded gene, which we term a gRNA-mediated effector (GME). This design enabled us to assess homing and knockout efficiencies of two target genes simultaneously, and also explore the timing and tissue specificity of Cas9 expression on cleavage/homing rates. We demonstrate that inclusion of a GME can result in high efficiency of disruption of both genes during super-Mendelian propagation of split-HGD. Furthermore, both genes were knocked out one generation earlier than expected indicating the robust somatic expression of Cas9 driven by Drosophila germline-limited promoters. We also assess the efficiency of 'shadow drive' generated by maternally deposited Cas9 protein and accumulation of drive-induced resistance alleles along multiple generations, and discuss design principles of HGD that could mitigate the accumulation of resistance alleles while incorporating a GME.
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Affiliation(s)
| | - Junru Liu
- Section of Cell and Developmental Biology and
| | | | | | - Ethan Bier
- Section of Cell and Developmental Biology and
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093
| | - Omar S Akbari
- Section of Cell and Developmental Biology and
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093
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12
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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: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Marshall JM, Raban RR, Kandul NP, Edula JR, León TM, Akbari OS. Winning the Tug-of-War Between Effector Gene Design and Pathogen Evolution in Vector Population Replacement Strategies. Front Genet 2019; 10:1072. [PMID: 31737050 PMCID: PMC6831721 DOI: 10.3389/fgene.2019.01072] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/07/2019] [Indexed: 12/19/2022] Open
Abstract
While efforts to control malaria with available tools have stagnated, and arbovirus outbreaks persist around the globe, the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-based gene editing has provided exciting new opportunities for genetics-based strategies to control these diseases. In one such strategy, called "population replacement", mosquitoes, and other disease vectors are engineered with effector genes that render them unable to transmit pathogens. These effector genes can be linked to "gene drive" systems that can bias inheritance in their favor, providing novel opportunities to replace disease-susceptible vector populations with disease-refractory ones over the course of several generations. While promising for the control of vector-borne diseases on a wide scale, this sets up an evolutionary tug-of-war between the introduced effector genes and the pathogen. Here, we review the disease-refractory genes designed to date to target Plasmodium falciparum malaria transmitted by Anopheles gambiae, and arboviruses transmitted by Aedes aegypti, including dengue serotypes 2 and 3, chikungunya, and Zika viruses. We discuss resistance concerns for these effector genes, and genetic approaches to prevent parasite and viral escape variants. One general approach is to increase the evolutionary hurdle required for the pathogen to evolve resistance by attacking it at multiple sites in its genome and/or multiple stages of development. Another is to reduce the size of the pathogen population by other means, such as with vector control and antimalarial drugs. We discuss lessons learned from the evolution of resistance to antimalarial and antiviral drugs and implications for the management of resistance after its emergence. Finally, we discuss the target product profile for population replacement strategies for vector-borne disease control. This differs between early phase field trials and wide-scale disease control. In the latter case, the demands on effector gene efficacy are great; however, with new possibilities ushered in by CRISPR-based gene editing, and when combined with surveillance, monitoring, and rapid management of pathogen resistance, the odds are increasingly favoring effector genes in the upcoming evolutionary tug-of-war.
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Affiliation(s)
- John M. Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, United States
- Innovative Genomics Institute, Berkeley, CA, United States
| | - Robyn R. Raban
- Section of Cell and Developmental Biology, University of California, San Diego, CA, United States
| | - Nikolay P. Kandul
- Section of Cell and Developmental Biology, University of California, San Diego, CA, United States
| | - Jyotheeswara R. Edula
- Section of Cell and Developmental Biology, University of California, San Diego, CA, United States
| | - Tomás M. León
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, United States
| | - Omar S. Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, CA, United States
- Tata Institute for Genetics and Society, University of California, San Diego, CA, United States
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14
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Kandul NP, Liu J, Sanchez C HM, Wu SL, Marshall JM, Akbari OS. Reply to 'Concerns about the feasibility of using "precision guided sterile males" to control insects'. Nat Commun 2019; 10:3955. [PMID: 31477702 PMCID: PMC6718384 DOI: 10.1038/s41467-019-11617-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/10/2019] [Indexed: 11/09/2022] Open
Affiliation(s)
- Nikolay P Kandul
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Hector M Sanchez C
- Division of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA, United States of America
| | - Sean L Wu
- Division of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA, United States of America
| | - John M Marshall
- Division of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA, United States of America
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, United States of America.
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, United States of America.
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15
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Kandul NP, Liu J, Sanchez C HM, Wu SL, Marshall JM, Akbari OS. Transforming insect population control with precision guided sterile males with demonstration in flies. Nat Commun 2019; 10:84. [PMID: 30622266 PMCID: PMC6325135 DOI: 10.1038/s41467-018-07964-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/05/2018] [Indexed: 01/03/2023] Open
Abstract
The sterile insect technique (SIT) is an environmentally safe and proven technology to suppress wild populations. To further advance its utility, a novel CRISPR-based technology termed precision guided SIT (pgSIT) is described. PgSIT mechanistically relies on a dominant genetic technology that enables simultaneous sexing and sterilization, facilitating the release of eggs into the environment ensuring only sterile adult males emerge. Importantly, for field applications, the release of eggs will eliminate burdens of manually sexing and sterilizing males, thereby reducing overall effort and increasing scalability. Here, to demonstrate efficacy, we systematically engineer multiple pgSIT systems in Drosophila which consistently give rise to 100% sterile males. Importantly, we demonstrate that pgSIT-generated sterile males are fit and competitive. Using mathematical models, we predict pgSIT will induce substantially greater population suppression than can be achieved by currently-available self-limiting suppression technologies. Taken together, pgSIT offers to potentially transform our ability to control insect agricultural pests and disease vectors.
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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, CA 92093, California, USA
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, California, USA
| | - Hector M Sanchez C
- Division of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA 94720, California, USA
| | - Sean L Wu
- Division of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA 94720, California, USA
| | - John M Marshall
- Division of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA 94720, California, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, California, USA.
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, California, USA.
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16
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Kandul NP, Zhang T, Hay BA, Guo M. Selective removal of deletion-bearing mitochondrial DNA in heteroplasmic Drosophila. Nat Commun 2016; 7:13100. [PMID: 27841259 PMCID: PMC5114534 DOI: 10.1038/ncomms13100] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/01/2016] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial DNA (mtDNA) often exists in a state of heteroplasmy, in which mutant mtDNA co-exists in cells with wild-type mtDNA. High frequencies of pathogenic mtDNA result in maternally inherited diseases; maternally and somatically acquired mutations also accumulate over time and contribute to diseases of ageing. Reducing heteroplasmy is therefore a therapeutic goal and in vivo models in post-mitotic tissues are needed to facilitate these studies. Here we describe a transgene-based model of a heteroplasmic lethal mtDNA deletion (mtDNAΔ) in adult Drosophila muscle. Stimulation of autophagy, activation of the PINK1/parkin pathway or decreased levels of mitofusin result in a selective decrease in mtDNAΔ. Decreased levels of mitofusin and increased levels of ATPIF1, an inhibitor of ATP synthase reversal-dependent mitochondrial repolarization, result in a further decrease in mtDNAΔ levels. These results show that an adult post-mitotic tissue can be cleansed of a deleterious genome, suggesting that therapeutic removal of mutant mtDNA can be achieved.
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Affiliation(s)
- Nikolay P. Kandul
- Division of Biology and Biological Engineering, California Institute of Technology, Mail Code 156-29, 1200 E. California blvd., Pasadena, California 91125, USA
| | - Ting Zhang
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Molecular and Medical Pharmacology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Bruce A. Hay
- Division of Biology and Biological Engineering, California Institute of Technology, Mail Code 156-29, 1200 E. California blvd., Pasadena, California 91125, USA
| | - Ming Guo
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Molecular and Medical Pharmacology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
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