1
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Li Z, You L, Hermann A, Bier E. Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier. Nat Commun 2024; 15:2629. [PMID: 38521791 PMCID: PMC10960810 DOI: 10.1038/s41467-024-46479-2] [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: 11/13/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024] Open
Abstract
DNA double-strand breaks (DSBs) are repaired by a hierarchically regulated network of pathways. Factors influencing the choice of particular repair pathways, however remain poorly characterized. Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects. The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components. We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms and a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion. These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
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Affiliation(s)
- 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
| | - Lang You
- 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
| | - Anita Hermann
- 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
| | - 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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2
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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] [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: 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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3
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Green EI, Jaouen E, Klug D, Proveti Olmo R, Gautier A, Blandin S, Marois E. A population modification gene drive targeting both Saglin and Lipophorin impairs Plasmodium transmission in Anopheles mosquitoes. eLife 2023; 12:e93142. [PMID: 38051195 PMCID: PMC10786457 DOI: 10.7554/elife.93142] [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: 10/02/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023] Open
Abstract
Lipophorin is an essential, highly expressed lipid transport protein that is secreted and circulates in insect hemolymph. We hijacked the Anopheles coluzzii Lipophorin gene to make it co-express a single-chain version of antibody 2A10, which binds sporozoites of the malaria parasite Plasmodium falciparum. The resulting transgenic mosquitoes show a markedly decreased ability to transmit Plasmodium berghei expressing the P. falciparum circumsporozoite protein to mice. To force the spread of this antimalarial transgene in a mosquito population, we designed and tested several CRISPR/Cas9-based gene drives. One of these is installed in, and disrupts, the pro-parasitic gene Saglin and also cleaves wild-type Lipophorin, causing the anti-malarial modified Lipophorin version to replace the wild type and hitch-hike together with the Saglin drive. Although generating drive-resistant alleles and showing instability in its gRNA-encoding multiplex array, the Saglin-based gene drive reached high levels in caged mosquito populations and efficiently promoted the simultaneous spread of the antimalarial Lipophorin::Sc2A10 allele. This combination is expected to decrease parasite transmission via two different mechanisms. This work contributes to the design of novel strategies to spread antimalarial transgenes in mosquitoes, and illustrates some expected and unexpected outcomes encountered when establishing a population modification gene drive.
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Affiliation(s)
- Emily I Green
- Inserm U1257, CNRS UPR9022, University of StrasbourgStrasbourgFrance
| | - Etienne Jaouen
- Inserm U1257, CNRS UPR9022, University of StrasbourgStrasbourgFrance
| | - Dennis Klug
- Inserm U1257, CNRS UPR9022, University of StrasbourgStrasbourgFrance
| | | | - Amandine Gautier
- Inserm U1257, CNRS UPR9022, University of StrasbourgStrasbourgFrance
| | - Stéphanie Blandin
- Inserm U1257, CNRS UPR9022, University of StrasbourgStrasbourgFrance
| | - Eric Marois
- Inserm U1257, CNRS UPR9022, University of StrasbourgStrasbourgFrance
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4
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Kumam Y, Trick HN, Vara Prasad P, Jugulam M. Transformative Approaches for Sustainable Weed Management: The Power of Gene Drive and CRISPR-Cas9. Genes (Basel) 2023; 14:2176. [PMID: 38136999 PMCID: PMC10742955 DOI: 10.3390/genes14122176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/25/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Weeds can negatively impact crop yields and the ecosystem's health. While many weed management strategies have been developed and deployed, there is a greater need for the development of sustainable methods for employing integrated weed management. Gene drive systems can be used as one of the approaches to suppress the aggressive growth and reproductive behavior of weeds, although their efficacy is yet to be tested. Their popularity in insect pest management has increased, however, with the advent of CRISPR-Cas9 technology, which provides specificity and precision in editing the target gene. This review focuses on the different types of gene drive systems, including the use of CRISPR-Cas9-based systems and their success stories in pest management, while also exploring their possible applications in weed species. Factors that govern the success of a gene drive system in weeds, including the mode of reproduction, the availability of weed genome databases, and well-established transformation protocols are also discussed. Importantly, the risks associated with the release of weed populations with gene drive-bearing alleles into wild populations are also examined, along with the importance of addressing ecological consequences and ethical concerns.
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Affiliation(s)
- Yaiphabi Kumam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA;
| | - P.V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (Y.K.); (P.V.V.P.)
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5
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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] [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: 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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6
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Sanz Juste S, Okamoto EM, Nguyen C, Feng X, López Del Amo V. Next-generation CRISPR gene-drive systems using Cas12a nuclease. Nat Commun 2023; 14:6388. [PMID: 37821497 PMCID: PMC10567717 DOI: 10.1038/s41467-023-42183-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023] Open
Abstract
One method for reducing the impact of vector-borne diseases is through the use of CRISPR-based gene drives, which manipulate insect populations due to their ability to rapidly propagate desired genetic traits into a target population. However, all current gene drives employ a Cas9 nuclease that is constitutively active, impeding our control over their propagation abilities and limiting the generation of alternative gene drive arrangements. Yet, other nucleases such as the temperature sensitive Cas12a have not been explored for gene drive designs in insects. To address this, we herein present a proof-of-concept gene-drive system driven by Cas12a that can be regulated via temperature modulation. Furthermore, we combined Cas9 and Cas12a to build double gene drives capable of simultaneously spreading two independent engineered alleles. The development of Cas12a-mediated gene drives provides an innovative option for designing next-generation vector control strategies to combat disease vectors and agricultural pests.
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Affiliation(s)
- Sara Sanz Juste
- Department of Epigenetics & Molecular Carcinogenesis at MD Anderson, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Emily M Okamoto
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Christina Nguyen
- University of Texas Health Science Center, School of Public Health, Department of Epidemiology, Human Genetics, and Environmental Sciences, Center for Infectious Diseases, Houston, TX, 77030, USA
| | - Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA.
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518106, China.
| | - Víctor López Del Amo
- University of Texas Health Science Center, School of Public Health, Department of Epidemiology, Human Genetics, and Environmental Sciences, Center for Infectious Diseases, Houston, TX, 77030, USA.
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7
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Vidal-Albalat A, Kindahl T, Rajeshwari R, Lindgren C, Forsgren N, Kitur S, Tengo LS, Ekström F, Kamau L, Linusson A. Structure-Activity Relationships Reveal Beneficial Selectivity Profiles of Inhibitors Targeting Acetylcholinesterase of Disease-Transmitting Mosquitoes. J Med Chem 2023; 66:6333-6353. [PMID: 37094110 PMCID: PMC10184127 DOI: 10.1021/acs.jmedchem.3c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Insecticide resistance jeopardizes the prevention of infectious diseases such as malaria and dengue fever by vector control of disease-transmitting mosquitoes. Effective new insecticidal compounds with minimal adverse effects on humans and the environment are therefore urgently needed. Here, we explore noncovalent inhibitors of the well-validated insecticidal target acetylcholinesterase (AChE) based on a 4-thiazolidinone scaffold. The 4-thiazolidinones inhibit AChE1 from the mosquitoes Anopheles gambiae and Aedes aegypti at low micromolar concentrations. Their selectivity depends primarily on the substitution pattern of the phenyl ring; halogen substituents have complex effects. The compounds also feature a pendant aliphatic amine that was important for activity; little variation of this group is tolerated. Molecular docking studies suggested that the tight selectivity profiles of these compounds are due to competition between two binding sites. Three 4-thiazolidinones tested for in vivo insecticidal activity had similar effects on disease-transmitting mosquitoes despite a 10-fold difference in their in vitro activity.
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Affiliation(s)
| | - Tomas Kindahl
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
| | | | | | - Nina Forsgren
- CBRN Defence and Security, Swedish Defence Research Agency, SE-90621 Umeå, Sweden
| | - Stanley Kitur
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, PO Box 54840-00200 Nairobi, Kenya
| | - Laura Sela Tengo
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, PO Box 54840-00200 Nairobi, Kenya
| | - Fredrik Ekström
- CBRN Defence and Security, Swedish Defence Research Agency, SE-90621 Umeå, Sweden
| | - Luna Kamau
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, PO Box 54840-00200 Nairobi, Kenya
| | - Anna Linusson
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
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8
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Frieß JL, Lalyer CR, Giese B, Simon S, Otto M. Review of gene drive modelling and implications for risk assessment of gene drive organisms. Ecol Modell 2023. [DOI: 10.1016/j.ecolmodel.2023.110285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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9
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Zhu Y, Champer J. Simulations Reveal High Efficiency and Confinement of a Population Suppression CRISPR Toxin-Antidote Gene Drive. ACS Synth Biol 2023; 12:809-819. [PMID: 36825354 DOI: 10.1021/acssynbio.2c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Though engineered gene drives hold great promise for spreading through and suppressing populations of disease vectors or invasive species, complications such as resistance alleles and spatial population structure can prevent their success. Additionally, most forms of suppression drives, such as homing drives or driving Y chromosomes, will generally spread uncontrollably between populations with even small levels of migration. The previously proposed CRISPR-based toxin-antidote system called toxin-antidote dominant embryo (TADE) suppression drive could potentially address the issues of confinement and resistance. However, it is a relatively weak form of drive compared to homing drives, which might make it particularly vulnerable to spatial population structure. In this study, we investigate TADE suppression drive using individual-based simulations in a continuous spatial landscape. We find that the drive is actually more confined than in simple models without space, even in its most efficient form with low cleavage rate in embryos from maternally deposited Cas9. Furthermore, the drive performed well in continuous space scenarios if the initial release requirements were met, suppressing the population in a timely manner without being severely affected by chasing, a phenomenon in which wild-type individuals avoid the drive by recolonizing empty areas. At higher embryo cut rates, the drive loses its ability to spread, but a single, widespread release can often still induce rapid population collapse. Thus, if TADE suppression gene drives can be successfully constructed, they may play an important role in control of disease vectors and invasive species when stringent confinement to target populations is desired.
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Affiliation(s)
- Yutong Zhu
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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10
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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: 11] [Impact Index Per Article: 11.0] [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: 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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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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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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13
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Verkuijl SAN, Anderson MAE, Alphey L, Bonsall MB. Daisy-chain gene drives: The role of low cut-rate, resistance mutations, and maternal deposition. PLoS Genet 2022; 18:e1010370. [PMID: 36121880 PMCID: PMC9521892 DOI: 10.1371/journal.pgen.1010370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 09/29/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022] Open
Abstract
The introgression of genetic traits through gene drive may serve as a powerful and widely applicable method of biological control. However, for many applications, a self-perpetuating gene drive that can spread beyond the specific target population may be undesirable and preclude use. Daisy-chain gene drives have been proposed as a means of tuning the invasiveness of a gene drive, allowing it to spread efficiently into the target population, but be self-limiting beyond that. Daisy-chain gene drives are made up of multiple independent drive elements, where each element, except one, biases the inheritance of another, forming a chain. Under ideal inheritance biasing conditions, the released drive elements remain linked in the same configuration, generating copies of most of their elements except for the last remaining link in the chain. Through mathematical modelling of populations connected by migration, we have evaluated the effect of resistance alleles, different fitness costs, reduction in the cut-rate, and maternal deposition on two alternative daisy-chain gene drive designs. We find that the self-limiting nature of daisy-chain gene drives makes their spread highly dependent on the efficiency and fidelity of the inheritance biasing mechanism. In particular, reductions in the cut-rate and the formation of non-lethal resistance alleles can cause drive elements to lose their linked configuration. This severely reduces the invasiveness of the drives and allows for phantom cutting, where an upstream drive element cuts a downstream target locus despite the corresponding drive element being absent, creating and biasing the inheritance of additional resistance alleles. This phantom cutting can be mitigated by an alternative indirect daisy-chain design. We further find that while dominant fitness costs and maternal deposition reduce daisy-chain invasiveness, if overcome with an increased release frequency, they can reduce the spread of the drive into a neighbouring population.
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Affiliation(s)
- Sebald A. N. Verkuijl
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
| | | | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
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14
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Roy S, Juste SS, Sneider M, Auradkar A, Klanseck C, Li Z, Julio AHF, Lopez del Amo V, Bier E, Guichard A. Cas9/Nickase-induced allelic conversion by homologous chromosome-templated repair in Drosophila somatic cells. Sci Adv 2022; 8:eabo0721. [PMID: 35776792 PMCID: PMC10883370 DOI: 10.1126/sciadv.abo0721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Repair of double-strand breaks (DSBs) in somatic cells is primarily accomplished by error-prone nonhomologous end joining and less frequently by precise homology-directed repair preferentially using the sister chromatid as a template. Here, a Drosophila system performs efficient somatic repair of both DSBs and single-strand breaks (SSBs) using intact sequences from the homologous chromosome in a process we refer to as homologous chromosome-templated repair (HTR). Unexpectedly, HTR-mediated allelic conversion at the white locus was more efficient (40 to 65%) in response to SSBs induced by Cas9-derived nickases D10A or H840A than to DSBs induced by fully active Cas9 (20 to 30%). Repair phenotypes elicited by Nickase versus Cas9 differ in both developmental timing (late versus early stages, respectively) and the production of undesired mutagenic events (rare versus frequent). Nickase-mediated HTR represents an efficient and unanticipated mechanism for allelic correction, with far-reaching potential applications in the field of gene editing.
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Affiliation(s)
- Sitara Roy
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Sara Sanz Juste
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Marketta Sneider
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Carissa Klanseck
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Zhiqian Li
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Alison Henrique Ferreira Julio
- Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Ilha do Fundão, Rio de Janeiro, 21941-902 RJ, Brazil
| | - Victor Lopez del Amo
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA 92093-0335, USA
| | - Annabel Guichard
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0335, USA
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15
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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) 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] [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: 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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16
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Del Amo VL, Juste SS, Gantz VM. A nickase Cas9 gene-drive system promotes super-Mendelian inheritance in Drosophila. Cell Rep 2022; 39:110843. [PMID: 35613590 DOI: 10.1016/j.celrep.2022.110843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/07/2022] [Accepted: 04/28/2022] [Indexed: 01/01/2023] Open
Abstract
CRISPR-based gene-drives have been proposed for managing insect populations, including disease-transmitting mosquitoes, due to their ability to bias their inheritance toward super-Mendelian rates (>50%). Current technologies use a Cas9 that introduces DNA double-strand breaks into the opposing wild-type allele to replace it with a copy of the gene-drive allele via DNA homology-directed repair. However, the use of different Cas9 versions is unexplored, and alternative approaches could increase the available toolkit for gene-drive designs. Here, we report a gene-drive that relies on Cas9 nickases that generate staggered paired nicks in DNA to propagate the engineered gene-drive cassette. We show that generating 5′ overhangs in the system yields efficient allelic conversion. The nickase gene-drive arrangement produces large, stereotyped deletions that are advantageous to eliminate viable animals carrying small mutations when targeting essential genes. Our nickase approach should expand the repertoire for gene-drive arrangements aimed at applications in mosquitoes and beyond. Gene-drives using wild-type Cas9 offer solutions to fight vector-borne diseases, yet alternative strategies are needed to increase the available toolkit. López Del Amo et al. describe a nickase-based gene-drive system that promotes super-Mendelian inheritance of an engineered cassette in the Drosophila germ line, providing alternative designs for CRISPR-based gene-drive.
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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] [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: 08/27/2021] [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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Bishop AL, López Del Amo V, Okamoto EM, Bodai Z, Komor AC, Gantz VM. Double-tap gene drive uses iterative genome targeting to help overcome resistance alleles. Nat Commun 2022; 13:2595. [PMID: 35534475 PMCID: PMC9085836 DOI: 10.1038/s41467-022-29868-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 09/21/2021] [Accepted: 02/28/2022] [Indexed: 01/07/2023] Open
Abstract
Homing CRISPR gene drives could aid in curbing the spread of vector-borne diseases and controlling crop pest and invasive species populations due to an inheritance rate that surpasses Mendelian laws. However, this technology suffers from resistance alleles formed when the drive-induced DNA break is repaired by error-prone pathways, which creates mutations that disrupt the gRNA recognition sequence and prevent further gene-drive propagation. Here, we attempt to counteract this by encoding additional gRNAs that target the most commonly generated resistance alleles into the gene drive, allowing a second opportunity at gene-drive conversion. Our presented "double-tap" strategy improved drive efficiency by recycling resistance alleles. The double-tap drive also efficiently spreads in caged populations, outperforming the control drive. Overall, this double-tap strategy can be readily implemented in any CRISPR-based gene drive to improve performance, and similar approaches could benefit other systems suffering from low HDR frequencies, such as mammalian cells or mouse germline transformations.
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Affiliation(s)
- Alena L Bishop
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Víctor López Del Amo
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Emily M Okamoto
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Zsolt Bodai
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Valentino M Gantz
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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19
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Chae K, Dawson C, Valentin C, Contreras B, Zapletal J, Myles KM, Adelman ZN. Engineering a self-eliminating transgene in the yellow fever mosquito, Aedes aegypti. PNAS Nexus 2022; 1:pgac037. [PMID: 36713320 PMCID: PMC9802104 DOI: 10.1093/pnasnexus/pgac037] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023]
Abstract
Promising genetics-based approaches are being developed to reduce or prevent the transmission of mosquito-vectored diseases. Less clear is how such transgenes can be removed from the environment, a concern that is particularly relevant for highly invasive gene drive transgenes. Here, we lay the groundwork for a transgene removal system based on single-strand annealing (SSA), a eukaryotic DNA repair mechanism. An SSA-based rescuer strain (kmoRG ) was engineered to have direct repeat sequences (DRs) in the Aedes aegypti kynurenine 3-monooxygenase (kmo) gene flanking the intervening transgenic cargo genes, DsRED and EGFP. Targeted induction of DNA double-strand breaks (DSBs) in the DsRED transgene successfully triggered complete elimination of the entire cargo from the kmoRG strain, restoring the wild-type kmo gene, and thereby, normal eye pigmentation. Our work establishes the framework for strategies to remove transgene sequences during the evaluation and testing of modified strains for genetics-based mosquito control.
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Affiliation(s)
- Keun Chae
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Chanell Dawson
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Collin Valentin
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Bryan Contreras
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Josef Zapletal
- Department of Industrial and Systems Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Kevin M Myles
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Xu X, Harvey-Samuel T, Siddiqui HA, Ang JXD, Anderson ME, Reitmayer CM, Lovett E, Leftwich PT, You M, Alphey L. Toward a CRISPR-Cas9-based Gene Drive in the Diamondback Moth Plutella xylostella. CRISPR J 2022; 5:224-236. [PMID: 35285719 DOI: 10.1089/crispr.2021.0129] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Promising to provide powerful genetic control tools, gene drives have been constructed in multiple dipteran insects, yeast, and mice for the purposes of population elimination or modification. However, it remains unclear whether these techniques can be applied to lepidopterans. Here, we used endogenous regulatory elements to drive Cas9 and single guide RNA (sgRNA) expression in the diamondback moth (DBM), Plutella xylostella, and test the first split gene drive system in a lepidopteran. The DBM is an economically important global agriculture pest of cruciferous crops and has developed severe resistance to various insecticides, making it a prime candidate for such novel control strategy development. A very high level of somatic editing was observed in Cas9/sgRNA transheterozygotes, although no significant homing was revealed in the subsequent generation. Although heritable Cas9-medated germline cleavage as well as maternal and paternal Cas9 deposition were observed, rates were far lower than for somatic cleavage events, indicating robust somatic but limited germline activity of Cas9/sgRNA under the control of selected regulatory elements. Our results provide valuable experience, paving the way for future construction of gene drives or other Cas9-based genetic control strategies in DBM and other lepidopterans.
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Affiliation(s)
- Xuejiao Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, P.R. China.,School of Life Sciences, Peking University, Beijing, P.R. China
| | - Tim Harvey-Samuel
- Arthropod Genetics Group, The Pirbright Institute, Woking, Pirbright, United Kingdom
| | - Hamid Anees Siddiqui
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Joshua Xin De Ang
- Arthropod Genetics Group, The Pirbright Institute, Woking, Pirbright, United Kingdom
| | | | - Christine M Reitmayer
- Arthropod Genetics Group, The Pirbright Institute, Woking, Pirbright, United Kingdom
| | - Erica Lovett
- Arthropod Genetics Group, The Pirbright Institute, Woking, Pirbright, United Kingdom
| | - Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, P.R. China
| | - Luke Alphey
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, P.R. China.,Arthropod Genetics Group, The Pirbright Institute, Woking, Pirbright, United Kingdom
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22
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Ang JXD, Nevard K, Ireland R, Purusothaman DK, Verkuijl SAN, Shackleford L, Gonzalez E, Anderson MAE, Alphey L. Considerations for homology-based DNA repair in mosquitoes: Impact of sequence heterology and donor template source. PLoS Genet 2022; 18:e1010060. [PMID: 35180218 PMCID: PMC8893643 DOI: 10.1371/journal.pgen.1010060] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 03/03/2022] [Accepted: 01/28/2022] [Indexed: 12/23/2022] Open
Abstract
The increasing prevalence of insecticide resistance and the ongoing global burden of vector-borne diseases have encouraged new efforts in mosquito control. For Aedes aegypti, the most important arboviral vector, integration rates achieved in Cas9-based knock-ins so far have been rather low, highlighting the need to understand gene conversion patterns and other factors that influence homology-directed repair (HDR) events in this species. In this study, we report the effects of sequence mismatches or donor template forms on integration rates. We found that modest sequence differences between construct homology arms [DNA sequence in the donor template which resembles the region flanking the target cut] and genomic target comprising 1.2% nucleotide dissimilarity (heterology) significantly reduced integration rates. While most integrations (59–88%) from plasmid templates were the result of canonical [on target, perfect repair] HDR events, no canonical events were identified from other donor types (i.e. ssDNA, biotinylated ds/ssDNA). Sequencing of the transgene flanking region in 69 individuals with canonical integrations revealed 60% of conversion tracts to be unidirectional and extend up to 220 bp proximal to the break, though in three individuals bidirectional conversion of up to 725 bp was observed. The field of genetic control of mosquito vectors has progressed rapidly in recent years, especially in Cas9-based control systems, due to its robustness to elicit a species-specific and dispersive control of mosquito population. To generate a Cas9-based integration, Cas9 and sgRNA are used to cleave a chromosomal locus while a plasmid DNA donor, containing a genetic cargo flanked by sequences homologous to the chromosomal locus, is supplied as a repair template. This results in the cargo being copied into the genome through HDR. This form of integration, however, is currently one of the major bottlenecks for researchers as it involves a laborious process of microinjecting mosquito embryos and has rather low integration rates. In this study, we assessed the effects of homologous sequence mismatches and various donor template forms (i.e. plasmid, ssDNA, biotinylated ds/ssDNA) on HDR. We found that sequence mismatches and non-plasmid donors reduced the efficiency and integrity of integration, respectively. By analysing the direction and length of homologous sequence that was copied into the genome concurrently with the cargo, we inferred the mechanism responsible for the integrations observed in our study. These findings will be useful to guide future construct designs for optimal HDR rates in mosquitoes.
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Affiliation(s)
| | | | | | | | - Sebald A. N. Verkuijl
- The Pirbright Institute, Pirbright, Woking, United Kingdom
- Mathematical Ecology Research Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | | | | | - Luke Alphey
- The Pirbright Institute, Pirbright, Woking, United Kingdom
- * E-mail: (MAEA); (LA)
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23
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Kaduskar B, Kushwah RBS, Auradkar A, Guichard A, Li M, Bennett JB, Julio AHF, Marshall JM, Montell C, Bier E. Reversing insecticide resistance with allelic-drive in Drosophila melanogaster. Nat Commun 2022; 13:291. [PMID: 35022402 PMCID: PMC8755802 DOI: 10.1038/s41467-021-27654-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 05/14/2021] [Accepted: 12/02/2021] [Indexed: 12/27/2022] Open
Abstract
A recurring target-site mutation identified in various pests and disease vectors alters the voltage gated sodium channel (vgsc) gene (often referred to as knockdown resistance or kdr) to confer resistance to commonly used insecticides, pyrethroids and DDT. The ubiquity of kdr mutations poses a major global threat to the continued use of insecticides as a means for vector control. In this study, we generate common kdr mutations in isogenic laboratory Drosophila strains using CRISPR/Cas9 editing. We identify differential sensitivities to permethrin and DDT versus deltamethrin among these mutants as well as contrasting physiological consequences of two different kdr mutations. Importantly, we apply a CRISPR-based allelic-drive to replace a resistant kdr mutation with a susceptible wild-type counterpart in population cages. This successful proof-of-principle opens-up numerous possibilities including targeted reversion of insecticide-resistant populations to a native susceptible state or replacement of malaria transmitting mosquitoes with those bearing naturally occurring parasite resistant alleles. Insecticide resistance (IR) poses a major global health challenge. Here, the authors generate common IR mutations in laboratory Drosophila strains and use a CRISPR-based allelic-drive to replace an IR allele with a susceptible wild-type counterpart, providing a potent new tool for vector control.
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Affiliation(s)
- Bhagyashree Kaduskar
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India.,Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Raja Babu Singh Kushwah
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India.,Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Annabel Guichard
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Menglin Li
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Jared B Bennett
- Biophysics Graduate Group, Division of Biological Sciences, College of Letters and Science, University of California, Berkeley, CA, 94720, USA
| | | | - John M Marshall
- Division of Biostatistics and Epidemiology - School of Public Health, University of California, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Craig Montell
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA. .,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA.
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24
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Siddall A, Harvey-Samuel T, Chapman T, Leftwich PT. Manipulating Insect Sex Determination Pathways for Genetic Pest Management: Opportunities and Challenges. Front Bioeng Biotechnol 2022; 10:867851. [PMID: 35837548 PMCID: PMC9274970 DOI: 10.3389/fbioe.2022.867851] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
Sex determination pathways in insects are generally characterised by an upstream primary signal, which is highly variable across species, and that regulates the splicing of a suite of downstream but highly-conserved genes (transformer, doublesex and fruitless). In turn, these downstream genes then regulate the expression of sex-specific characteristics in males and females. Identification of sex determination pathways has and continues to be, a critical component of insect population suppression technologies. For example, "first-generation" transgenic technologies such as fsRIDL (Female-Specific Release of Insects carrying Dominant Lethals) enabled efficient selective removal of females from a target population as a significant improvement on the sterile insect technique (SIT). Second-generation technologies such as CRISPR/Cas9 homing gene drives and precision-guided SIT (pgSIT) have used gene editing technologies to manipulate sex determination genes in vivo. The development of future, third-generation control technologies, such as Y-linked drives, (female to male) sex-reversal, or X-shredding, will require additional knowledge of aspects of sexual development, including a deeper understanding of the nature of primary signals and dosage compensation. This review shows how knowledge of sex determination in target pest species is fundamental to all phases of the development of control technologies.
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Affiliation(s)
- Alex Siddall
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Tim Harvey-Samuel
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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25
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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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26
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Grunwald HA, Weitzel AJ, Cooper KL. Applications of and considerations for using CRISPR-Cas9-mediated gene conversion systems in rodents. Nat Protoc 2022; 17:3-14. [PMID: 34949863 DOI: 10.1038/s41596-021-00646-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/13/2021] [Indexed: 01/23/2023]
Abstract
Genetic elements that are inherited at super-Mendelian frequencies could be used in a 'gene drive' to spread an allele to high prevalence in a population with the goal of eliminating invasive species or disease vectors. We recently demonstrated that the gene conversion mechanism underlying a CRISPR-Cas9-mediated gene drive is feasible in mice. Although substantial technical hurdles remain, overcoming these could lead to strategies that might decrease the spread of rodent-borne Lyme disease or eliminate invasive populations of mice and rats that devastate island ecology. Perhaps more immediately achievable at moderate gene conversion efficiency, applications in a laboratory setting could produce complex genotypes that reduce the time and cost in both dollars and animal lives compared with Mendelian inheritance strategies. Here, we discuss what we have learned from early efforts to achieve CRISPR-Cas9-mediated gene conversion, potential for broader applications in the laboratory, current limitations, and plans for optimizing this potentially powerful technology.
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Affiliation(s)
- Hannah A Grunwald
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Alexander J Weitzel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
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27
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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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28
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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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29
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Lacy K, Schaefer KA, Scheitrum DP, Klein EY. The economic value of genetically engineered mosquitoes as a Malaria control strategy depends on local transmission rates. Biotechnol J 2021; 17:e2100373. [PMID: 34873849 DOI: 10.1002/biot.202100373] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/05/2022]
Abstract
This paper assesses the economic value of genetically engineered (GE) Anopheles gambiae mosquitoes as a malaria control strategy. We use an epidemiological-economic model of malaria transmission to evaluate this technology for a range of village-level transmission settings. In each setting, we evaluate public health outcomes following introduction of GE mosquitoes relative to a "status quo" baseline scenario. We also assess results both in contrast to-and in combination with-a Mass Drug Administration (MDA) strategy. We find that-in low transmission settings-the present value (PV) public health benefits of GE mosquito release are substantial, both relative to status quo dynamics and MDA. In contrast, in high transmission settings, the release of GE mosquitoes may increase steady-state infection rates. Our results indicate that there are substantial policy complementarities when GE mosquito release is combined with local MDA-the combined control strategy can lead to local eradication.
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Affiliation(s)
- Katherine Lacy
- Department of Economics, University of Nevada, Reno, USA
| | - K Aleks Schaefer
- Department of Agricultural Economics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Daniel P Scheitrum
- Department of Agricultural and Resource Economics, University of Arizona, Tucson, USA
| | - Eili Y Klein
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, USA.,Center for Disease Dynamics, Economics and Policy, Washington, DC, USA
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30
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Zhu GH, Albishi NM, Chen X, Brown RL, Palli SR. Expanding the Toolkit for Genome Editing in a Disease Vector, Aedes aegypti: Transgenic Lines Expressing Cas9 and Single Guide RNA Induce Efficient Mutagenesis. CRISPR J 2021; 4:846-853. [PMID: 33450159 PMCID: PMC8742270 DOI: 10.1089/crispr.2020.0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
CRISPR-Cas9 mediated genome editing methods are being used for the analysis of gene function. However, it is hard to identify gene knockout mutants for genes whose knockout does not cause distinct phenotypes. To overcome this issue in the disease vector, Aedes aegypti, a transgenic Cas9/single guide RNA (sgRNA) method, was used to knock out the eye marker gene, kynurenine 3-monooxygenase (kmo), and the juvenile hormone receptor, Methoprene-tolerant (Met). PiggyBac transformation vectors were prepared to express sgRNAs targeting kmo and Met under the control of the U6 promoter. Transgenic Ae. aegypti expressing kmo-sgRNA or Met-sgRNA under the control of the U6 promoter and enhanced green fluorescent protein (eGFP) under the control of the hr5ie1 promoter were produced. The U6-sgRNA adults were mated with AAEL010097-Cas9 adults. The progeny were screened, and the insects expressing eGFP and DsRed were selected and evaluated for mutations in target genes. About 77% and 78% of the progeny that were positive for both eGFP and DsRed in kmo-sgRNA and Met-sgRNA groups, respectively, showed mutations in their target genes.
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Affiliation(s)
- Guan-Heng Zhu
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA
| | - Najla M. Albishi
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA
| | - Xien Chen
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA
| | - Rachel L. Brown
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA
| | - Subba Reddy Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, USA
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31
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Xu X, Harvey-Samuel T, Yang J, You M, Alphey L. CRISPR/Cas9-based functional characterization of the pigmentation gene ebony in Plutella xylostella. Insect Mol Biol 2021; 30:615-623. [PMID: 34414615 DOI: 10.1111/imb.12730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/26/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Body pigmentation is an important character of insects in adapting to biotic and abiotic environmental challenges. Additionally, based on the relative ease of screening, several genes involved in insect melanization have been used in classic genetic studies or as visual markers in constructing transgenic insects. Here, a homologue of the Bombyx mori melanization-inhibiting gene ebony, associated with the conversion of dopamine to N-β-alanyl dopamine, was identified in a global pest, Plutella xylostella. The CRISPR/Cas9 system was applied to generate multiple Pxebony knockout alleles which were crossed to produce a Pxebony knockout strain, showing darker pigmentation in larvae, pupae and adults, compared with wildtype. Interestingly, we observed that Pxebony heterozygotes displayed an intermediate darkened phenotype, indicating partial dominance between the knockout and wildtype alleles. The fitness costs of Pxebony deficiency were also assessed in the mutant strain, indicating that embryo hatchability and larval survival were significantly reduced, while the eclosion rate was not obviously affected. Our work provides a potential target for exploring CRISPR-based genetics-control systems in this economically important pest lepidopteran.
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Affiliation(s)
- X Xu
- 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, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
| | - T Harvey-Samuel
- Arthropod Genetics Group, The Pirbright Institute, Woking, UK
| | - J 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, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
| | - M You
- 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, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
| | - L Alphey
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Arthropod Genetics Group, The Pirbright Institute, Woking, UK
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32
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Adelman ZN. Demystifying the Risk Assessment Process for Laboratory-Based Experiments Utilizing Invasive Genetic Elements: It Is More Than Gene Drive. Appl Biosaf 2021; 26:154-163. [PMID: 36035544 PMCID: PMC9134331 DOI: 10.1089/apb.20.0074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Advances in recombinant DNA approaches have resulted in the development of transgene architectures that severely bias their own inheritance, a process commonly referred to as "gene drive." The rapid pace of development, combined with the complexity of many gene drive approaches, threatens to overwhelm those responsible for ensuring its safe use in the laboratory, as even identifying that a specific transgene is capable of gene drive may not be intuitive. Although currently gene drive experiments have been limited to just a few species (mosquitoes, flies, mice, and yeast), the range of organisms used in gene drive research is expected to increase substantially in the coming years. Here the defining features of different gene drive approaches are discussed. Although this will start with a focus on identifying when gene drive could or could not occur, the emphasis will also be on establishing risk profiles based on anticipated level of invasiveness and persistence of transgenes in the surrounding environment. Attention is also called to the fact that transgenes can be considered invasive without being considered gene drive (and vice versa). This further supports the notion that adequate risk assessment requires information regarding the specific circumstances a given transgene or set of transgenes is capable of invading a corresponding population. Finally, challenges in the review and evaluation of work involving gene drive organisms are discussed.
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Affiliation(s)
- Zach N. Adelman
- Department of Entomology and Agrilife Research, Texas A&M University, College Station, Texas, USA
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33
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Feng X, López Del Amo V, Mameli E, Lee M, Bishop AL, Perrimon N, Gantz VM. Optimized CRISPR tools and site-directed transgenesis towards gene drive development in Culex quinquefasciatus mosquitoes. Nat Commun 2021; 12:2960. [PMID: 34017003 PMCID: PMC8137705 DOI: 10.1038/s41467-021-23239-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 02/10/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
Culex mosquitoes are a global vector for multiple human and animal diseases, including West Nile virus, lymphatic filariasis, and avian malaria, posing a constant threat to public health, livestock, companion animals, and endangered birds. While rising insecticide resistance has threatened the control of Culex mosquitoes, advances in CRISPR genome-editing tools have fostered the development of alternative genetic strategies such as gene drive systems to fight disease vectors. However, though gene-drive technology has quickly progressed in other mosquitoes, advances have been lacking in Culex. Here, we develop a Culex-specific Cas9/gRNA expression toolkit and use site-directed homology-based transgenesis to generate and validate a Culex quinquefasciatus Cas9-expressing line. We show that gRNA scaffold variants improve transgenesis efficiency in both Culex quinquefasciatus and Drosophila melanogaster and boost gene-drive performance in the fruit fly. These findings support future technology development to control Culex mosquitoes and provide valuable insight for improving these tools in other species.
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Affiliation(s)
- Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Víctor López Del Amo
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Enzo Mameli
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, School of Medicine, Boston, MA, USA
| | - Megan Lee
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Alena L Bishop
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- HHMI, Harvard Medical School, Boston, MA, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
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34
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Li Z, Marcel N, Devkota S, Auradkar A, Hedrick SM, Gantz VM, Bier E. CopyCatchers are versatile active genetic elements that detect and quantify inter-homolog somatic gene conversion. Nat Commun 2021; 12:2625. [PMID: 33976171 PMCID: PMC8113449 DOI: 10.1038/s41467-021-22927-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 02/10/2021] [Accepted: 04/01/2021] [Indexed: 11/08/2022] Open
Abstract
CRISPR-based active genetic elements, or gene-drives, copied via homology-directed repair (HDR) in the germline, are transmitted to progeny at super-Mendelian frequencies. Active genetic elements also can generate widespread somatic mutations, but the genetic basis for such phenotypes remains uncertain. It is generally assumed that such somatic mutations are generated by non-homologous end-joining (NHEJ), the predominant double stranded break repair pathway active in somatic cells. Here, we develop CopyCatcher systems in Drosophila to detect and quantify somatic gene conversion (SGC) events. CopyCatchers inserted into two independent genetic loci reveal unexpectedly high rates of SGC in the Drosophila eye and thoracic epidermis. Focused RNAi-based genetic screens identify several unanticipated loci altering SGC efficiency, one of which (c-MYC), when downregulated, promotes SGC mediated by both plasmid and homologous chromosome-templates in human HEK293T cells. Collectively, these studies suggest that CopyCatchers can serve as effective discovery platforms to inform potential gene therapy strategies.
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Affiliation(s)
- Zhiqian Li
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Nimi Marcel
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Stephen M Hedrick
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Valentino M Gantz
- 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-UCSD, La Jolla, CA, USA.
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35
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Piergentili R, Del Rio A, Signore F, Umani Ronchi F, Marinelli E, Zaami S. CRISPR-Cas and Its Wide-Ranging Applications: From Human Genome Editing to Environmental Implications, Technical Limitations, Hazards and Bioethical Issues. Cells 2021; 10:cells10050969. [PMID: 33919194 PMCID: PMC8143109 DOI: 10.3390/cells10050969] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/14/2022] Open
Abstract
The CRISPR-Cas system is a powerful tool for in vivo editing the genome of most organisms, including man. During the years this technique has been applied in several fields, such as agriculture for crop upgrade and breeding including the creation of allergy-free foods, for eradicating pests, for the improvement of animal breeds, in the industry of bio-fuels and it can even be used as a basis for a cell-based recording apparatus. Possible applications in human health include the making of new medicines through the creation of genetically modified organisms, the treatment of viral infections, the control of pathogens, applications in clinical diagnostics and the cure of human genetic diseases, either caused by somatic (e.g., cancer) or inherited (mendelian disorders) mutations. One of the most divisive, possible uses of this system is the modification of human embryos, for the purpose of preventing or curing a human being before birth. However, the technology in this field is evolving faster than regulations and several concerns are raised by its enormous yet controversial potential. In this scenario, appropriate laws need to be issued and ethical guidelines must be developed, in order to properly assess advantages as well as risks of this approach. In this review, we summarize the potential of these genome editing techniques and their applications in human embryo treatment. We will analyze CRISPR-Cas limitations and the possible genome damage caused in the treated embryo. Finally, we will discuss how all this impacts the law, ethics and common sense.
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Affiliation(s)
- Roberto Piergentili
- Institute of Molecular Biology and Pathology, Italian National Research Council (CNR-IBPM), 00185 Rome, Italy;
| | - Alessandro Del Rio
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences, Sapienza University of Rome, 00161 Rome, Italy; (F.U.R.); (E.M.); (S.Z.)
- Correspondence: or
| | - Fabrizio Signore
- Obstetrics and Gynecology Department, USL Roma2, Sant’Eugenio Hospital, 00144 Rome, Italy;
| | - Federica Umani Ronchi
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences, Sapienza University of Rome, 00161 Rome, Italy; (F.U.R.); (E.M.); (S.Z.)
| | - Enrico Marinelli
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences, Sapienza University of Rome, 00161 Rome, Italy; (F.U.R.); (E.M.); (S.Z.)
| | - Simona Zaami
- Department of Anatomical, Histological, Forensic, and Orthopedic Sciences, Sapienza University of Rome, 00161 Rome, Italy; (F.U.R.); (E.M.); (S.Z.)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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37
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Abstract
Synthetic gene drive constructs could, in principle, provide the basis for highly efficient interventions to control disease vectors and other pest species. This efficiency derives in part from leveraging natural processes of dispersal and gene flow to spread the construct and its impacts from one population to another. However, sometimes (for example, with invasive species) only specific populations are in need of control, and impacts on non-target populations would be undesirable. Many gene drive designs use nucleases that recognise and cleave specific genomic sequences, and one way to restrict their spread would be to exploit sequence differences between target and non-target populations. In this paper we propose and model a series of low threshold double drive designs for population suppression, each consisting of two constructs, one imposing a reproductive load on the population and the other inserted into a differentiated locus and controlling the drive of the first. Simple deterministic, discrete-generation computer simulations are used to assess the alternative designs. We find that the simplest double drive designs are significantly more robust to pre-existing cleavage resistance at the differentiated locus than single drive designs, and that more complex designs incorporating sex ratio distortion can be more efficient still, even allowing for successful control when the differentiated locus is neutral and there is up to 50% pre-existing resistance in the target population. Similar designs can also be used for population replacement, with similar benefits. A population genomic analysis of CRISPR PAM sites in island and mainland populations of the malaria mosquito Anopheles gambiae indicates that the differentiation needed for our methods to work can exist in nature. Double drives should be considered when efficient but localised population genetic control is needed and there is some genetic differentiation between target and non-target populations.
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Affiliation(s)
- Katie Willis
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
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38
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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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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41
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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] [What about the content of this article? (0)] [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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Xu XRS, Bulger EA, Gantz VM, Klanseck C, Heimler SR, Auradkar A, Bennett JB, Miller LA, Leahy S, Juste SS, Buchman A, Akbari OS, Marshall JM, Bier E. Active Genetic Neutralizing Elements for Halting or Deleting Gene Drives. Mol Cell 2020; 80:246-262.e4. [PMID: 32949493 PMCID: PMC10962758 DOI: 10.1016/j.molcel.2020.09.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 11/23/2019] [Revised: 05/03/2020] [Accepted: 09/01/2020] [Indexed: 01/02/2023]
Abstract
CRISPR-Cas9-based gene drive systems possess the inherent capacity to spread progressively throughout target populations. Here we describe two self-copying (or active) guide RNA-only genetic elements, called e-CHACRs and ERACRs. These elements use Cas9 produced in trans by a gene drive either to inactivate the cas9 transgene (e-CHACRs) or to delete and replace the gene drive (ERACRs). e-CHACRs can be inserted at various genomic locations and carry two or more gRNAs, the first copying the e-CHACR and the second mutating and inactivating the cas9 transgene. Alternatively, ERACRs are inserted at the same genomic location as a gene drive, carrying two gRNAs that cut on either side of the gene drive to excise it. e-CHACRs efficiently inactivate Cas9 and can drive to completion in cage experiments. Similarly, ERACRs, particularly those carrying a recoded cDNA-restoring endogenous gene activity, can drive reliably to fully replace a gene drive. We compare the strengths of these two systems.
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Affiliation(s)
- Xiang-Ru Shannon Xu
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Emily A Bulger
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, and Gladstone Institutes, San Francisco, CA, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Carissa Klanseck
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Stephanie R Heimler
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Jared B Bennett
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lauren Ashley Miller
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Sarah Leahy
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Sara Sanz Juste
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Anna Buchman
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Omar S Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, Berkeley, CA, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA.
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43
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Abstract
CRISPR-based synthetic gene drives have the potential to deliver a more effective and humane method of invasive vertebrate pest control than current strategies. Relatively efficient CRISPR gene drive systems have been developed in insects and yeast but not in mammals. Here, we investigated the efficiency of CRISPR-Cas9-based gene drives in Mus musculus by constructing "split drive" systems where gRNA expression occurs on a separate chromosome to Cas9, which is under the control of either a zygotic (CAG) or germline (Vasa) promoter. While both systems generated double-strand breaks at their intended target site in vivo, no homology-directed repair between chromosomes ("homing") was detectable. Our data indicate that robust and specific Cas9 expression during meiosis is a critical requirement for the generation of efficient CRISPR-based synthetic gene drives in rodents.
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Affiliation(s)
- Chandran Pfitzner
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
- Precision Medicine, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Melissa A White
- Precision Medicine, South Australian Health and Medical Research Institute, Adelaide, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Sandra G Piltz
- Precision Medicine, South Australian Health and Medical Research Institute, Adelaide, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Michaela Scherer
- Precision Medicine, South Australian Health and Medical Research Institute, Adelaide, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Fatwa Adikusuma
- Precision Medicine, South Australian Health and Medical Research Institute, Adelaide, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, Australia
| | - James N Hughes
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Paul Q Thomas
- Precision Medicine, South Australian Health and Medical Research Institute, Adelaide, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, Australia
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Rode NO, Courtier-Orgogozo V, Débarre F. Can a Population Targeted by a CRISPR-Based Homing Gene Drive Be Rescued? G3 (Bethesda) 2020; 10:3403-3415. [PMID: 32727921 PMCID: PMC7466991 DOI: 10.1534/g3.120.401484] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022]
Abstract
CRISPR-based homing gene drive is a genetic control technique aiming to modify or eradicate natural populations. This technique is based on the release of individuals carrying an engineered piece of DNA that can be preferentially inherited by the progeny. The development of countermeasures is important to control the spread of gene drives, should they result in unanticipated damages. One proposed countermeasure is the introduction of individuals carrying a brake construct that targets and inactivates the drive allele but leaves the wild-type allele unaffected. Here we develop models to investigate the efficiency of such brakes. We consider a variable population size and use a combination of analytical and numerical methods to determine the conditions where a brake can prevent the extinction of a population targeted by an eradication drive. We find that a brake is not guaranteed to prevent eradication and that characteristics of both the brake and the drive affect the likelihood of recovering the wild-type population. In particular, brakes that restore fitness are more efficient than brakes that do not. Our model also indicates that threshold-dependent drives (drives that can spread only when introduced above a threshold) are more amenable to control with a brake than drives that can spread from an arbitrary low introduction frequency (threshold-independent drives). Based on our results, we provide practical recommendations and discuss safety issues.
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Affiliation(s)
- Nicolas O Rode
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - Florence Débarre
- Sorbonne Université, CNRS, IRD, INRA, Institute of Ecology and Environmental Sciences-Paris (IEES Paris), place Jussieu, 75005, France
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45
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Ni XY, Zhou ZD, Huang J, Qiao X. Targeted gene disruption by CRISPR/xCas9 system in Drosophila melanogaster. Arch Insect Biochem Physiol 2020; 104:e21662. [PMID: 32027059 DOI: 10.1002/arch.21662] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Although the Cas9 protein from Streptococcus pyogenes (SpCas9) is the most widely used clustered regularly interspaced short palindromic repeats (CRISPR) variant in genome engineering experiments, it does have certain limitations. First, the stringent requirement for the protospacer adjacent motif (PAM) sequence limits the target DNA that can be manipulated using this method in insects. Second, its complementarity specifications are not very stringent, meaning that it can sometimes cause off-target effects at the target site. A recent study reported that an evolved SpCas9 variant, xCas9(3.7), with preference for various 5'-NG-3' PAM sequences not only has the broadest PAM compatibility but also has much greater DNA specificity and lower genome-wide off-target activity than SpCas9 in mammalian cells. Here we applied the CRISPR/xCas9 system to target the white gene in Drosophila melanogaster, testing the genome-editing efficiency of xCas9 at different PAM sites. On the GGG PAM site, xCas9 showed less activity than SpCas9. For the non-NGG PAM site TGA, xCas9 could produce DNA cleavage and indel-mediated disruption on the target gene. However, for other non-NGG PAM sites, xCas9 showed no activity. These findings show that the evolved Cas9 variant with broad PAM compatibility is functional in Drosophila to induce heritable gene alterations, increasing the targeting range for the applications of genome editing in insects.
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Affiliation(s)
- Xu-Yang Ni
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhen-Dong Zhou
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jia Huang
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xiaomu Qiao
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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46
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Abstract
Gene drive-based strategies for modifying populations face the problem that genes encoding cargo and the drive mechanism are subject to separation, mutational inactivation, and loss of efficacy. Resilience, an ability to respond to these eventualities in ways that restore population modification with functional genes, is needed for long-term success. Here, we show that resilience can be achieved through cycles of population modification with "Cleave and Rescue" (ClvR) selfish genetic elements. ClvR comprises a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene and a recoded version of the essential gene resistant to cleavage. ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. Cycles of modification can, in principle, be carried out if two ClvR elements targeting different essential genes are located at the same genomic position, and one of them, ClvRn+1, carries a Rescue transgene from an earlier element, ClvRnClvRn+1 should spread within a population of ClvRn, while also bringing about a decrease in its frequency. To test this hypothesis, we first show that multiple ClvRs, each targeting a different essential gene, function when located at a common chromosomal position in Drosophila We then show that when several of these also carry the Rescue from a different ClvR, they spread to transgene fixation in populations fixed for the latter and at its expense. Therefore, genetic modifications of populations can be overwritten with new content, providing an ongoing point of control.
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Affiliation(s)
- Georg Oberhofer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Tobin Ivy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Bruce A Hay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;
- St John's College, University of Cambridge, CB2 1TP Cambridge, United Kingdom
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