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Harvey-Samuel T, Feng X, Okamoto EM, Purusothaman DK, Leftwich PT, Alphey L, Gantz VM. CRISPR-based gene drives generate super-Mendelian inheritance in the disease vector Culex quinquefasciatus. Nat Commun 2023; 14:7561. [PMID: 37985762 PMCID: PMC10662442 DOI: 10.1038/s41467-023-41834-1] [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: 06/12/2023] [Accepted: 09/21/2023] [Indexed: 11/22/2023] Open
Abstract
Culex mosquitoes pose a significant public health threat as vectors for a variety of diseases including West Nile virus and lymphatic filariasis, and transmit pathogens threatening livestock, companion animals, and endangered birds. Rampant insecticide resistance makes controlling these mosquitoes challenging and necessitates the development of new control strategies. Gene drive technologies have made significant progress in other mosquito species, although similar advances have been lagging in Culex. Here we test a CRISPR-based homing gene drive for Culex quinquefasciatus, and show that the inheritance of two split-gene-drive transgenes, targeting different loci, are biased in the presence of a Cas9-expressing transgene although with modest efficiencies. Our findings extend the list of disease vectors where engineered homing gene drives have been demonstrated to include Culex alongside Anopheles and Aedes, and pave the way for future development of these technologies to control Culex mosquitoes.
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Affiliation(s)
- Tim Harvey-Samuel
- Arthropod Genetics Group, The Pirbright Institute, Woking, GU24 0NF, UK
| | - 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, Guangdong, 518106, Shenzhen, China.
| | - Emily M Okamoto
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Deepak-Kumar Purusothaman
- Arthropod Genetics Group, The Pirbright Institute, Woking, GU24 0NF, UK
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Luke Alphey
- Arthropod Genetics Group, The Pirbright Institute, Woking, GU24 0NF, UK.
- Biology Department, University of York, York, YO10 5DD, UK.
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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2
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Harvey-Samuel T, Feng X, Okamoto EM, Purusothaman DK, Leftwich PT, Alphey L, Gantz VM. CRISPR-based gene drives generate super-Mendelian inheritance in the disease vector Culex quinquefasciatus. bioRxiv 2023:2023.06.12.544656. [PMID: 37398284 PMCID: PMC10312623 DOI: 10.1101/2023.06.12.544656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Culex mosquitoes pose a significant public health threat as vectors for a variety of diseases including West Nile virus and lymphatic filariasis, and transmit pathogens threatening livestock, companion animals, and endangered birds. Rampant insecticide resistance makes controlling these mosquitoes challenging and necessitates the development of new control strategies. Gene drive technologies have made significant progress in other mosquito species, although similar advances have been lagging in Culex. Here we test the first CRISPR-based homing gene drive for Culex quinquefasciatus, demonstrating the possibility of using this technology to control Culex mosquitoes. Our results show that the inheritance of two split-gene-drive transgenes, targeting different loci, are biased in the presence of a Cas9-expressing transgene although with modest efficiencies. Our findings extend the list of disease vectors where engineered homing gene drives have been demonstrated to include Culex alongside Anopheles and Aedes, and pave the way for future development of these technologies to control Culex mosquitoes.
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Affiliation(s)
- Tim Harvey-Samuel
- Arthropod Genetics Group, The Pirbright Institute, Woking, UK, GU24 0NF
| | - Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA 92093
| | - Emily M Okamoto
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA 92093
| | - Deepak-Kumar Purusothaman
- Arthropod Genetics Group, The Pirbright Institute, Woking, UK, GU24 0NF
- Present address: MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK G12 8QQ
| | - Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK, NR4 7TJ
| | - Luke Alphey
- Present address: Biology Department, University of York, York, UK, YO10 5DD
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA 92093
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3
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Gantz VM, Bier E. Active genetics comes alive: Exploring the broad applications of CRISPR-based selfish genetic elements (or gene-drives): Exploring the broad applications of CRISPR-based selfish genetic elements (or gene-drives). Bioessays 2022; 44:e2100279. [PMID: 35686327 PMCID: PMC9397133 DOI: 10.1002/bies.202100279] [Citation(s) in RCA: 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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/11/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based "active genetic" elements developed in 2015 bypassed the fundamental rules of traditional genetics. Inherited in a super-Mendelian fashion, such selfish genetic entities offered a variety of potential applications including: gene-drives to disseminate gene cassettes carrying desired traits throughout insect populations to control disease vectors or pest species, allelic drives biasing inheritance of preferred allelic variants, neutralizing genetic elements to delete and replace or to halt the spread of gene-drives, split-drives with the core constituent Cas9 endonuclease and guide RNA (gRNA) components inserted at separate genomic locations to accelerate assembly of complex arrays of genetic traits or to gain genetic entry into novel organisms (vertebrates, plants, bacteria), and interhomolog based copying systems in somatic cells to develop tools for treating inherited or infectious diseases. Here, we summarize the substantial advances that have been made on all of these fronts and look forward to the next phase of this rapidly expanding and impactful field.
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Affiliation(s)
- Valentino M Gantz
- Department of Cell and Developmental Biology, University of California, La Jolla, California, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, La Jolla, California, USA
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4
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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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5
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Bodai Z, Bishop AL, Gantz VM, Komor AC. Targeting double-strand break indel byproducts with secondary guide RNAs improves Cas9 HDR-mediated genome editing efficiencies. Nat Commun 2022; 13:2351. [PMID: 35534455 PMCID: PMC9085776 DOI: 10.1038/s41467-022-29989-9] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/07/2022] [Indexed: 12/26/2022] Open
Abstract
Programmable double-strand DNA breaks (DSBs) can be harnessed for precision genome editing through manipulation of the homology-directed repair (HDR) pathway. However, end-joining repair pathways often outcompete HDR and introduce insertions and deletions of bases (indels) at the DSB site, decreasing precision outcomes. It has been shown that indel sequences for a given DSB site are reproducible and can even be predicted. Here, we report a general strategy (the "double tap" method) to improve HDR-mediated precision genome editing efficiencies that takes advantage of the reproducible nature of indel sequences. The method simply involves the use of multiple gRNAs: a primary gRNA that targets the wild-type genomic sequence, and one or more secondary gRNAs that target the most common indel sequence(s), which in effect provides a "second chance" at HDR-mediated editing. This proof-of-principle study presents the double tap method as a simple yet effective option for enhancing precision editing in mammalian cells.
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Affiliation(s)
- Zsolt Bodai
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alena L Bishop
- Division of Biological Sciences, Section of Cell and Developmental Biology, 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
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
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Weitzel AJ, Grunwald HA, Weber C, Levina R, Gantz VM, Hedrick SM, Bier E, Cooper KL. Meiotic Cas9 expression mediates gene conversion in the male and female mouse germline. PLoS Biol 2021; 19:e3001478. [PMID: 34941868 PMCID: PMC8699911 DOI: 10.1371/journal.pbio.3001478] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 04/20/2021] [Accepted: 11/10/2021] [Indexed: 11/18/2022] Open
Abstract
Highly efficient gene conversion systems have the potential to facilitate the study of complex genetic traits using laboratory mice and, if implemented as a "gene drive," to limit loss of biodiversity and disease transmission caused by wild rodent populations. We previously showed that such a system of gene conversion from heterozygous to homozygous after a sequence targeted CRISPR/Cas9 double-strand DNA break (DSB) is feasible in the female mouse germline. In the male germline, however, all DSBs were instead repaired by end joining (EJ) mechanisms to form an "insertion/deletion" (indel) mutation. These observations suggested that timing Cas9 expression to coincide with meiosis I is critical to favor conditions when homologous chromosomes are aligned and interchromosomal homology-directed repair (HDR) mechanisms predominate. Here, using a Cas9 knock-in allele at the Spo11 locus, we show that meiotic expression of Cas9 does indeed mediate gene conversion in the male as well as in the female germline. However, the low frequency of both HDR and indel mutation in both male and female germlines suggests that Cas9 may be expressed from the Spo11 locus at levels too low for efficient DSB formation. We suggest that more robust Cas9 expression initiated during early meiosis I may improve the efficiency of gene conversion and further increase the rate of "super-mendelian" inheritance from both male and female mice.
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Affiliation(s)
- Alexander J. Weitzel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Hannah A. Grunwald
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Ceri Weber
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Rimma Levina
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Valentino M. Gantz
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Stephen M. Hedrick
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, California, United States of America
| | - Ethan Bier
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
- Tata Institute for Genetics and Society, University of California San Diego, La Jolla, California, United States of America
| | - Kimberly L. Cooper
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
- Tata Institute for Genetics and Society, University of California San Diego, La Jolla, California, United States of America
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7
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Feng X, Kambic L, Nishimoto JH, Reed FA, Denton JA, Sutton JT, Gantz VM. Evaluation of Gene Knockouts by CRISPR as Potential Targets for the Genetic Engineering of the Mosquito Culex quinquefasciatus. CRISPR J 2021; 4:595-608. [PMID: 34280034 PMCID: PMC8392076 DOI: 10.1089/crispr.2021.0028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Culex quinquefasciatus mosquitoes are a globally widespread vector of several human and animal pathogens. Their biology and behavior allow them to thrive in proximity to urban areas, rendering them a constant public health threat. Their mixed bird/mammal feeding behavior further offers a vehicle for zoonotic pathogens transmission to people and, separately, poses a threat to the conservation of insular birds. The advent of CRISPR has led to the development of novel technologies for the genetic engineering of wild mosquito populations. Yet, research into Cx. quinquefasciatus has been lagging compared to other disease vectors. Here, we use this tool to disrupt a set of five pigmentation genes in Cx. quinquefasciatus that, when altered, lead to visible, homozygous-viable phenotypes. We further validate this approach in separate laboratories and in two distinct strains of Cx. quinquefasciatus that are relevant to potential future public health and bird conservation applications. We generate a double-mutant line, demonstrating the possibility of sequentially combining multiple such mutations in a single individual. Lastly, we target two loci, doublesex in the sex-determination pathway and proboscipedia, a hox gene, demonstrating the flexibility of these methods applied to novel targets. Our work provides a platform of seven validated loci that could be used for targeted mutagenesis in Cx. quinquefasciatus and the future development of genetic suppression strategies for this species. Furthermore, the mutant lines generated here could have widespread utility to the research community using this model organism, as they could be used as targets for transgene delivery, where a copy of the disrupted gene could be included as an easily scored transgenesis marker.
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Affiliation(s)
- Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
| | - Lukas Kambic
- Department of Biology, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, USA
| | | | - Floyd A. Reed
- School of Life Sciences, University of Hawaiʻi at Mānoa, Honolulu, Hawai‘i, USA
| | - Jai A. Denton
- Institute of Vector-borne Disease, University of Monash, Clayton, Australia
| | - Jolene T. Sutton
- Department of Biology, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, USA
| | - Valentino M. Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, USA
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8
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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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9
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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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10
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López Del Amo V, Leger BS, Cox KJ, Gill S, Bishop AL, Scanlon GD, Walker JA, Gantz VM, Choudhary A. Small-Molecule Control of Super-Mendelian Inheritance in Gene Drives. Cell Rep 2021; 31:107841. [PMID: 32610142 PMCID: PMC7587219 DOI: 10.1016/j.celrep.2020.107841] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 12/12/2019] [Revised: 02/20/2020] [Accepted: 06/09/2020] [Indexed: 11/29/2022] Open
Abstract
Synthetic CRISPR-based gene-drive systems have tremendous potential in public health and agriculture, such as for fighting vector-borne diseases or suppressing crop pest populations. These elements can rapidly spread in a population by breaching the inheritance limit of 50% dictated by Mendel's law of gene segregation, making them a promising tool for population engineering. However, current technologies lack control over their propagation capacity, and there are important concerns about potential unchecked spreading. Here, we describe a gene-drive system in Drosophila that generates an analog inheritance output that can be tightly and conditionally controlled to between 50% and 100%. This technology uses a modified SpCas9 that responds to a synthetic, orally available small molecule, fine-tuning the inheritance probability. This system opens a new avenue to feasibility studies for spatial and temporal control of gene drives using small molecules.
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Affiliation(s)
- Víctor López Del Amo
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Brittany S Leger
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kurt J Cox
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Shubhroz Gill
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alena L Bishop
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Garrett D Scanlon
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - James A Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA.
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11
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Long KC, Alphey L, Annas GJ, Bloss CS, Campbell KJ, Champer J, Chen CH, Choudhary A, Church GM, Collins JP, Cooper KL, Delborne JA, Edwards OR, Emerson CI, Esvelt K, Evans SW, Friedman RM, Gantz VM, Gould F, Hartley S, Heitman E, Hemingway J, Kanuka H, Kuzma J, Lavery JV, Lee Y, Lorenzen M, Lunshof JE, Marshall JM, Messer PW, Montell C, Oye KA, Palmer MJ, Papathanos PA, Paradkar PN, Piaggio AJ, Rasgon JL, Rašić G, Rudenko L, Saah JR, Scott MJ, Sutton JT, Vorsino AE, Akbari OS. Core commitments for field trials of gene drive organisms. Science 2020; 370:1417-1419. [DOI: 10.1126/science.abd1908] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Adolfi A, Gantz VM, Jasinskiene N, Lee HF, Hwang K, Terradas G, Bulger EA, Ramaiah A, Bennett JB, Emerson JJ, Marshall JM, Bier E, James AA. Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi. Nat Commun 2020; 11:5553. [PMID: 33144570 PMCID: PMC7609566 DOI: 10.1038/s41467-020-19426-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [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: 05/19/2020] [Accepted: 10/13/2020] [Indexed: 12/27/2022] Open
Abstract
Cas9/gRNA-mediated gene-drive systems have advanced development of genetic technologies for controlling vector-borne pathogen transmission. These technologies include population suppression approaches, genetic analogs of insecticidal techniques that reduce the number of insect vectors, and population modification (replacement/alteration) approaches, which interfere with competence to transmit pathogens. Here, we develop a recoded gene-drive rescue system for population modification of the malaria vector, Anopheles stephensi, that relieves the load in females caused by integration of the drive into the kynurenine hydroxylase gene by rescuing its function. Non-functional resistant alleles are eliminated via a dominantly-acting maternal effect combined with slower-acting standard negative selection, and rare functional resistant alleles do not prevent drive invasion. Small cage trials show that single releases of gene-drive males robustly result in efficient population modification with ≥95% of mosquitoes carrying the drive within 5-11 generations over a range of initial release ratios.
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Affiliation(s)
- Adriana Adolfi
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697-3900, USA
- Liverpool School of Tropical Medicine, Vector Biology Department, L3 5QA, Liverpool, UK
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0349, USA
| | - Nijole Jasinskiene
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697-3900, USA
| | - Hsu-Feng Lee
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697-3900, USA
| | - Kristy Hwang
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697-3900, USA
| | - Gerard Terradas
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0349, USA
- Tata Institute for Genetics and Society (TIGS)-UCSD, La Jolla, CA, 92093-0335, USA
| | - Emily A Bulger
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0349, USA
- Tata Institute for Genetics and Society (TIGS)-UCSD, La Jolla, CA, 92093-0335, USA
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, CA, 94158, USA
- The Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Arunachalam Ramaiah
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697-2525, USA
- Tata Institute for Genetics and Society (TIGS)-India, Bangalore, KA, 560065, India
| | - Jared B Bennett
- Biophysics Graduate Group, Division of Biological Sciences, College of Letters and Science, University of California, Berkeley, CA, 94720, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697-2525, USA
| | - John M Marshall
- Division of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0349, USA
- Tata Institute for Genetics and Society (TIGS)-UCSD, La Jolla, CA, 92093-0335, USA
| | - Anthony A James
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697-3900, USA.
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-4025, USA.
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13
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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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14
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Kandul NP, Liu J, Buchman A, Gantz VM, Bier E, Akbari OS. Assessment of a Split Homing Based Gene Drive for Efficient Knockout of Multiple Genes. G3 (Bethesda) 2020; 10:827-837. [PMID: 31882406 PMCID: PMC7003086 DOI: 10.1534/g3.119.400985] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/19/2019] [Indexed: 01/08/2023]
Abstract
Homing based gene drives (HGD) possess the potential to spread linked cargo genes into natural populations and are poised to revolutionize population control of animals. Given that host encoded genes have been identified that are important for pathogen transmission, targeting these genes using guide RNAs as cargo genes linked to drives may provide a robust method to prevent disease transmission. However, effectiveness of the inclusion of additional guide RNAs that target separate genes has not been thoroughly explored. To test this approach, we generated a split-HGD in Drosophila melanogaster that encoded a drive linked effector consisting of a second gRNA engineered to target a separate host-encoded gene, which we term a gRNA-mediated effector (GME). This design enabled us to assess homing and knockout efficiencies of two target genes simultaneously, and also explore the timing and tissue specificity of Cas9 expression on cleavage/homing rates. We demonstrate that inclusion of a GME can result in high efficiency of disruption of both genes during super-Mendelian propagation of split-HGD. Furthermore, both genes were knocked out one generation earlier than expected indicating the robust somatic expression of Cas9 driven by Drosophila germline-limited promoters. We also assess the efficiency of 'shadow drive' generated by maternally deposited Cas9 protein and accumulation of drive-induced resistance alleles along multiple generations, and discuss design principles of HGD that could mitigate the accumulation of resistance alleles while incorporating a GME.
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Affiliation(s)
| | - Junru Liu
- Section of Cell and Developmental Biology and
| | | | | | - Ethan Bier
- Section of Cell and Developmental Biology and
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093
| | - Omar S Akbari
- Section of Cell and Developmental Biology and
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093
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15
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López Del Amo V, Bishop AL, Sánchez C HM, Bennett JB, Feng X, Marshall JM, Bier E, Gantz VM. A transcomplementing gene drive provides a flexible platform for laboratory investigation and potential field deployment. Nat Commun 2020; 11:352. [PMID: 31953404 PMCID: PMC6969112 DOI: 10.1038/s41467-019-13977-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [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: 07/03/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
CRISPR-based gene drives can spread through wild populations by biasing their own transmission above the 50% value predicted by Mendelian inheritance. These technologies offer population-engineering solutions for combating vector-borne diseases, managing crop pests, and supporting ecosystem conservation efforts. Current technologies raise safety concerns for unintended gene propagation. Herein, we address such concerns by splitting the drive components, Cas9 and gRNAs, into separate alleles to form a trans-complementing split-gene-drive (tGD) and demonstrate its ability to promote super-Mendelian inheritance of the separate transgenes. This dual-component configuration allows for combinatorial transgene optimization and increases safety by restricting escape concerns to experimentation windows. We employ the tGD and a small-molecule-controlled version to investigate the biology of component inheritance and resistant allele formation, and to study the effects of maternal inheritance and impaired homology on efficiency. Lastly, mathematical modeling of tGD spread within populations reveals potential advantages for improving current gene-drive technologies for field population modification.
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Affiliation(s)
- Víctor López Del Amo
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alena L Bishop
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Héctor M Sánchez C
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Jared B Bennett
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720, USA
| | - Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0349, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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16
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Grunwald HA, Gantz VM, Poplawski G, Xu XRS, Bier E, Cooper KL. Author Correction: Super-Mendelian inheritance mediated by CRISPR-Cas9 in the female mouse germline. Nature 2020; 577:E8. [PMID: 31911657 DOI: 10.1038/s41586-019-1861-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Hannah A Grunwald
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Valentino M Gantz
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Gunnar Poplawski
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Xiang-Ru S Xu
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Ethan Bier
- Division of Biological Sciences, Section of Cellular 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
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cellular 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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17
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Guichard A, Haque T, Bobik M, Xu XRS, Klanseck C, Kushwah RBS, Berni M, Kaduskar B, Gantz VM, Bier E. Efficient allelic-drive in Drosophila. Nat Commun 2019; 10:1640. [PMID: 30967548 PMCID: PMC6456580 DOI: 10.1038/s41467-019-09694-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [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: 08/09/2018] [Accepted: 03/21/2019] [Indexed: 01/08/2023] Open
Abstract
Gene-drive systems developed in several organisms result in super-Mendelian inheritance of transgenic insertions. Here, we generalize this "active genetic" approach to preferentially transmit allelic variants (allelic-drive) resulting from only a single or a few nucleotide alterations. We test two configurations for allelic-drive: one, copy-cutting, in which a non-preferred allele is selectively targeted for Cas9/guide RNA (gRNA) cleavage, and a more general approach, copy-grafting, that permits selective inheritance of a desired allele located in close proximity to the gRNA cut site. We also characterize a phenomenon we refer to as lethal-mosaicism that dominantly eliminates NHEJ-induced mutations and favors inheritance of functional cleavage-resistant alleles. These two efficient allelic-drive methods, enhanced by lethal mosaicism and a trans-generational drive process we refer to as "shadow-drive", have broad practical applications in improving health and agriculture and greatly extend the active genetics toolbox.
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Affiliation(s)
- Annabel Guichard
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Tisha Haque
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Marketta Bobik
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Xiang-Ru S Xu
- 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
| | - Raja Babu Singh Kushwah
- 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-India (TIGS), TIGS Center at inStem, Bangalore, 560065, India
| | - Mateus Berni
- 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
- Post-graduate Program in Morphological Sciences, Federal University of Rio de Janeiro (PCM/UFRJ), Rio de Janeiro, 21941-902, RJ, Brazil
| | - Bhagyashree Kaduskar
- 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-India (TIGS), TIGS Center at inStem, Bangalore, 560065, India
| | - Valentino M Gantz
- 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.
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18
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Grunwald HA, Gantz VM, Poplawski G, Xu XRS, Bier E, Cooper KL. Super-Mendelian inheritance mediated by CRISPR-Cas9 in the female mouse germline. Nature 2019; 566:105-109. [PMID: 30675057 PMCID: PMC6367021 DOI: 10.1038/s41586-019-0875-2] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [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: 07/04/2018] [Accepted: 12/07/2018] [Indexed: 01/02/2023]
Abstract
A gene drive biases the transmission of one of the two copies of a gene such that it is inherited more frequently than by random segregation. Highly efficient gene drive systems have recently been developed in insects, which leverage the sequence-targeted DNA cleavage activity of CRISPR-Cas9 and endogenous homology-directed repair mechanisms to convert heterozygous genotypes to homozygosity1-4. If implemented in laboratory rodents, similar systems would enable the rapid assembly of currently impractical genotypes that involve multiple homozygous genes (for example, to model multigenic human diseases). To our knowledge, however, such a system has not yet been demonstrated in mammals. Here we use an active genetic element that encodes a guide RNA, which is embedded in the mouse tyrosinase (Tyr) gene, to evaluate whether targeted gene conversion can occur when CRISPR-Cas9 is active in the early embryo or in the developing germline. Although Cas9 efficiently induces double-stranded DNA breaks in the early embryo and male germline, these breaks are not corrected by homology-directed repair. By contrast, Cas9 expression limited to the female germline induces double-stranded breaks that are corrected by homology-directed repair, which copies the active genetic element from the donor to the receiver chromosome and increases its rate of inheritance in the next generation. These results demonstrate the feasibility of CRISPR-Cas9-mediated systems that bias inheritance of desired alleles in mice and that have the potential to transform the use of rodent models in basic and biomedical research.
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Affiliation(s)
- Hannah A Grunwald
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Valentino M Gantz
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Gunnar Poplawski
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Xiang-Ru S Xu
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Ethan Bier
- Division of Biological Sciences, Section of Cellular 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
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cellular 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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19
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Gantz VM, Akbari OS. Gene editing technologies and applications for insects. Curr Opin Insect Sci 2018; 28:66-72. [PMID: 30551769 PMCID: PMC6296244 DOI: 10.1016/j.cois.2018.05.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 05/09/2023]
Abstract
Initially discovered in bacteria, CRISPR-based genome editing endonucleases have proven remarkably amenable for adaptation to insects. To date, these endonucleases have been utilized in a plethora of both model and non-model insects including diverse flies, bees, beetles, butterflies, moths, and grasshoppers, to name a few, thereby revolutionizing functional genomics of insects. In addition to basic genome editing, they have also been invaluable for advanced genome engineering and synthetic biology applications. Here we explore the recent genome editing advancements in insects for generating site-specific genomic mutations, insertions, deletions, as well as more advanced applications such as Homology Assisted Genome Knock-in (HACK), potential to utilize DNA base editing, generating predictable reciprocal chromosomal translocations, and development gene drives to control the fate of wild populations.
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Affiliation(s)
- Valentino M Gantz
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92092, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92092, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, USA.
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20
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Abstract
On December 18, 2014, a yellow female fly quietly emerged from her pupal case. What made her unique was that she had only one parent carrying a mutant allele of this classic recessive locus. Then, one generation later, after mating with a wild-type male, all her offspring displayed the same recessive yellow phenotype. Further analysis of other such yellow females revealed that the construct causing the mutation was converting the opposing chromosome with 95% efficiency. These simple results, seen also in mosquitoes and yeast, open the door to a new era of genetics wherein the laws of traditional Mendelian inheritance can be bypassed for a broad variety of purposes. Here, we consider the implications of this fundamentally new form of "active genetics," its applications for gene drives, reversal and amplification strategies, its potential for contributing to cell and gene therapy strategies, and ethical/biosafety considerations associated with such active genetic elements. Also watch the Video Abstract.
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Affiliation(s)
- 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
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21
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Akbari OS, Bellen HJ, Bier E, Bullock SL, Burt A, Church GM, Cook KR, Duchek P, Edwards OR, Esvelt KM, Gantz VM, Golic KG, Gratz SJ, Harrison MM, Hayes KR, James AA, Kaufman TC, Knoblich J, Malik HS, Matthews KA, O'Connor-Giles KM, Parks AL, Perrimon N, Port F, Russell S, Ueda R, Wildonger J. BIOSAFETY. Safeguarding gene drive experiments in the laboratory. Science 2015; 349:927-9. [PMID: 26229113 PMCID: PMC4692367 DOI: 10.1126/science.aac7932] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [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: 01/18/2023]
Abstract
Multiple stringent confinement strategies should be used whenever possible
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Affiliation(s)
- Omar S Akbari
- Department of Entomology, Univ. of California, Riverside, CA 92507, USA. Center for Disease Vector Research, Institute for Integrative Genome Biology, Univ. of California, Riverside, CA 92507, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, Univ. of California, San Diego, La Jolla, CA 92095, USA.
| | - Simon L Bullock
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berks SL5 7PY, UK
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin R Cook
- Bloomington Drosophila Stock Center, Department of Biology, Indiana Univ., Bloomington, IN 47405, USA
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Owain R Edwards
- CSIRO Centre for Environment and Life Sciences, Underwood Avenue, Floreat, WA 6014, Australia
| | - Kevin M Esvelt
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA.
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, Univ. of California, San Diego, La Jolla, CA 92095, USA
| | - Kent G Golic
- Department of Biology, Univ. of Utah, Salt Lake City, UT 84112, USA
| | - Scott J Gratz
- Laboratory of Genetics, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
| | - Keith R Hayes
- CSIRO Biosecurity Flagship, General Post Of ce Box 1538, Hobart, Tasmania, 7001, Australia
| | - Anthony A James
- Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry, Univ. of California at Irvine, Irvine, CA 92697, USA
| | - Thomas C Kaufman
- Bloomington Drosophila Stock Center, Department of Biology, Indiana Univ., Bloomington, IN 47405, USA
| | - Juergen Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kathy A Matthews
- Bloomington Drosophila Stock Center, Department of Biology, Indiana Univ., Bloomington, IN 47405, USA
| | - Kate M O'Connor-Giles
- Laboratory of Genetics, Univ. of Wisconsin-Madison, Madison, WI 53706, USA. Laboratory of Cell and Molecular Biology, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
| | - Annette L Parks
- Bloomington Drosophila Stock Center, Department of Biology, Indiana Univ., Bloomington, IN 47405, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fillip Port
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Steven Russell
- Department of Genetics, Univ. of Cambridge, Cambridge, Cambridgeshire CB2 3EH, UK
| | - Ryu Ueda
- Department of Genetics, Graduate Univ. for Advanced Studies, Mishima, Shizuoka 411-8540, Japan. NIG-Fly Stock Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jill Wildonger
- Department of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
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Gantz VM, Bier E. Genome editing. The mutagenic chain reaction: a method for converting heterozygous to homozygous mutations. Science 2015; 348:442-4. [PMID: 25908821 PMCID: PMC4687737 DOI: 10.1126/science.aaa5945] [Citation(s) in RCA: 336] [Impact Index Per Article: 37.3] [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: 12/31/2014] [Accepted: 03/10/2015] [Indexed: 12/20/2022]
Abstract
An organism with a single recessive loss-of-function allele will typically have a wild-type phenotype, whereas individuals homozygous for two copies of the allele will display a mutant phenotype. We have developed a method called the mutagenic chain reaction (MCR), which is based on the CRISPR/Cas9 genome-editing system for generating autocatalytic mutations, to produce homozygous loss-of-function mutations. In Drosophila, we found that MCR mutations efficiently spread from their chromosome of origin to the homologous chromosome, thereby converting heterozygous mutations to homozygosity in the vast majority of somatic and germline cells. MCR technology should have broad applications in diverse organisms.
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Affiliation(s)
- Valentino M Gantz
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92095, USA.
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92095, USA.
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