A multiplexed, confinable CRISPR/Cas9 gene drive can propagate in caged Aedes aegypti populations.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
25 Jan 2024
25 Jan 2024
Historique:
received:
09
08
2023
accepted:
11
01
2024
medline:
26
1
2024
pubmed:
26
1
2024
entrez:
25
1
2024
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 38272895
doi: 10.1038/s41467-024-44956-2
pii: 10.1038/s41467-024-44956-2
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
729Subventions
Organisme : United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)
ID : N66001-17-2-4054
Organisme : United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)
ID : N66001-17-2-4054
Organisme : United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)
ID : N66001-17-2-4054
Organisme : United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)
ID : N66001-17-2-4054
Organisme : United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)
ID : N66001-17-2-4054
Organisme : United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)
ID : N66001-17-2-4054
Organisme : United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)
ID : N66001-17-2-4054
Organisme : United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)
ID : N66001-17-2-4054
Organisme : Wellcome Trust (Wellcome)
ID : 110117/Z/15/Z
Organisme : Wellcome Trust (Wellcome)
ID : 110117/Z/15/Z
Organisme : Wellcome Trust (Wellcome)
ID : 110117/Z/15/Z
Organisme : RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
ID : BBS/E/I/00007033, BBS/E/I/00007038, and BBS/E/I/00007039
Organisme : RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
ID : BBS/E/I/00007033, BBS/E/I/00007038, and BBS/E/I/00007039
Informations de copyright
© 2024. The Author(s).
Références
Brady, O. J. & Hay, S. I. The global expansion of dengue: how Aedes aegypti mosquitoes enabled the first pandemic arbovirus. Annu. Rev. Entomol. 65, 191–208 (2020).
pubmed: 31594415
doi: 10.1146/annurev-ento-011019-024918
World Health Organization, A global brief on vector-borne diseases. World Heal. Organ. 9, 1–56 (2014).
Bhatt, S. et al. The global distribution and burden of dengue. Nature 496, 504–507 (2013).
pubmed: 23563266
pmcid: 3651993
doi: 10.1038/nature12060
Messina, J. P. et al. The current and future global distribution and population at risk of dengue. Nat. Microbiol. 4, 1508–1515 (2019).
pubmed: 31182801
pmcid: 6784886
doi: 10.1038/s41564-019-0476-8
Alphey, L. Genetic control of mosquitoes. Annu. Rev. Entomol. 59, 205–224 (2014).
pubmed: 24160434
doi: 10.1146/annurev-ento-011613-162002
Burt, A. Site-specific selfish genes as tools for the control and genetic engineering of natural populations. Proc. R. Soc. B Biol. Sci. 270, 921–928 (2003).
doi: 10.1098/rspb.2002.2319
Alphey, L. S., Crisanti, A., Randazzo, F. & Akbari, O. S. Opinion: standardizing the definition of gene drive. Proc. Natl. Acad. Sci. 117, 30864–30867 (2020).
pubmed: 33208534
pmcid: 7733814
doi: 10.1073/pnas.2020417117
Esvelt, K. M., Smidler, A. L., Catteruccia, F. & Church, G. M. Concerning RNA-guided gene drives for the alteration of wild populations. Elife 3, 1–21 (2014).
doi: 10.7554/eLife.03401
Gantz, V. M. et al. Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephensi. Proc. Natl. Acad. Sci. 112, E6736–E6743 (2015).
pubmed: 26598698
pmcid: 4679060
doi: 10.1073/pnas.1521077112
Hammond, A. et al. A CRISPR-Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae. Nat. Biotechnol. 34, 78–83 (2016).
pubmed: 26641531
doi: 10.1038/nbt.3439
DiCarlo, J. E., Chavez, A., Dietz, S. L., Esvelt, K. M. & Church, G. M. Safeguarding CRISPR-Cas9 gene drives in yeast. Nat. Biotechnol. 33, 1250–1255 (2015).
pubmed: 26571100
pmcid: 4675690
doi: 10.1038/nbt.3412
Gantz, V. M. & Bier, E. The mutagenic chain reaction: a method for converting heterozygous to homozygous mutations. Science (80-.). 348, 442–444 (2015).
doi: 10.1126/science.aaa5945
Gerdes, J. A., Mannix, K. M., Hudson, A. M. & Cooley, L. HtsRC-mediated accumulation of F-actin regulates ring canal size during Drosophila melanogaster Oogenesis. Genetics 216, 717–734 (2020).
pubmed: 32883702
pmcid: 7648574
doi: 10.1534/genetics.120.303629
Grunwald, H. A. et al. Super-Mendelian inheritance mediated by CRISPR–Cas9 in the female mouse germline. Nature 566, 105–109 (2019).
pubmed: 30675057
pmcid: 6367021
doi: 10.1038/s41586-019-0875-2
Hammond, A. M. et al. The creation and selection of mutations resistant to a gene drive over multiple generations in the malaria mosquito. PLoS Genet. 13, e1007039 (2017).
pubmed: 28976972
pmcid: 5648257
doi: 10.1371/journal.pgen.1007039
Unckless, R. L., Clark, A. G. & Messer, P. W. Evolution of resistance against CRISPR/Cas9 gene drive. Genetics 205, 827–841 (2017).
pubmed: 27941126
doi: 10.1534/genetics.116.197285
Noble, C., Olejarz, J., Esvelt, K. M., Church, G. M. & Nowak, M. A. Evolutionary dynamics of CRISPR gene drives. Sci. Adv. 3, 3–9 (2017).
doi: 10.1126/sciadv.1601964
Pham, T. B. et al. Experimental population modification of the malaria vector mosquito, Anopheles stephensi. PLOS Genet. 15, e1008440 (2019).
pubmed: 31856182
pmcid: 6922335
doi: 10.1371/journal.pgen.1008440
Oberhofer, G., Ivy, T. & Hay, B. A. Behavior of homing endonuclease gene drives targeting genes required for viability or female fertility with multiplexed guide RNAs. Proc. Natl. Acad. Sci. 115, E9343–E9352 (2018).
pubmed: 30224454
pmcid: 6176634
doi: 10.1073/pnas.1805278115
Champer, J. et al. Reducing resistance allele formation in CRISPR gene drive. Proc. Natl. Acad. Sci. 115, 5522–5527 (2018).
pubmed: 29735716
pmcid: 6003519
doi: 10.1073/pnas.1720354115
Champer, J. et al. A CRISPR homing gene drive targeting a haplolethal gene removes resistance alleles and successfully spreads through a cage population. Proc. Natl. Acad. Sci. 117, 24377–24383 (2020).
pubmed: 32929034
pmcid: 7533649
doi: 10.1073/pnas.2004373117
Marshall, J. M., Buchman, A., Sánchez, H. M. C. & Akbari, O. S. Overcoming evolved resistance to population-suppressing homing-based gene drives. Sci. Rep. 7, 1–12 (2017).
doi: 10.1038/s41598-017-02744-7
Edgington, M. P., Harvey-Samuel, T. & Alphey, L. Population-level multiplexing: a promising strategy to manage the evolution of resistance against gene drives targeting a neutral locus. Evol. Appl. 13, 1939–1948 (2020).
pubmed: 32908596
pmcid: 7463328
doi: 10.1111/eva.12945
Champer, S. E. et al. Computational and experimental performance of CRISPR homing gene drive strategies with multiplexed gRNAs. Sci. Adv. 6, eaaz0525 (2020).
de Ang, J. X. et al. Considerations for homology-based DNA repair in mosquitoes: impact of sequence heterology and donor template source. PLOS Genet. 18, e1010060 (2022).
pubmed: 35180218
pmcid: 8893643
doi: 10.1371/journal.pgen.1010060
Oberhofer, G., Ivy, T. & Hay, B. A. Cleave and Rescue, a novel selfish genetic element and general strategy for gene drive. Proc. Natl. Acad. Sci. 116, 6250–6259 (2019).
pubmed: 30760597
pmcid: 6442612
doi: 10.1073/pnas.1816928116
Leftwich, P. T. et al. Recent advances in threshold-dependent gene drives for mosquitoes. Biochem. Soc. Trans. 0, BST20180076 (2018).
Akbari, O. S. et al. A synthetic gene drive system for local, reversible modification and suppression of insect populations. Curr. Biol. 23, 671–677 (2013).
pubmed: 23541732
pmcid: 8459379
doi: 10.1016/j.cub.2013.02.059
Champer, J. et al. Molecular safeguarding of CRISPR gene drive experiments. Elife 8, 1–10 (2019).
doi: 10.7554/eLife.41439
Champer, J. et al. A toxin-antidote CRISPR gene drive system for regional population modification. Nat. Commun. 11, 1–10 (2020).
doi: 10.1038/s41467-020-14960-3
Maselko, M. et al. Engineering multiple species-like genetic incompatibilities in insects. Nat. Commun. 11, 1–7 (2020).
doi: 10.1038/s41467-020-18348-1
Terradas, G. et al. Inherently confinable split-drive systems in Drosophila. Nat. Commun. 12, 1–12 (2021).
doi: 10.1038/s41467-021-21771-7
Han, Q. et al. Analysis of the wild-type and mutant genes encoding the enzyme kynurenine monooxygenase of the yellow fever mosquito, Aedes aegypti. Insect Mol. Biol. 12, 483–490 (2003).
pubmed: 12974953
pmcid: 2629591
doi: 10.1046/j.1365-2583.2003.00433.x
Coates, C. J., Schaub, T. L., Besansky, N. J., Collins, F. H. & James, A. A. The white gene from the yellow fever mosquito, Aedes aegypti. Insect Mol. Biol. 6, 291–299 (1997).
pubmed: 9272447
doi: 10.1046/j.1365-2583.1997.00183.x
Chan, Y. S., Huen, D. S., Glauert, R., Whiteway, E. & Russell, S. Optimising homing endonuclease gene drive performance in a semi-refractory species: The Drosophila melanogaster Experience. PLoS One 8, 54130 (2013).
doi: 10.1371/journal.pone.0054130
Verkuijl, S. A. N., Ang, J. X. D., Alphey, L., Bonsall, M. B. & Anderson, M. A. E. The challenges in developing efficient and robust synthetic homing endonuclease gene drives. Front. Bioeng. Biotechnol. 0, 426 (2022).
Anderson, M. A. E. et al. Expanding the CRISPR toolbox in culicine mosquitoes: in vitro validation of Pol III promoters. ACS Synth. Biol. 9, 678–681 (2020).
pubmed: 32129976
pmcid: 7093051
doi: 10.1021/acssynbio.9b00436
Li, M. et al. Development of a confinable gene drive system in the human disease vector Aedes aegypti. Elife 9 (2020).
Basu, S. et al. Silencing of end-joining repair for efficient site-specific gene insertion after TALEN/CRISPR mutagenesis in Aedes aegypti. Proc. Natl. Acad. Sci. 112, 4038–4043 (2015).
pubmed: 25775608
pmcid: 4386333
doi: 10.1073/pnas.1502370112
Noble, C. et al. Daisy-chain gene drives for the alteration of local populations. Proc. Natl. Acad. Sci. 116, 8275–8282 (2019).
pubmed: 30940750
pmcid: 6486765
doi: 10.1073/pnas.1716358116
López Del Amo, V. et al. A transcomplementing gene drive provides a flexible platform for laboratory investigation and potential field deployment. Nat. Commun. 11, 1–12 (2020).
doi: 10.1038/s41467-019-13977-7
Bottino-Rojas, V. et al. Beyond the eye: Kynurenine pathway impairment causes midgut homeostasis dysfunction and survival and reproductive costs in blood-feeding mosquitoes. Insect Biochem. Mol. Biol. 142, 103720 (2022).
Purusothaman, D.-K., Shackleford, L., Anderson, M. A. E., Harvey-Samuel, T. & Alphey, L. CRISPR/Cas-9 mediated knock-in by homology dependent repair in the West Nile Virus vector Culex quinquefasciatus Say. Sci. Rep. 11, 1–8 (2021).
doi: 10.1038/s41598-021-94065-z
Anderson, M. E. et al. CRISPR/Cas9 gene editing in the West Nile Virus vector, Culex quinquefasciatus Say. PLoS One 14, e0224857 (2019).
pubmed: 31714905
pmcid: 6850532
doi: 10.1371/journal.pone.0224857
Kyrou, K. et al. A CRISPR–Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes. Nat. Biotechnol. https://doi.org/10.1038/nbt.4245 (2018).
Adolfi, A. et al. Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi. Nat. Commun. 11, 1–13 (2020).
doi: 10.1038/s41467-020-19426-0
Hammond, A. et al. Regulating the expression of gene drives is key to increasing their invasive potential and the mitigation of resistance. PLoS Genet. 17, 1–21 (2021).
doi: 10.1371/journal.pgen.1009321
Akbari, O. S. et al. The developmental transcriptome of the mosquito Aedes aegypti, an invasive species and major arbovirus vector. G3 (Bethesda) 3, 1493–1509 (2013).
pubmed: 23833213
doi: 10.1534/g3.113.006742
Matthews, B. J., McBride, C. S., DeGennaro, M., Despo, O. & Vosshall, L. B. The neurotranscriptome of the Aedes aegypti mosquito. BMC Genom 17, 1–20 (2016).
doi: 10.1186/s12864-015-2239-0
Ohlstein, B., Lavoie, C. A., Vef, O., Gateff, E. & McKearin, D. M. The drosophila cystoblast differentiation factor, benign gonial cell neoplasm, is related to DExH-box proteins and interacts genetically with bag-of-marbles. Genetics 155, 1809–1819 (2000).
pubmed: 10924476
pmcid: 1461197
doi: 10.1093/genetics/155.4.1809
Anderson, M. A. E. et al. Closing the gap to effective gene drive in Aedes aegypti by exploiting germline regulatory elements. Nat. Commun. 14, 1–9 (2023).
doi: 10.1038/s41467-023-36029-7
Kandul, N. P. et al. Assessment of a split homing based gene drive for efficient knockout of multiple genes. G3 Genes|Genomes|Genetics 10, 827–837 (2020).
pubmed: 31882406
doi: 10.1534/g3.119.400985
Guichard, A. et al. Efficient allelic-drive in Drosophila. Nat. Commun. 10, 1–10 (2019).
doi: 10.1038/s41467-019-09694-w
Otte, M. et al. Improving genetic transformation rates in honeybees. Sci. Rep. 8, 1–6 (2018).
doi: 10.1038/s41598-018-34724-w
Daniel, E. et al. ATGme: open-source web application for rare codon identification and custom DNA sequence optimization. BMC Bioinform. 16, 303 (2015).
doi: 10.1186/s12859-015-0743-5
Coates, C. J., Jasinskiene, N., Miyashiro, L. & James, A. A. Mariner transposition and transformation of the yellow fever mosquito, Aedes aegypti. Proc. Natl. Acad. Sci. 95, 3748–3751 (1998).
pubmed: 9520438
pmcid: 19908
doi: 10.1073/pnas.95.7.3748
Bassett, A. R., Tibbit, C., Ponting, C. P. & Liu, J. L. Highly efficient targeted mutagenesis of drosophila with the CRISPR/Cas9 system. Cell Rep. 4, 220–228 (2013).
pubmed: 23827738
pmcid: 3714591
doi: 10.1016/j.celrep.2013.06.020
Martins, S. et al. Germline transformation of the diamondback moth, Plutella xylostella L., using the piggyBac transposable element. Insect Mol. Biol. 21, 414–421 (2012).
pubmed: 22621377
doi: 10.1111/j.1365-2583.2012.01146.x
Liu, Y. G. & Chen, Y. High-efficiency thermal asymmetric interlaced PCR for amplification of unknown flanking sequences. Biotechniques 43, 649–656 (2007).
pubmed: 18072594
doi: 10.2144/000112601
Kistler, K. E., Vosshall, L. B. & Matthews, B. J. Genome engineering with CRISPR-Cas9 in the mosquito Aedes aegypti. Cell Rep. 11, 51–60 (2015).
pubmed: 25818303
pmcid: 4394034
doi: 10.1016/j.celrep.2015.03.009
Carvalho, D. O. et al. Mass production of genetically modified Aedes aegypti for field releases in Brazil. J. Vis. Exp. 83, 1–10 (2014).
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).
pubmed: 30809026
pmcid: 6533916
doi: 10.1038/s41587-019-0032-3
R Core Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, https://www.r-project.org/ (2021).
Wickham, H. et al. Welcome to the Tidyverse. J. Open Source Softw. 4, 1686 (2019).
doi: 10.21105/joss.01686
Wickham, H. Elegant Graphics for Data Analysis, R. Gentleman, K. Hornik, G. Parmigiani, Eds., Second (Springer Nature, 2016) (August 10, 2021).
Signorell, A. DescTools: Tools for descriptive statistics. R package version 0.99.42. https://cran.r-project.org/web/packages/DescTools/index.html (2020).
Bates, D., Mächler, M., Zurich, E., Bolker, B. M. & Walker, S. C. Fitting linear mixed-effects models using lme4. JSS J. Stat. Softw. 67 1–48 (2015).
Lenth, R. emmeans: estimated marginal means, aka least-squares means. R package version 1.4.6. https://cran.r-project.org/web/packages/emmeans/index.html (2020).
Lüdecke, D. sjPlot - data visualization for statistics in Social Science. https://doi.org/10.5281/ZENODO.2400856 (2021) (August 12, 2021).
Hartig, F. DHARMa: residual diagnostics for hierarchical (multi-level/mixed) regression models https://cran.r-project.org/web/packages/DHARMa/vignettes/DHARMa.html (2020) (August 12, 2021).