1
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Traoré N, Kientega M, Maïga H, Nebié K, Zida I, Galizi R, Kiendrebeogo E, Sow BBD, Belem AMG, Dabiré RA, Diabaté A. Genetic Diversity and Population Structure of the Invasive Oriental Fruit Fly, Bactrocera dorsalis (Diptera: Tephritidae) in Burkina Faso. Insects 2024; 15:298. [PMID: 38786854 DOI: 10.3390/insects15050298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Bactrocera dorsalis Hendel is a highly invasive horticultural pest that is of major economic importance worldwide. In Burkina Faso, it is one of the main insect pests that affects the production and exportation of mangos. Understanding the biology and the genetic dynamics of this insect pest provides crucial information for the development of effective control measures. The aim of this study was to understand the distribution, diversity, and genetic structure of B. dorsalis in Burkina Faso. Male flies were collected transversally in Burkina Faso and analyzed by PCR using 10 microsatellite markers. The results showed an abundance of B. dorsalis varying from 87 to 2986 flies per trap per day at the different sampling sites. The genetic diversity was high at all sites, with an average Shannon's Information Index (I) of 0.72 per site. The gene flow was high between study populations and ranged from 10.62 to 27.53 migrants. Bayesian admixture analysis showed no evidence of structure, while Discriminant Analysis of Principal Components identified three weakly separated clusters in the population of B. dorsalis in Burkina Faso. The results of this study could be used to optimize the effectiveness of current control interventions and to guide the implementation of new, innovative, and sustainable strategies.
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Affiliation(s)
- Nouhoun Traoré
- Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso 01 BP 545, Burkina Faso
- Laboratoire de Santé Animale Tropicale, Institut du Développement Rural, Université Nazi Boni (UNB), Bobo-Dioulasso 01 BP 1091, Burkina Faso
| | - Mahamadi Kientega
- Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso 01 BP 545, Burkina Faso
- Laboratoire de Santé Animale Tropicale, Institut du Développement Rural, Université Nazi Boni (UNB), Bobo-Dioulasso 01 BP 1091, Burkina Faso
| | - Hamidou Maïga
- Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso 01 BP 545, Burkina Faso
| | - Karim Nebié
- Institut de l'Environnement et de Recherches Agricoles (INERA), Bobo-Dioulasso 01 BP 910, Burkina Faso
| | - Issaka Zida
- Institut de l'Environnement et de Recherches Agricoles (INERA), Bobo-Dioulasso 01 BP 910, Burkina Faso
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK
| | - Emmanuel Kiendrebeogo
- Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso 01 BP 545, Burkina Faso
| | - Bazoumana B D Sow
- Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso 01 BP 545, Burkina Faso
| | - Adrien M G Belem
- Laboratoire de Santé Animale Tropicale, Institut du Développement Rural, Université Nazi Boni (UNB), Bobo-Dioulasso 01 BP 1091, Burkina Faso
| | - Remy A Dabiré
- Institut de l'Environnement et de Recherches Agricoles (INERA), Bobo-Dioulasso 01 BP 910, Burkina Faso
| | - Abdoulaye Diabaté
- Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso 01 BP 545, Burkina Faso
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2
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Hasan MN, Khalil I, Chowdhury MAB, Rahman M, Asaduzzaman M, Billah M, Banu LA, Alam MU, Ahsan A, Traore T, Uddin MJ, Galizi R, Russo I, Zumla A, Haider N. Two decades of endemic dengue in Bangladesh (2000-2022): trends, seasonality, and impact of temperature and rainfall patterns on transmission dynamics. J Med Entomol 2024; 61:345-353. [PMID: 38253990 PMCID: PMC10936167 DOI: 10.1093/jme/tjae001] [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] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 12/17/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
The objectives of this study were to compare dengue virus (DENV) cases, deaths, case-fatality ratio [CFR], and meteorological parameters between the first and the recent decades of this century (2000-2010 vs. 2011-2022) and to describe the trends, seasonality, and impact of change of temperature and rainfall patterns on transmission dynamics of dengue in Bangladesh. For the period 2000-2022, dengue cases and death data from Bangladesh's Ministry of Health and Family Welfare's website, and meteorological data from the Bangladesh Meteorological Department were analyzed. A Poisson regression model was performed to identify the impact of meteorological parameters on the monthly dengue cases. A forecast of dengue cases was performed using an autoregressive integrated moving average model. Over the past 23 yr, a total of 244,246 dengue cases were reported including 849 deaths (CFR = 0.35%). The mean annual number of dengue cases increased 8 times during the second decade, with 2,216 cases during 2000-2010 vs. 18,321 cases during 2011-2022. The mean annual number of deaths doubled (21 vs. 46), but the overall CFR has decreased by one-third (0.69% vs. 0.23%). Concurrently, the annual mean temperature increased by 0.49 °C, and rainfall decreased by 314 mm with altered precipitation seasonality. Monthly mean temperature (Incidence risk ratio [IRR]: 1.26), first-lagged rainfall (IRR: 1.08), and second-lagged rainfall (IRR: 1.17) were significantly associated with monthly dengue cases. The increased local temperature and changes in rainfall seasonality might have contributed to the increased dengue cases in Bangladesh.
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Affiliation(s)
- Mohammad Nayeem Hasan
- Department of Statistics, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Ibrahim Khalil
- Department of Livestock Services, Ministry of Fisheries and Livestock, Bangladesh, Dhaka, Bangladesh
| | | | - Mahbubur Rahman
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, UK
- Institute of Epidemiology, Disease Control and Research (IEDCR), Ministry of Health and Family Welfare, Mohakhali, Dhaka, Bangladesh
| | - Md Asaduzzaman
- School of Digital, Technologies, and Arts, Staffordshire University, Stoke on Trent ST4 2DE, UK
| | - Masum Billah
- School of Digital, Technologies, and Arts, Staffordshire University, Stoke on Trent ST4 2DE, UK
| | - Laila Arjuman Banu
- Department of Anatomy, Bangabandhu Sheik Mujib Medical University, Dhaka, Bangladesh
| | - Mahbub-Ul Alam
- Environmental Intervention Unit, International Centre for Diarrhoeal Diseases Research, Bangladesh (ICDDR,B), Dhaka 1212, Bangladesh
| | - Atik Ahsan
- Environmental Intervention Unit, International Centre for Diarrhoeal Diseases Research, Bangladesh (ICDDR,B), Dhaka 1212, Bangladesh
| | - Tieble Traore
- Emergency Preparedness and Response Programme, WHO Regional Office for Africa, Dakar Hub, Dakar, Senegal
| | - Md Jamal Uddin
- Department of Statistics, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
- Department of General Educational and Development, Daffodil International University, Dhaka, Bangladesh
| | - Roberto Galizi
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK
| | - Ilaria Russo
- School of Medicine, Faculty of Medicine and Health Sciences, Keele University, Staffordshire ST5 5BG, UK
| | - Alimuddin Zumla
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London and NIHR-BRC, University College London Hospitals, London, UK
| | - Najmul Haider
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, Staffordshire ST5 5BG, UK
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3
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D'Amato R, Taxiarchi C, Galardini M, Trusso A, Minuz RL, Grilli S, Somerville AGT, Shittu D, Khalil AS, Galizi R, Crisanti A, Simoni A, Müller R. Anti-CRISPR Anopheles mosquitoes inhibit gene drive spread under challenging behavioural conditions in large cages. Nat Commun 2024; 15:952. [PMID: 38296981 PMCID: PMC10830555 DOI: 10.1038/s41467-024-44907-x] [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: 04/18/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
CRISPR-based gene drives have the potential to spread within populations and are considered as promising vector control tools. A doublesex-targeting gene drive was able to suppress laboratory Anopheles mosquito populations in small and large cages, and it is considered for field application. Challenges related to the field-use of gene drives and the evolving regulatory framework suggest that systems able to modulate or revert the action of gene drives, could be part of post-release risk-mitigation plans. In this study, we challenge an AcrIIA4-based anti-drive to inhibit gene drive spread in age-structured Anopheles gambiae population under complex feeding and behavioural conditions. A stochastic model predicts the experimentally-observed genotype dynamics in age-structured populations in medium-sized cages and highlights the necessity of large-sized cage trials. These experiments and experimental-modelling framework demonstrate the effectiveness of the anti-drive in different scenarios, providing further corroboration for its use in controlling the spread of gene drive in Anopheles.
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Affiliation(s)
- Rocco D'Amato
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy
| | | | - Marco Galardini
- Biological Design Center, Boston University, Boston, MA, USA
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - Alessandro Trusso
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy
| | - Roxana L Minuz
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy
| | - Silvia Grilli
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Dammy Shittu
- Department of Life Sciences, Imperial College London, London, UK
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, UK
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alekos Simoni
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
| | - Ruth Müller
- Genetics and Ecology Research Centre, Polo of Genomics, Genetics and Biology (Polo GGB), Terni, Italy.
- Unit of Entomology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
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4
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Page N, Taxiarchi C, Tonge D, Kuburic J, Chesters E, Kriezis A, Kyrou K, Game L, Nolan T, Galizi R. Single-cell profiling of Anopheles gambiae spermatogenesis defines the onset of meiotic silencing and premeiotic overexpression of the X chromosome. Commun Biol 2023; 6:850. [PMID: 37582841 PMCID: PMC10427639 DOI: 10.1038/s42003-023-05224-z] [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: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 08/17/2023] Open
Abstract
Understanding development and genetic regulation in the Anopheles gambiae germline is essential to engineer effective genetic control strategies targeting this malaria mosquito vector. These include targeting the germline to induce sterility or using regulatory sequences to drive transgene expression for applications such as gene drive. However, only very few germline-specific regulatory elements have been characterised with the majority showing leaky expression. This has been shown to considerably reduce the efficiency of current genetic control strategies, which rely on regulatory elements with more tightly restricted spatial and/or temporal expression. Meiotic silencing of the sex chromosomes limits the flexibility of transgene expression to develop effective sex-linked genetic control strategies. Here, we build on our previous study, dissecting gametogenesis into four distinct cell populations, using single-cell RNA sequencing to define eight distinct cell clusters and associated germline cell-types using available marker genes. We reveal overexpression of X-linked genes in a distinct cluster of pre-meiotic cells and document the onset of meiotic silencing of the X chromosome in a subcluster of cells in the latter stages of spermatogenesis. This study provides a comprehensive dataset, characterising the expression of distinct cell types through spermatogenesis and widening the toolkit for genetic control of malaria mosquitoes.
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Affiliation(s)
- Nicole Page
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Daniel Tonge
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
| | - Jasmina Kuburic
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
| | - Emily Chesters
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
| | - Antonios Kriezis
- Department of Life Sciences, Imperial College London, London, UK
| | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, London, UK
| | - Laurence Game
- Genomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Tony Nolan
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK.
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5
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Prakash S, Racovita A, Petrucci T, Galizi R, Jaramillo A. qSanger: Quantification of Genetic Variants in Bacterial Cultures by Sanger Sequencing. Biodes Res 2023; 5:0007. [PMID: 37849461 PMCID: PMC10521659 DOI: 10.34133/bdr.0007] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/25/2022] [Indexed: 10/19/2023] Open
Abstract
Genetic variations such as mutations and recombinations arise spontaneously in all cultured organisms. Although it is possible to identify nonneutral mutations by selection or counterselection, the identification of neutral mutations in a heterogeneous population usually requires expensive and time-consuming methods such as quantitative or droplet polymerase chain reaction and high-throughput sequencing. Neutral mutations could even become dominant under changing environmental conditions enforcing transitory selection or counterselection. We propose a novel method, which we called qSanger, to quantify DNA using amplitude ratios of aligned electropherogram peaks from mixed Sanger sequencing reads. Plasmids expressing enhanced green fluorescent protein and mCherry fluorescent markers were used to validate qSanger both in vitro and in cotransformed Escherichia coli via quantitative polymerase chain reaction and fluorescence quantifications. We show that qSanger allows the quantification of genetic variants, including single-base natural polymorphisms or de novo mutations, from mixed Sanger sequencing reads, with substantial reduction of labor and costs compared to canonical approaches.
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Affiliation(s)
- Satya Prakash
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Adrian Racovita
- De Novo Synthetic Biology Lab, I2SysBio, CSIC-University of Valencia, Paterna, Spain
| | - Teresa Petrucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
| | - Alfonso Jaramillo
- School of Life Sciences, University of Warwick, Coventry, UK
- De Novo Synthetic Biology Lab, I2SysBio, CSIC-University of Valencia, Paterna, Spain
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6
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Alcalay Y, Fuchs S, Galizi R, Bernardini F, Haghighat-Khah RE, Rusch DB, Adrion JR, Hahn MW, Tortosa P, Rotenberry R, Papathanos PA. The Potential for a Released Autosomal X-Shredder Becoming a Driving-Y Chromosome and Invasively Suppressing Wild Populations of Malaria Mosquitoes. Front Bioeng Biotechnol 2021; 9:752253. [PMID: 34957064 PMCID: PMC8698249 DOI: 10.3389/fbioe.2021.752253] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
Sex-ratio distorters based on X-chromosome shredding are more efficient than sterile male releases for population suppression. X-shredding is a form of sex distortion that skews spermatogenesis of XY males towards the preferential transmission of Y-bearing gametes, resulting in a higher fraction of sons than daughters. Strains harboring X-shredders on autosomes were first developed in the malaria mosquito Anopheles gambiae, resulting in strong sex-ratio distortion. Since autosomal X-shredders are transmitted in a Mendelian fashion and can be selected against, their frequency in the population declines once releases are halted. However, unintended transfer of X-shredders to the Y-chromosome could produce an invasive meiotic drive element, that benefits from its biased transmission to the predominant male-biased offspring and its effective shielding from female negative selection. Indeed, linkage to the Y-chromosome of an active X-shredder instigated the development of the nuclease-based X-shredding system. Here, we analyze mechanisms whereby an autosomal X-shredder could become unintentionally Y-linked after release by evaluating the stability of an established X-shredder strain that is being considered for release, exploring its potential for remobilization in laboratory and wild-type genomes of An. gambiae and provide data regarding expression on the mosquito Y-chromosome. Our data suggest that an invasive X-shredder resulting from a post-release movement of such autosomal transgenes onto the Y-chromosome is unlikely.
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Affiliation(s)
- Yehonatan Alcalay
- Department of Entomology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Silke Fuchs
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, United Kingdom
| | - Federica Bernardini
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, United States
| | - Jeffrey R Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN, United States.,Department of Computer Science, Indiana University, Bloomington, IN, United States
| | - Pablo Tortosa
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), Université de La Réunion, INSERM 1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, France
| | - Rachel Rotenberry
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Philippos Aris Papathanos
- Department of Entomology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
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7
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Fuchs S, Garrood WT, Beber A, Hammond A, Galizi R, Gribble M, Morselli G, Hui TYJ, Willis K, Kranjc N, Burt A, Crisanti A, Nolan T. Resistance to a CRISPR-based gene drive at an evolutionarily conserved site is revealed by mimicking genotype fixation. PLoS Genet 2021; 17:e1009740. [PMID: 34610011 PMCID: PMC8519452 DOI: 10.1371/journal.pgen.1009740] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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: 07/23/2021] [Revised: 10/15/2021] [Accepted: 09/24/2021] [Indexed: 01/06/2023] Open
Abstract
CRISPR-based homing gene drives can be designed to disrupt essential genes whilst biasing their own inheritance, leading to suppression of mosquito populations in the laboratory. This class of gene drives relies on CRISPR-Cas9 cleavage of a target sequence and copying ('homing') therein of the gene drive element from the homologous chromosome. However, target site mutations that are resistant to cleavage yet maintain the function of the essential gene are expected to be strongly selected for. Targeting functionally constrained regions where mutations are not easily tolerated should lower the probability of resistance. Evolutionary conservation at the sequence level is often a reliable indicator of functional constraint, though the actual level of underlying constraint between one conserved sequence and another can vary widely. Here we generated a novel adult lethal gene drive (ALGD) in the malaria vector Anopheles gambiae, targeting an ultra-conserved target site in a haplosufficient essential gene (AGAP029113) required during mosquito development, which fulfils many of the criteria for the target of a population suppression gene drive. We then designed a selection regime to experimentally assess the likelihood of generation and subsequent selection of gene drive resistant mutations at its target site. We simulated, in a caged population, a scenario where the gene drive was approaching fixation, where selection for resistance is expected to be strongest. Continuous sampling of the target locus revealed that a single, restorative, in-frame nucleotide substitution was selected. Our findings show that ultra-conservation alone need not be predictive of a site that is refractory to target site resistance. Our strategy to evaluate resistance in vivo could help to validate candidate gene drive targets for their resilience to resistance and help to improve predictions of the invasion dynamics of gene drives in field populations.
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Affiliation(s)
- Silke Fuchs
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - William T. Garrood
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Anna Beber
- Department of Biology, University of Padua, Padua, Italy
| | - Andrew Hammond
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, United States of America
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Matthew Gribble
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Giulia Morselli
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tin-Yu J. Hui
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Katie Willis
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Molecular Medicine, University of Padua, Padua, Italy
- * E-mail: (AC); (TN)
| | - Tony Nolan
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail: (AC); (TN)
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8
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Annas GJ, Beisel CL, Clement K, Crisanti A, Francis S, Galardini M, Galizi R, Grünewald J, Immobile G, Khalil AS, Müller R, Pattanayak V, Petri K, Paul L, Pinello L, Simoni A, Taxiarchi C, Joung JK. A Code of Ethics for Gene Drive Research. CRISPR J 2021; 4:19-24. [PMID: 33571044 PMCID: PMC7898401 DOI: 10.1089/crispr.2020.0096] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Gene drives hold promise for use in controlling insect vectors of diseases, agricultural pests, and for conservation of ecosystems against invasive species. At the same time, this technology comes with potential risks that include unknown downstream effects on entire ecosystems as well as the accidental or nefarious spread of organisms that carry the gene drive machinery. A code of ethics can be a useful tool for all parties involved in the development and regulation of gene drives and can be used to help ensure that a balanced analysis of risks, benefits, and values is taken into consideration in the interest of society and humanity. We have developed a code of ethics for gene drive research with the hope that this code will encourage the development of an international framework that includes ethical guidance of gene drive research and is incorporated into scientific practice by gaining broad agreement and adherence.
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Affiliation(s)
- George J Annas
- Center for Health Law, Ethics & Human Rights, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Chase L Beisel
- Helmholtz Institute of RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Kendell Clement
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, United Kingdom.,Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Stacy Francis
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marco Galardini
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, United Kingdom
| | - Julian Grünewald
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Greta Immobile
- Polo d'Innovazione Genomica Genetica e Biologia SCaRL, Siena, Italy
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Ruth Müller
- Polo d'Innovazione Genomica Genetica e Biologia SCaRL, Siena, Italy.,Unit Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Vikram Pattanayak
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Karl Petri
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ligi Paul
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alekos Simoni
- Polo d'Innovazione Genomica Genetica e Biologia SCaRL, Siena, Italy
| | | | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
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9
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Prakash S, Racovita A, Varela C, Walsh M, Galizi R, Isalan M, Jaramillo A. Engineering Adaptive Gene Circuits in Bacteria Mastering Game Playing by Reinforcement Learning. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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10
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Hammond A, Karlsson X, Morianou I, Kyrou K, Beaghton A, Gribble M, Kranjc N, Galizi R, Burt A, Crisanti A, Nolan T. Regulating the expression of gene drives is key to increasing their invasive potential and the mitigation of resistance. PLoS Genet 2021; 17:e1009321. [PMID: 33513149 PMCID: PMC7886172 DOI: 10.1371/journal.pgen.1009321] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [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: 07/29/2020] [Revised: 02/16/2021] [Accepted: 12/22/2020] [Indexed: 12/27/2022] Open
Abstract
Homing-based gene drives use a germline source of nuclease to copy themselves at specific target sites in a genome and bias their inheritance. Such gene drives can be designed to spread and deliberately suppress populations of malaria mosquitoes by impairing female fertility. However, strong unintended fitness costs of the drive and a propensity to generate resistant mutations can limit a gene drive’s potential to spread. Alternative germline regulatory sequences in the drive element confer improved fecundity of carrier individuals and reduced propensity for target site resistance. This is explained by reduced rates of end-joining repair of DNA breaks from parentally deposited nuclease in the embryo, which can produce heritable mutations that reduce gene drive penetrance. We tracked the generation and selection of resistant mutations over the course of a gene drive invasion of a population. Improved gene drives show faster invasion dynamics, increased suppressive effect and later onset of target site resistance. Our results show that regulation of nuclease expression is as important as the choice of target site when developing a robust homing-based gene drive for population suppression. Gene drives are selfish genetic elements that are able to drastically bias their own inheritance. They can rapidly invade populations, even starting from a very low frequency. Recent advances have allowed the engineering of gene drives deliberately designed to spread genetic traits of choice into populations of malaria-transmitting mosquito species–for example traits that impair a mosquito’s ability to reproduce or its ability to transmit parasites. The class of gene drive in question uses a very precise cutting and copying mechanism, termed ‘homing’, that allows it to increase its numbers in the cells that go on to form sperm or eggs, thereby increasing the chances that a copy of the gene drive is transmitted to offspring. However, while this type of gene drive can rapidly invade a mosquito population, mosquitoes can also eventually become resistant to the gene drive in some cases. Here we show that restricting the cutting activity of the gene drive to the germline tissue is crucial to maintaining its potency and we illustrate how failure to restrict this activity can lead to the generation of mutations that can make mosquitoes resistant to the gene drive.
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Affiliation(s)
- Andrew Hammond
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Xenia Karlsson
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Ioanna Morianou
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Andrea Beaghton
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Matthew Gribble
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, United Kingdom
- University of Padova, Padova, Italy
- * E-mail: (AC); (TN)
| | - Tony Nolan
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail: (AC); (TN)
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11
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Rocha EM, Katak RDM, Campos de Oliveira J, Araujo MDS, Carlos BC, Galizi R, Tripet F, Marinotti O, Souza-Neto JA. Vector-Focused Approaches to Curb Malaria Transmission in the Brazilian Amazon: An Overview of Current and Future Challenges and Strategies. Trop Med Infect Dis 2020; 5:E161. [PMID: 33092228 PMCID: PMC7709627 DOI: 10.3390/tropicalmed5040161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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: 09/18/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 01/05/2023] Open
Abstract
In Brazil, malaria transmission is mostly confined to the Amazon, where substantial progress has been made towards disease control in the past decade. Vector control has been historically considered a fundamental part of the main malaria control programs implemented in Brazil. However, the conventional vector-control tools have been insufficient to control or eliminate local vector populations due to the complexity of the Amazonian rainforest environment and ecological features of malaria vector species in the Amazon, especially Anopheles darlingi. Malaria elimination in Brazil and worldwide eradication will require a combination of conventional and new approaches that takes into account the regional specificities of vector populations and malaria transmission dynamics. Here we present an overview on both conventional and novel promising vector-focused tools to curb malaria transmission in the Brazilian Amazon. If well designed and employed, vector-based approaches may improve the implementation of malaria-control programs, particularly in remote or difficult-to-access areas and in regions where existing interventions have been unable to eliminate disease transmission. However, much effort still has to be put into research expanding the knowledge of neotropical malaria vectors to set the steppingstones for the optimization of conventional and development of innovative vector-control tools.
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Affiliation(s)
- Elerson Matos Rocha
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Amazonas—PPGBIOTEC/UFAM, Manaus 69067-005, Brazil; (E.M.R.); (R.d.M.K.); (J.C.d.O.)
| | - Ricardo de Melo Katak
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Amazonas—PPGBIOTEC/UFAM, Manaus 69067-005, Brazil; (E.M.R.); (R.d.M.K.); (J.C.d.O.)
| | - Juan Campos de Oliveira
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Amazonas—PPGBIOTEC/UFAM, Manaus 69067-005, Brazil; (E.M.R.); (R.d.M.K.); (J.C.d.O.)
| | - Maisa da Silva Araujo
- Laboratory of Medical Entomology, Oswaldo Cruz Foundation, FIOCRUZ RONDONIA, Porto Velho, RO 76812-245, Brazil;
| | - Bianca Cechetto Carlos
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil;
- Central Multiuser Laboratory, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
| | - Roberto Galizi
- Centre of Applied Entomology and Parasitology, School of Life Sciences, Keele University, Staffordshire ST5 5GB, UK; (R.G.); (F.T.)
| | - Frederic Tripet
- Centre of Applied Entomology and Parasitology, School of Life Sciences, Keele University, Staffordshire ST5 5GB, UK; (R.G.); (F.T.)
| | | | - Jayme A. Souza-Neto
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil;
- Central Multiuser Laboratory, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
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12
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Galizi R, Duncan JN, Rostain W, Quinn CM, Storch M, Kushwaha M, Jaramillo A. Engineered RNA-Interacting CRISPR Guide RNAs for Genetic Sensing and Diagnostics. CRISPR J 2020; 3:398-408. [PMID: 33095053 DOI: 10.1089/crispr.2020.0029] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CRISPR guide RNAs (gRNAs) can be programmed with relative ease to allow the genetic editing of nearly any DNA or RNA sequence. Here, we propose novel molecular architectures to achieve RNA-dependent modulation of CRISPR activity in response to specific RNA molecules. We designed and tested, in both living Escherichia coli cells and cell-free assays for rapid prototyping, cis-repressed RNA-interacting guide RNA (igRNA) that switch to their active state only upon interaction with small RNA fragments or long RNA transcripts, including pathogen-derived mRNAs of medical relevance such as the human immunodeficiency virus infectivity factor. The proposed CRISPR-igRNAs are fully customizable and easily adaptable to the majority if not all the available CRISPR-Cas variants to modulate a variety of genetic functions in response to specific cellular conditions, providing orthogonal activation and increased specificity. We thereby foresee a large scope of application for therapeutic, diagnostic, and biotech applications in both prokaryotic and eukaryotic systems.
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Affiliation(s)
- Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, United Kingdom
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - John N Duncan
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - William Rostain
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Charlotte M Quinn
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Marko Storch
- Department of Life Sciences, Imperial College London, London, United Kingdom
- London Biofoundry, Imperial College London, London, United Kingdom
| | - Manish Kushwaha
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Université Paris-Saclay, INRAE, AgroParisTech, MIcalis Institute, Paris, France
| | - Alfonso Jaramillo
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
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13
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Haghighat-Khah RE, Sharma A, Wunderlich MR, Morselli G, Marston LA, Bamikole C, Hall A, Kranjc N, Taxiarchi C, Sharakhov I, Galizi R. Cellular mechanisms regulating synthetic sex ratio distortion in the Anopheles gambiae germline. Pathog Glob Health 2020; 114:370-378. [PMID: 33043870 PMCID: PMC7580827 DOI: 10.1080/20477724.2020.1803628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Genetic control strategies aimed to bias the sex of progenies towards males present a promising new paradigm to eliminate malaria-transmitting mosquitoes. A synthetic sex-ratio distortion (SD) system was successfully engineered in Anopheles gambiae by exploiting the meiotic activity of the I-PpoI endonuclease targeting ribosomal DNA (rDNA) repeats, exclusively located on the X chromosome. Males carrying the SD construct produce highly male-biased progenies without evident reduction in fertility. In this study, we investigated the fate of X and Y chromosomes in these SD males and found that ratios of mature X:Y-bearing sperm were comparable to wild-type insects, indicating absence of selection mechanisms during sperm maturation. We therefore tested the effect of meiotic cleavage of both X and Y chromosomes in a lab-generated SD strain carrying rDNA on both sex chromosomes, showing fertility comparable to wild-type and a reduced male-bias compared to SD males in which only the X is targeted. Exposure of Y-linked rDNA to I-PpoI cleavage for consecutive generations rapidly restored the male-bias to typical high frequencies, indicating a correlation between the number of cleavable targets in each sex chromosome and the sex-ratios found in the progeny. Altogether our results indicate that meiotic cleavage of rDNA repeats, located in the sex chromosomes of A. gambiae SD males, affects the competitiveness of mature sperm to fertilize the female oocyte, thereby generating sex-biased progenies. We also show that the presence of rDNA copies on the Y chromosome does not impair the effectiveness of engineered synthetic SD systems for the control of human malaria mosquitoes.
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Affiliation(s)
| | - Atashi Sharma
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | | | - Giulia Morselli
- Department of Life Sciences, Imperial College London, London, UK
| | | | | | - Ann Hall
- Department of Life Sciences, Imperial College London, London, UK
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Igor Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Department of Cytology and Genetics, Tomsk State University, Tomsk, Russian Federation
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London, UK
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, UK
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14
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Simoni A, Hammond AM, Beaghton AK, Galizi R, Taxiarchi C, Kyrou K, Meacci D, Gribble M, Morselli G, Burt A, Nolan T, Crisanti A. A male-biased sex-distorter gene drive for the human malaria vector Anopheles gambiae. Nat Biotechnol 2020; 38:1054-1060. [PMID: 32393821 PMCID: PMC7473848 DOI: 10.1038/s41587-020-0508-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [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: 08/03/2019] [Accepted: 04/01/2020] [Indexed: 12/21/2022]
Abstract
Only female insects transmit diseases such as malaria, dengue and Zika; therefore, control methods that bias the sex ratio of insect offspring have long been sought. Genetic elements such as sex-chromosome drives can distort sex ratios to produce unisex populations that eventually collapse, but the underlying molecular mechanisms are unknown. We report a male-biased sex-distorter gene drive (SDGD) in the human malaria vector Anopheles gambiae. We induced super-Mendelian inheritance of the X-chromosome-shredding I-PpoI nuclease by coupling this to a CRISPR-based gene drive inserted into a conserved sequence of the doublesex (dsx) gene. In modeling of invasion dynamics, SDGD was predicted to have a quicker impact on female mosquito populations than previously developed gene drives targeting female fertility. The SDGD at the dsx locus led to a male-only population from a 2.5% starting allelic frequency in 10–14 generations, with population collapse and no selection for resistance. Our results support the use of SDGD for malaria vector control. A sex-distorter gene drive causes population collapse in the malaria mosquito.
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Affiliation(s)
- Alekos Simoni
- Department of Life Sciences, Imperial College London, London, UK.,Polo d'Innovazione Genomica, Genetica e Biologia, Terni, Italy
| | - Andrew M Hammond
- Department of Life Sciences, Imperial College London, London, UK.,W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA
| | | | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London, UK.,Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
| | | | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, London, UK
| | - Dario Meacci
- Department of Life Sciences, Imperial College London, London, UK
| | - Matthew Gribble
- Department of Life Sciences, Imperial College London, London, UK
| | - Giulia Morselli
- Department of Life Sciences, Imperial College London, London, UK
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, UK
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, London, UK.,Liverpool School of Tropical Medicine, Liverpool, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, UK. .,Department of Molecular Medicine, University of Padova, Padova, Italy.
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15
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Bernardini F, Kriezis A, Galizi R, Nolan T, Crisanti A. Introgression of a synthetic sex ratio distortion system from Anopheles gambiae into Anopheles arabiensis. Sci Rep 2019; 9:5158. [PMID: 30914785 PMCID: PMC6435806 DOI: 10.1038/s41598-019-41646-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 01/04/2019] [Accepted: 03/14/2019] [Indexed: 12/04/2022] Open
Abstract
I-PpoI is a homing endonuclease that has a high cleavage activity and specificity for a conserved sequence within the ribosomal rDNA repeats, located in a single cluster on the Anopheles gambiae X chromosome. This property has been exploited to develop a synthetic sex ratio distortion system in this mosquito species. When I-PpoI is expressed from a transgene during spermatogenesis in mosquitoes, the paternal X chromosome is shredded and only Y chromosome-bearing sperm are viable, resulting in a male-biased sex ratio of >95% in the progeny. These distorter male mosquitoes can efficiently suppress caged wild-type populations, providing a powerful tool for vector control strategies. Given that malaria mosquito vectors belong to a species complex comprising at least two major vectors, we investigated whether the sex distorter I-PpoI, originally integrated in the A. gambiae genome, could be transferred via introgression to the sibling vector species Anopheles arabiensis. In compliance with Haldane’s rule, F1 hybrid male sterility is known to occur in all intercrosses among members of the Anopheles gambiae complex. A scheme based on genetic crosses and transgene selection was used to bypass F1 hybrid male sterility and introgress the sex distorter I-PpoI into the A. arabiensis genetic background. Our data suggest that this sex distortion technique can be successfully applied to target A. arabiensis mosquitoes.
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Affiliation(s)
- Federica Bernardini
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Antonios Kriezis
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
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16
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Galizi R, Jaramillo A. Engineering CRISPR guide RNA riboswitches for in vivo applications. Curr Opin Biotechnol 2019; 55:103-113. [PMID: 30265865 DOI: 10.1016/j.copbio.2018.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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] [Received: 07/06/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 02/07/2023]
Abstract
CRISPR-based genome editing provides a simple and scalable toolbox for a variety of therapeutic and biotechnology applications. Whilst the fundamental properties of CRISPR proved easily transferable from the native prokaryotic hosts to eukaryotic and multicellular organisms, the tight control of the CRISPR-editing activity remains a major challenge. Here we summarise recent developments of CRISPR and riboswitch technologies and recommend novel functionalised synthetic-gRNA (sgRNA) designs to achieve inducible and spatiotemporal regulation of CRISPR-based genetic editors in response to cellular or extracellular stimuli. We believe that future advances of these tools will have major implications for both basic and applied research, spanning from fundamental genetic studies and synthetic biology to genetic editing and gene therapy.
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Affiliation(s)
- Roberto Galizi
- Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom; ISSB, CNRS, Univ Evry, CEA, Université Paris-Saclay, 91025 Evry, France; Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, 46980 Paterna, Spain.
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17
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Kyrou K, Hammond AM, Galizi R, Kranjc N, Burt A, Beaghton AK, Nolan T, Crisanti A. A CRISPR-Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes. Nat Biotechnol 2018; 36:1062-1066. [PMID: 30247490 PMCID: PMC6871539 DOI: 10.1038/nbt.4245] [Citation(s) in RCA: 441] [Impact Index Per Article: 73.5] [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: 04/06/2018] [Accepted: 08/03/2018] [Indexed: 01/13/2023]
Abstract
Complete population collapse of malaria vector Anopheles gambiae in cages is achieved using a gene drive that targets doublesex. In the human malaria vector Anopheles gambiae, the gene doublesex (Agdsx) encodes two alternatively spliced transcripts, dsx-female (AgdsxF) and dsx-male (AgdsxM), that control differentiation of the two sexes. The female transcript, unlike the male, contains an exon (exon 5) whose sequence is highly conserved in all Anopheles mosquitoes so far analyzed. We found that CRISPR–Cas9-targeted disruption of the intron 4–exon 5 boundary aimed at blocking the formation of functional AgdsxF did not affect male development or fertility, whereas females homozygous for the disrupted allele showed an intersex phenotype and complete sterility. A CRISPR–Cas9 gene drive construct targeting this same sequence spread rapidly in caged mosquitoes, reaching 100% prevalence within 7–11 generations while progressively reducing egg production to the point of total population collapse. Owing to functional constraint of the target sequence, no selection of alleles resistant to the gene drive occurred in these laboratory experiments. Cas9-resistant variants arose in each generation at the target site but did not block the spread of the drive.
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Affiliation(s)
- Kyros Kyrou
- Department of Life Sciences, Imperial College London, UK
| | | | - Roberto Galizi
- Department of Life Sciences, Imperial College London, UK
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, UK
| | - Austin Burt
- Department of Life Sciences, Imperial College London, UK
| | | | - Tony Nolan
- Department of Life Sciences, Imperial College London, UK
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18
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Abstract
Self-propagating gene drive technologies have a number of desirable characteristics that warrant their development for the control of insect pest and vector populations, such as the malaria-transmitting mosquitoes. Theoretically easy to deploy and self-sustaining, these tools may be used to generate cost-effective interventions that benefit society without obvious bias related to wealth, age or education. Their species-specific design offers the potential to reduce environmental risks and aim to be compatible and complementary with other control strategies, potentially expediting the elimination and eradication of malaria. A number of strategies have been proposed for gene-drive based control of the malaria mosquito and recent demonstrations have shown proof-of-principle in the laboratory. Though several technical, ethical and regulatory challenges remain, none appear insurmountable if research continues in a step-wise and open manner.
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Affiliation(s)
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London, UK
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19
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Hammond AM, Kyrou K, Bruttini M, North A, Galizi R, Karlsson X, Kranjc N, Carpi FM, D’Aurizio R, Crisanti A, Nolan T. The creation and selection of mutations resistant to a gene drive over multiple generations in the malaria mosquito. PLoS Genet 2017; 13:e1007039. [PMID: 28976972 PMCID: PMC5648257 DOI: 10.1371/journal.pgen.1007039] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [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: 08/08/2017] [Revised: 10/19/2017] [Accepted: 09/20/2017] [Indexed: 11/19/2022] Open
Abstract
Gene drives have enormous potential for the control of insect populations of medical and agricultural relevance. By preferentially biasing their own inheritance, gene drives can rapidly introduce genetic traits even if these confer a negative fitness effect on the population. We have recently developed gene drives based on CRISPR nuclease constructs that are designed to disrupt key genes essential for female fertility in the malaria mosquito. The construct copies itself and the associated genetic disruption from one homologous chromosome to another during gamete formation, a process called homing that ensures the majority of offspring inherit the drive. Such drives have the potential to cause long-lasting, sustainable population suppression, though they are also expected to impose a large selection pressure for resistance in the mosquito. One of these population suppression gene drives showed rapid invasion of a caged population over 4 generations, establishing proof of principle for this technology. In order to assess the potential for the emergence of resistance to the gene drive in this population we allowed it to run for 25 generations and monitored the frequency of the gene drive over time. Following the initial increase of the gene drive we observed a gradual decrease in its frequency that was accompanied by the spread of small, nuclease-induced mutations at the target gene that are resistant to further cleavage and restore its functionality. Such mutations showed rates of increase consistent with positive selection in the face of the gene drive. Our findings represent the first documented example of selection for resistance to a synthetic gene drive and lead to important design recommendations and considerations in order to mitigate for resistance in future gene drive applications.
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Affiliation(s)
- Andrew M. Hammond
- Dept. of Life Sciences, Imperial College London, London, United Kingdom
| | - Kyros Kyrou
- Dept. of Life Sciences, Imperial College London, London, United Kingdom
| | - Marco Bruttini
- Polo d’Innovazione Genomica, Genetica e Biologia, Siena, Italy
| | - Ace North
- Department of Zoology, University of Oxford, Oxford, England
| | - Roberto Galizi
- Dept. of Life Sciences, Imperial College London, London, United Kingdom
| | - Xenia Karlsson
- Dept. of Life Sciences, Imperial College London, London, United Kingdom
| | - Nace Kranjc
- Dept. of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Romina D’Aurizio
- Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics (IIT), CNR, Pisa, Italy
| | - Andrea Crisanti
- Dept. of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail: (AC); (TN)
| | - Tony Nolan
- Dept. of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail: (AC); (TN)
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20
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Bernardini F, Galizi R, Wunderlich M, Taxiarchi C, Kranjc N, Kyrou K, Hammond A, Nolan T, Lawniczak MNK, Papathanos PA, Crisanti A, Windbichler N. Cross-Species Y Chromosome Function Between Malaria Vectors of the Anopheles gambiae Species Complex. Genetics 2017; 207:729-740. [PMID: 28860320 PMCID: PMC5629335 DOI: 10.1534/genetics.117.300221] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 06/19/2017] [Accepted: 08/21/2017] [Indexed: 02/03/2023] Open
Abstract
Y chromosome function, structure and evolution is poorly understood in many species, including the Anopheles genus of mosquitoes-an emerging model system for studying speciation that also represents the major vectors of malaria. While the Anopheline Y had previously been implicated in male mating behavior, recent data from the Anopheles gambiae complex suggests that, apart from the putative primary sex-determiner, no other genes are conserved on the Y. Studying the functional basis of the evolutionary divergence of the Y chromosome in the gambiae complex is complicated by complete F1 male hybrid sterility. Here, we used an F1 × F0 crossing scheme to overcome a severe bottleneck of male hybrid incompatibilities that enabled us to experimentally purify a genetically labeled A. gambiae Y chromosome in an A. arabiensis background. Whole genome sequencing (WGS) confirmed that the A. gambiae Y retained its original sequence content in the A. arabiensis genomic background. In contrast to comparable experiments in Drosophila, we find that the presence of a heterospecific Y chromosome has no significant effect on the expression of A. arabiensis genes, and transcriptional differences can be explained almost exclusively as a direct consequence of transcripts arising from sequence elements present on the A. gambiae Y chromosome itself. We find that Y hybrids show no obvious fertility defects, and no substantial reduction in male competitiveness. Our results demonstrate that, despite their radically different structure, Y chromosomes of these two species of the gambiae complex that diverged an estimated 1.85 MYA function interchangeably, thus indicating that the Y chromosome does not harbor loci contributing to hybrid incompatibility. Therefore, Y chromosome gene flow between members of the gambiae complex is possible even at their current level of divergence. Importantly, this also suggests that malaria control interventions based on sex-distorting Y drive would be transferable, whether intentionally or contingent, between the major malaria vector species.
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Affiliation(s)
- Federica Bernardini
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Mariana Wunderlich
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Chrysanthi Taxiarchi
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Andrew Hammond
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Mara N K Lawniczak
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, United Kingdom
| | - Philippos Aris Papathanos
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132, Italy
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, United Kingdom
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21
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Werther R, Hallinan JP, Lambert AR, Havens K, Pogson M, Jarjour J, Galizi R, Windbichler N, Crisanti A, Nolan T, Stoddard BL. Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity. Nucleic Acids Res 2017; 45:8621-8634. [PMID: 28637173 PMCID: PMC5737575 DOI: 10.1093/nar/gkx544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 04/27/2017] [Revised: 06/02/2017] [Accepted: 06/12/2017] [Indexed: 12/11/2022] Open
Abstract
The retargeting of protein-DNA specificity, outside of extremely modular DNA binding proteins such as TAL effectors, has generally proved to be quite challenging. Here, we describe structural analyses of five different extensively retargeted variants of a single homing endonuclease, that have been shown to function efficiently in ex vivo and in vivo applications. The redesigned proteins harbor mutations at up to 53 residues (18%) of their amino acid sequence, primarily distributed across the DNA binding surface, making them among the most significantly reengineered ligand-binding proteins to date. Specificity is derived from the combined contributions of DNA-contacting residues and of neighboring residues that influence local structural organization. Changes in specificity are facilitated by the ability of all those residues to readily exchange both form and function. The fidelity of recognition is not precisely correlated with the fraction or total number of residues in the protein-DNA interface that are actually involved in DNA contacts, including directional hydrogen bonds. The plasticity of the DNA-recognition surface of this protein, which allows substantial retargeting of recognition specificity without requiring significant alteration of the surrounding protein architecture, reflects the ability of the corresponding genetic elements to maintain mobility and persistence in the face of genetic drift within potential host target sites.
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Affiliation(s)
- Rachel Werther
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Jazmine P. Hallinan
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Abigail R. Lambert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Kyle Havens
- Bluebird Bio Inc., Suite 207 1616 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Mark Pogson
- Bluebird Bio Inc., Suite 207 1616 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Jordan Jarjour
- Bluebird Bio Inc., Suite 207 1616 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Roberto Galizi
- Imperial College of London, Department of Life Sciences, South Kensington Campus, London SW7 2AZ, UK
| | - Nikolai Windbichler
- Imperial College of London, Department of Life Sciences, South Kensington Campus, London SW7 2AZ, UK
| | - Andrea Crisanti
- Imperial College of London, Department of Life Sciences, South Kensington Campus, London SW7 2AZ, UK
| | - Tony Nolan
- Imperial College of London, Department of Life Sciences, South Kensington Campus, London SW7 2AZ, UK
| | - Barry L. Stoddard
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
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22
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Hall AB, Papathanos PA, Sharma A, Cheng C, Akbari OS, Assour L, Bergman NH, Cagnetti A, Crisanti A, Dottorini T, Fiorentini E, Galizi R, Hnath J, Jiang X, Koren S, Nolan T, Radune D, Sharakhova MV, Steele A, Timoshevskiy VA, Windbichler N, Zhang S, Hahn MW, Phillippy AM, Emrich SJ, Sharakhov IV, Tu ZJ, Besansky NJ. Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. Proc Natl Acad Sci U S A 2016; 113:E2114-23. [PMID: 27035980 PMCID: PMC4839409 DOI: 10.1073/pnas.1525164113] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [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: 11/18/2022] Open
Abstract
Y chromosomes control essential male functions in many species, including sex determination and fertility. However, because of obstacles posed by repeat-rich heterochromatin, knowledge of Y chromosome sequences is limited to a handful of model organisms, constraining our understanding of Y biology across the tree of life. Here, we leverage long single-molecule sequencing to determine the content and structure of the nonrecombining Y chromosome of the primary African malaria mosquito, Anopheles gambiae We find that the An. gambiae Y consists almost entirely of a few massively amplified, tandemly arrayed repeats, some of which can recombine with similar repeats on the X chromosome. Sex-specific genome resequencing in a recent species radiation, the An. gambiae complex, revealed rapid sequence turnover within An. gambiae and among species. Exploiting 52 sex-specific An. gambiae RNA-Seq datasets representing all developmental stages, we identified a small repertoire of Y-linked genes that lack X gametologs and are not Y-linked in any other species except An. gambiae, with the notable exception of YG2, a candidate male-determining gene. YG2 is the only gene conserved and exclusive to the Y in all species examined, yet sequence similarity to YG2 is not detectable in the genome of a more distant mosquito relative, suggesting rapid evolution of Y chromosome genes in this highly dynamic genus of malaria vectors. The extensive characterization of the An. gambiae Y provides a long-awaited foundation for studying male mosquito biology, and will inform novel mosquito control strategies based on the manipulation of Y chromosomes.
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Affiliation(s)
- Andrew Brantley Hall
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Philippos-Aris Papathanos
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Atashi Sharma
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Changde Cheng
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Omar S Akbari
- Department of Entomology, Riverside Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Lauren Assour
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702
| | - Alessia Cagnetti
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
| | - Andrea Crisanti
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy; Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Tania Dottorini
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Elisa Fiorentini
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jonathan Hnath
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702
| | - Xiaofang Jiang
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Diane Radune
- National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Laboratory of Evolutionary Cytogenetics, Tomsk State University, Tomsk 634050, Russia
| | - Aaron Steele
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Vladimir A Timoshevskiy
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Simo Zhang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405
| | - Matthew W Hahn
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405; Department of Biology, Indiana University, Bloomington, IN 47405
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Scott J Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556; Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Igor V Sharakhov
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Laboratory of Evolutionary Cytogenetics, Tomsk State University, Tomsk 634050, Russia;
| | - Zhijian Jake Tu
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Nora J Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556;
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23
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Hammond A, Galizi R, Kyrou K, Simoni A, Siniscalchi C, Katsanos D, Gribble M, Baker D, Marois E, Russell S, Burt A, Windbichler N, Crisanti A, Nolan T. A CRISPR-Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae. Nat Biotechnol 2015; 34:78-83. [PMID: 26641531 PMCID: PMC4913862 DOI: 10.1038/nbt.3439] [Citation(s) in RCA: 658] [Impact Index Per Article: 73.1] [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: 09/12/2015] [Accepted: 11/23/2015] [Indexed: 01/20/2023]
Abstract
Gene drive systems that enable super-Mendelian inheritance of a transgene have the potential to modify insect populations over a timeframe of a few years. We describe CRISPR-Cas9 endonuclease constructs that function as gene drive systems in Anopheles gambiae, the main vector for malaria. We identified three genes (AGAP005958, AGAP011377 and AGAP007280) that confer a recessive female-sterility phenotype upon disruption, and inserted into each locus CRISPR-Cas9 gene drive constructs designed to target and edit each gene. For each targeted locus we observed a strong gene drive at the molecular level, with transmission rates to progeny of 91.4 to 99.6%. Population modeling and cage experiments indicate that a CRISPR-Cas9 construct targeting one of these loci, AGAP007280, meets the minimum requirement for a gene drive targeting female reproduction in an insect population. These findings could expedite the development of gene drives to suppress mosquito populations to levels that do not support malaria transmission.
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Affiliation(s)
- Andrew Hammond
- Department of Life Sciences, Imperial College London, London, UK
| | - Roberto Galizi
- Department of Life Sciences, Imperial College London, London, UK
| | - Kyros Kyrou
- Department of Life Sciences, Imperial College London, London, UK
| | - Alekos Simoni
- Department of Life Sciences, Imperial College London, London, UK
| | - Carla Siniscalchi
- Dipartimento di Medicina Sperimentale Via Gambuli, Centro di Genomica Funzionale, University of Perugia, Perugia, Italy
| | | | - Matthew Gribble
- Department of Life Sciences, Imperial College London, London, UK
| | - Dean Baker
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Eric Marois
- INSERM U963, CNRS UPR9022, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Austin Burt
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, UK
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, London, UK
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24
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Lunghi M, Galizi R, Magini A, Carruthers VB, Di Cristina M. Expression of the glycolytic enzymes enolase and lactate dehydrogenase during the early phase ofToxoplasmadifferentiation is regulated by an intron retention mechanism. Mol Microbiol 2015; 96:1159-75. [DOI: 10.1111/mmi.12999] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Matteo Lunghi
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Perugia Italy
| | - Roberto Galizi
- Department of Experimental Medicine; University of Perugia; Perugia Italy
| | - Alessandro Magini
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Perugia Italy
| | - Vern B. Carruthers
- Department of Microbiology and Immunology; University of Michigan Medical School; Ann Arbor MI USA
| | - Manlio Di Cristina
- Department of Chemistry, Biology and Biotechnology; University of Perugia; Perugia Italy
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25
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Castellano L, Rizzi E, Krell J, Di Cristina M, Galizi R, Mori A, Tam J, De Bellis G, Stebbing J, Crisanti A, Nolan T. The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNAs. BMC Genomics 2015; 16:100. [PMID: 25766668 PMCID: PMC4345017 DOI: 10.1186/s12864-015-1257-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 01/19/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Small RNAs include different classes essential for endogenous gene regulation and cellular defence against genomic parasites. However, a comprehensive analysis of the small RNA pathways in the germline of the mosquito Anopheles gambiae has never been performed despite their potential relevance to reproductive capacity in this malaria vector. RESULTS We performed small RNA deep sequencing during larval and adult gonadogenesis and find that they predominantly express four classes of regulatory small RNAs. We identified 45 novel miRNA precursors some of which were sex-biased and gonad-enriched , nearly doubling the number of previously known miRNA loci. We also determine multiple genomic clusters of 24-30 nt Piwi-interacting RNAs (piRNAs) that map to transposable elements (TEs) and 3'UTR of protein coding genes. Unusually, many TEs and the 3'UTR of some endogenous genes produce an abundant peak of 29-nt small RNAs with piRNA-like characteristics. Moreover, both sense and antisense piRNAs from TEs in both Anopheles gambiae and Drosophila melanogaster reveal novel features of piRNA sequence bias. We also discovered endogenous small interfering RNAs (endo-siRNAs) that map to overlapping transcripts and TEs. CONCLUSIONS This is the first description of the germline miRNome in a mosquito species and should prove a valuable resource for understanding gene regulation that underlies gametogenesis and reproductive capacity. We also provide the first evidence of a piRNA pathway that is active against transposons in the germline and our findings suggest novel piRNA sequence bias. The contribution of small RNA pathways to germline TE regulation and genome defence in general is an important finding for approaches aimed at manipulating mosquito populations through the use of selfish genetic elements.
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Affiliation(s)
- Leandro Castellano
- Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK.
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate, Milan, Italy.
| | - Jonathan Krell
- Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK.
| | - Manlio Di Cristina
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy.
| | - Roberto Galizi
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
| | - Ayako Mori
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
| | - Janis Tam
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
| | - Gianluca De Bellis
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate, Milan, Italy.
| | - Justin Stebbing
- Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK.
| | - Andrea Crisanti
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
- Dipartimento di Medicina Sperimentale Via Gambuli, Centro di Genomica Funzionale, University of Perugia, 06132, Perugia, Italy.
| | - Tony Nolan
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
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26
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Galizi R, Doyle LA, Menichelli M, Bernardini F, Deredec A, Burt A, Stoddard BL, Windbichler N, Crisanti A. A synthetic sex ratio distortion system for the control of the human malaria mosquito. Nat Commun 2014; 5:3977. [PMID: 24915045 PMCID: PMC4057611 DOI: 10.1038/ncomms4977] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/28/2014] [Indexed: 01/09/2023] Open
Abstract
It has been theorized that inducing extreme reproductive sex ratios could be a method to suppress or eliminate pest populations. Limited knowledge about the genetic makeup and mode of action of naturally occurring sex distorters and the prevalence of co-evolving suppressors has hampered their use for control. Here we generate a synthetic sex distortion system by exploiting the specificity of the homing endonuclease I-PpoI, which is able to selectively cleave ribosomal gene sequences of the malaria vector Anopheles gambiae that are located exclusively on the mosquito’s X chromosome. We combine structure-based protein engineering and molecular genetics to restrict the activity of the potentially toxic endonuclease to spermatogenesis. Shredding of the paternal X chromosome prevents it from being transmitted to the next generation, resulting in fully fertile mosquito strains that produce >95% male offspring. We demonstrate that distorter male mosquitoes can efficiently suppress caged wild-type mosquito populations, providing the foundation for a new class of genetic vector control strategies. Extreme reproductive sex ratios could result in the suppression or elimination of pest populations. Here, the authors design a synthetic sex distortion system in Anopheles gambiae that gives rise to fertile mosquito strains that produce over 95% male offsprings and could therefore be used to suppress mosquito populations.
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Affiliation(s)
- Roberto Galizi
- 1] Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK [2] Centro di Genomica Funzionale, University of Perugia, Dipartimento di Medicina Sperimentale Via Gambuli, Edificio D, 3° Piano, 06132 Perugia, Italy
| | - Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Miriam Menichelli
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Federica Bernardini
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Anne Deredec
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Austin Burt
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Nikolai Windbichler
- 1] Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK [2]
| | - Andrea Crisanti
- 1] Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK [2] Centro di Genomica Funzionale, University of Perugia, Dipartimento di Medicina Sperimentale Via Gambuli, Edificio D, 3° Piano, 06132 Perugia, Italy [3]
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27
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Galizi R, Spano F, Giubilei MA, Capuccini B, Magini A, Urbanelli L, Ogawa T, Dubey JP, Spaccapelo R, Emiliani C, Di Cristina M. Evidence of tRNA cleavage in apicomplexan parasites: Half-tRNAs as new potential regulatory molecules of Toxoplasma gondii and Plasmodium berghei. Mol Biochem Parasitol 2013; 188:99-108. [DOI: 10.1016/j.molbiopara.2013.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 03/12/2013] [Accepted: 03/24/2013] [Indexed: 12/11/2022]
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