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Dunwell TL, Dailey SC, Ottestad AL, Yu J, Becker PW, Scaife S, Richman SD, Wood HM, Slaney H, Bottomley D, Yang X, Xiao H, Wahl SGF, Grønberg BH, Dai H, Fu G. Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA. Sci Rep 2021; 11:3138. [PMID: 33542447 PMCID: PMC7862664 DOI: 10.1038/s41598-021-82737-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 01/22/2021] [Indexed: 11/12/2022] Open
Abstract
Liquid biopsy testing utilising Next Generation Sequencing (NGS) is rapidly moving towards clinical adoption for personalised oncology. However, before NGS can fulfil its potential any novel testing approach must identify ways of reducing errors, allowing separation of true low-frequency mutations from procedural artefacts, and be designed to improve upon current technologies. Popular NGS technologies typically utilise two DNA capture approaches; PCR and ligation, which have known limitations and seem to have reached a development plateau with only small, stepwise improvements being made. To maximise the ultimate utility of liquid biopsy testing we have developed a highly versatile approach to NGS: Adaptor Template Oligo Mediated Sequencing (ATOM-Seq). ATOM-Seq's strengths and versatility avoid the major limitations of both PCR- and ligation-based approaches. This technology is ligation free, simple, efficient, flexible, and streamlined, and it offers novel advantages that make it perfectly suited for use on highly challenging clinical material. Using reference and clinical materials, we demonstrate detection of known SNVs down to allele frequencies of 0.1% using as little as 20–25 ng of cfDNA, as well as the ability to detect fusions from RNA. We illustrate ATOM-Seq’s suitability for clinical testing by showing high concordance rates between paired cfDNA and FFPE clinical samples.
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Affiliation(s)
- Thomas L Dunwell
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK
| | - Simon C Dailey
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK
| | - Anine L Ottestad
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jihang Yu
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK
| | - Philipp W Becker
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK
| | - Sarah Scaife
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK
| | - Susan D Richman
- Pathology and Data Analytics, Leeds Institute of Medical Research, University of Leeds, St James University Hospital, Leeds, LS9 7TF, UK
| | - Henry M Wood
- Pathology and Data Analytics, Leeds Institute of Medical Research, University of Leeds, St James University Hospital, Leeds, LS9 7TF, UK
| | - Hayley Slaney
- Pathology and Data Analytics, Leeds Institute of Medical Research, University of Leeds, St James University Hospital, Leeds, LS9 7TF, UK
| | - Daniel Bottomley
- Pathology and Data Analytics, Leeds Institute of Medical Research, University of Leeds, St James University Hospital, Leeds, LS9 7TF, UK
| | - Xiangsheng Yang
- Guangzhou Biotron Technology Co., Ltd, Room 204, Zone C, Science and Technology Innovation Base, No. 80, Lanyue Road, Science City, Guangzhou, China
| | - Hui Xiao
- Guangzhou Biotron Technology Co., Ltd, Room 204, Zone C, Science and Technology Innovation Base, No. 80, Lanyue Road, Science City, Guangzhou, China
| | - Sissel G F Wahl
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Bjørn H Grønberg
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Hongyan Dai
- Department of Oncology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Pathology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Guoliang Fu
- GeneFirst Ltd, Building E5, Culham Science Centre, Abingdon, OX14 3DB, UK.
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2
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Lech K, Correia L, Beckmann M, Busz M, Collison S, Davis S, Mallini P, Scaife S, Dukes J, Jakobsen BK, Williams L, Teng M. Abstract B024: Using single-cell paired sequencing to isolate cancer-specific T-cell receptors for cancer immunotherapy. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-b024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immunocore’s ImmTAC™ (Immune Mobilising Monoclonal TCR Against Cancer) platform combines affinity-enhanced T-cell receptor (TCR)-based targeting with an anti-CD3 scFv effector function to activate a cytotoxic T-cell response against cancer cells. A key part to this process is the identification of tumour epitope specific TCRs from tumor antigen-reactive T-cells. Here, we describe an integrated in-house process leading to the isolation of TCRs specific for validated cancer epitopes, coupled with rapid identification of TCR chains from individual clones using single cell sequencing. The process involves first strand cDNA generation and universal amplification using SmartSeq2 chemistry, followed by targeted sequencing of the TCR alpha and beta chains using next-generation sequencing (NGS). We have also leveraged the 10x Genomics VDJ/5’ counting platform to label and pool multiple experimental clones for repertoire sequencing within a single run. Together with Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-Seq), we can reliably assign each T-cell clone to its sample of origin paired with transcriptomic information of epitope specific T-cell populations, linking TCR sequences to their functional phenotype.
Citation Format: Karolina Lech, Lucia Correia, Max Beckmann, Maria Busz, Sean Collison, Sterenn Davis, Paraskevi Mallini, Sarah Scaife, Joseph Dukes, Bent K. Jakobsen, Luke Williams, Michelle Teng. Using single-cell paired sequencing to isolate cancer-specific T-cell receptors for cancer immunotherapy [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B024.
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Affiliation(s)
| | | | | | - Maria Busz
- Immunocore, Ltd., Abingdon, United Kingdom
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3
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Haghighat-Khah RE, Scaife S, Martins S, St John O, Matzen KJ, Morrison N, Alphey L. Site-specific cassette exchange systems in the Aedes aegypti mosquito and the Plutella xylostella moth. PLoS One 2015; 10:e0121097. [PMID: 25830287 PMCID: PMC4382291 DOI: 10.1371/journal.pone.0121097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/09/2015] [Indexed: 12/02/2022] Open
Abstract
Genetically engineered insects are being evaluated as potential tools to decrease the economic and public health burden of mosquitoes and agricultural pest insects. Here we describe a new tool for the reliable and targeted genome manipulation of pest insects for research and field release using recombinase mediated cassette exchange (RMCE) mechanisms. We successfully demonstrated the established ΦC31-RMCE method in the yellow fever mosquito, Aedes aegypti, which is the first report of RMCE in mosquitoes. A new variant of this RMCE system, called iRMCE, combines the ΦC31-att integration system and Cre or FLP-mediated excision to remove extraneous sequences introduced as part of the site-specific integration process. Complete iRMCE was achieved in two important insect pests, Aedes aegypti and the diamondback moth, Plutella xylostella, demonstrating the transferability of the system across a wide phylogenetic range of insect pests.
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Affiliation(s)
- Roya Elaine Haghighat-Khah
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | | | - Sara Martins
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | - Oliver St John
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | | | | | - Luke Alphey
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
- * E-mail: (LA); (KJM)
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4
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Wilke ABB, Scaife S, Alphey L, Marrelli MT. DsRed2 transient expression in Culex quinquefasciatus mosquitoes. Mem Inst Oswaldo Cruz 2013; 108:529-31. [PMID: 23828005 PMCID: PMC3970632 DOI: 10.1590/s0074-02762013000400023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 12/07/2012] [Indexed: 11/21/2022] Open
Abstract
Culex quinquefasciatus mosquitoes have been successfully genetically modified only once, despite the efforts of several laboratories to transform and establish a stable strain. We have developed a transient gene expression method, in Culex, that delivers plasmid DNA directly to the mosquito haemolymph and additional tissues. We were able to express DsRed2 fluorescent protein in adult Cx. quinquefasciatus mosquitoes by injecting plasmids directly into their thorax. The expression of DsRed2 in adult Cx. quinquefasciatus mosquitoes is an important stepping stone to genetic transformation and the potential use of new control strategies and genetic interactions.
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Affiliation(s)
- André Barretto Bruno Wilke
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brasil.
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5
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Wilke ABB, Scaife S, Alphey L, Marrelli MT. DsRed2 transient expression in Culex quinquefasciatus mosquitoes. Mem Inst Oswaldo Cruz 2013; 108. [PMID: 23828005 PMCID: PMC3970632 DOI: 10.1590/0074-0276108042013023] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Culex quinquefasciatus mosquitoes have been successfully genetically modified only once, despite the efforts of several laboratories to transform and establish a stable strain. We have developed a transient gene expression method, in Culex, that delivers plasmid DNA directly to the mosquito haemolymph and additional tissues. We were able to express DsRed2 fluorescent protein in adult Cx. quinquefasciatus mosquitoes by injecting plasmids directly into their thorax. The expression of DsRed2 in adult Cx. quinquefasciatus mosquitoes is an important stepping stone to genetic transformation and the potential use of new control strategies and genetic interactions.
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Affiliation(s)
- André Barretto Bruno Wilke
- Departamento de Epidemiologia, Faculdade de Saúde Pública,
Universidade de São Paulo, São Paulo, SP, Brasil,Corresponding author:
| | | | - Luke Alphey
- Oxitec Ltd, Oxford, United Kingdom,Department of Zoology, University of Oxford, Oxford, United
Kingdom
| | - Mauro Toledo Marrelli
- Departamento de Epidemiologia, Faculdade de Saúde Pública,
Universidade de São Paulo, São Paulo, SP, Brasil
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6
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Marinotti O, Jasinskiene N, Fazekas A, Scaife S, Fu G, Mattingly ST, Chow K, Brown DM, Alphey L, James AA. Development of a population suppression strain of the human malaria vector mosquito, Anopheles stephensi. Malar J 2013; 12:142. [PMID: 23622561 PMCID: PMC3648444 DOI: 10.1186/1475-2875-12-142] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/19/2013] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Transgenic mosquito strains are being developed to contribute to the control of dengue and malaria transmission. One approach uses genetic manipulation to confer conditional, female-specific dominant lethality phenotypes. Engineering of a female-specific flightless phenotype provides a sexing mechanism essential for male-only mosquito, release approaches that result in population suppression of target vector species. METHODS An approach that uses a female-specific gene promoter and antibiotic-repressible lethal factor to produce a sex-specific flightless phenotype was adapted to the human malaria vector, Anopheles stephensi. Transposon- and site-specific recombination-mediated technologies were used to generate a number of transgenic An. stephensi lines that when combined through mating produced the phenotype of flight-inhibited females and flight-capable males. RESULTS The data shown here demonstrate the successful engineering of a female-specific flightless phenotype in a malaria vector. The flightless phenotype was repressible by the addition of tetracycline to the larval diet. This conditional phenotype allows the rearing of the strains under routine laboratory conditions. The minimal level of tetracycline that rescues the flightless phenotype is higher than that found as an environmental contaminant in circumstances where there is intensive use of antibiotics. CONCLUSIONS These studies support the further development of flightless female technology for applications in malaria control programmes that target the vectors.
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Affiliation(s)
- Osvaldo Marinotti
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Nijole Jasinskiene
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Aniko Fazekas
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Sarah Scaife
- Oxitec Ltd, 71 Milton Park, Abingdon, Oxfordshire, OX14 4RX, UK
| | - Guoliang Fu
- Oxitec Ltd, 71 Milton Park, Abingdon, Oxfordshire, OX14 4RX, UK
| | - Stefanie T Mattingly
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - Karissa Chow
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA
| | - David M Brown
- Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry, 3205 McGaugh Hall, University of California, Irvine, CA, 92697-3900, USA
| | - Luke Alphey
- Oxitec Ltd, 71 Milton Park, Abingdon, Oxfordshire, OX14 4RX, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Anthony A James
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA
- Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry, 3205 McGaugh Hall, University of California, Irvine, CA, 92697-3900, USA
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7
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Harris AF, McKemey AR, Nimmo D, Curtis Z, Black I, Morgan SA, Oviedo MN, Lacroix R, Naish N, Morrison NI, Collado A, Stevenson J, Scaife S, Dafa'alla T, Fu G, Phillips C, Miles A, Raduan N, Kelly N, Beech C, Donnelly CA, Petrie WD, Alphey L. Successful suppression of a field mosquito population by sustained release of engineered male mosquitoes. Nat Biotechnol 2012; 30:828-30. [PMID: 22965050 DOI: 10.1038/nbt.2350] [Citation(s) in RCA: 284] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Angela F Harris
- Mosquito Research and Control Unit, Grand Cayman, Cayman Islands
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8
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Martins S, Naish N, Walker AS, Morrison NI, Scaife S, Fu G, Dafa'alla T, Alphey L. Germline transformation of the diamondback moth, Plutella xylostella L., using the piggyBac transposable element. Insect Mol Biol 2012; 21:414-421. [PMID: 22621377 DOI: 10.1111/j.1365-2583.2012.01146.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The diamondback moth, Plutella xylostella, is one of the most economically important agricultural pests. The larvae of this moth cause damage by feeding on the foliage of cruciferous vegetables such as cabbage, broccoli, cauliflower and rapeseed. Control generally comprises chemical treatment; however, the diamondback moth is renowned for rapid development of resistance to pesticides. Other methods, such as biological control, have not been able to provide adequate protection. Germline transformation of pest insects has become available in recent years as an enabling technology for new genetics-based control methods, such as the Release of Insects carrying a Dominant Lethal (RIDL(®) ). In the present study, we report the first transformation of the diamondback moth, using the piggyBac transposable element, by embryo microinjection. In generating transgenic strains using four different constructs, the function of three regulatory sequences in this moth was demonstrated in driving expression of fluorescent proteins. The transformation rates achieved, 0.48-0.68%, are relatively low compared with those described in other Lepidoptera, but not prohibitive, and are likely to increase with experience. We anticipate that germline transformation of the diamondback moth will permit the development of RIDL strains for use against this pest and facilitate the wider use of this species as a model organism for basic studies.
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Affiliation(s)
- S Martins
- Department of Zoology, University of Oxford, Oxford, UK
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9
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Labbé GMC, Scaife S, Morgan SA, Curtis ZH, Alphey L. Female-specific flightless (fsRIDL) phenotype for control of Aedes albopictus. PLoS Negl Trop Dis 2012; 6:e1724. [PMID: 22802980 PMCID: PMC3393675 DOI: 10.1371/journal.pntd.0001724] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 05/23/2012] [Indexed: 12/21/2022] Open
Abstract
Background Aedes albopictus, the Asian tiger mosquito, is a vector of several arboviruses including dengue and chikungunya, and is also a significant nuisance mosquito. It is one of the most invasive of mosquitoes with a relentlessly increasing geographic distribution. Conventional control methods have so far failed to control Ae. albopictus adequately. Novel genetics-based strategies offer a promising alternative or aid towards efficient control of this mosquito. Methodology/Principal Findings We describe here the isolation, characterisation and use of the Ae. albopictus Actin-4 gene to drive a dominant lethal gene in the indirect flight muscles of Ae. albopictus, thus inducing a conditional female-specific late-acting flightless phenotype. We also show that in this context, the Actin-4 regulatory regions from both Ae. albopictus and Ae. aegypti can be used to provide conditional female-specific flightlessness in either species. Conclusion/Significance With the disease-transmitting females incapacitated, the female flightless phenotype encompasses a genetic sexing mechanism and would be suitable for controlling Ae. albopictus using a male-only release approach as part of an integrated pest management strategy. The Asian Tiger mosquito, Aedes albopictus, is a highly invasive species which took advantage of human activity to spread from South-East Asia to Africa, North and South America, and Europe in the past forty years. Beyond the annoying biting nuisance, this mosquito is also a significant public health threat, capable of transmitting dengue and responsible for an important chikungunya outbreak in the Indian Ocean in 2007. This mosquito is notoriously difficult to control using current methods, but control techniques involving the release of genetically sterile males have recently shown promising results against the closely related yellow fever mosquito, Aedes aegypti. Wild females inseminated by sterile males have non-viable progeny so if enough sterile males are released, the target population crashes. Female mosquitoes, even if sterile, would bite and potentially acquire and transmit pathogens, so it is crucial to minimise the release of such females. Here we describe the development of genetically engineered strains of the Asian Tiger mosquito to use in such control programmes: the females are unable to fly unless reared with an antidote, thus facilitating male-only releases. The daughters of released males will also be flightless, a lethal phenotype in the field, thus reducing the population and preventing disease transmission.
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Affiliation(s)
- Geneviève M. C. Labbé
- Oxitec Limited, Oxford, United Kingdom
- Division of Biology, Imperial College London Silwood Park, Ascot, United Kingdom
| | | | | | | | - Luke Alphey
- Oxitec Limited, Oxford, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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10
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Harris AF, Nimmo D, McKemey AR, Kelly N, Scaife S, Donnelly CA, Beech C, Petrie WD, Alphey L. Field performance of engineered male mosquitoes. Nat Biotechnol 2011; 29:1034-7. [PMID: 22037376 DOI: 10.1038/nbt.2019] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 09/27/2011] [Indexed: 11/09/2022]
Abstract
Dengue is the most medically important arthropod-borne viral disease, with 50-100 million cases reported annually worldwide. As no licensed vaccine or dedicated therapy exists for dengue, the most promising strategies to control the disease involve targeting the predominant mosquito vector, Aedes aegypti. However, the current methods to do this are inadequate. Various approaches involving genetically engineered mosquitoes have been proposed, including the release of transgenic sterile males. However, the ability of laboratory-reared, engineered male mosquitoes to effectively compete with wild males in terms of finding and mating with wild females, which is critical to the success of these strategies, has remained untested. We report data from the first open-field trial involving a strain of engineered mosquito. We demonstrated that genetically modified male mosquitoes, released across 10 hectares for a 4-week period, mated successfully with wild females and fertilized their eggs. These findings suggest the feasibility of this technology to control dengue by suppressing field populations of A. aegypti.
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Affiliation(s)
- Angela F Harris
- Mosquito Research and Control Unit (MRCU), Grand Cayman, Cayman Islands
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11
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Fu G, Lees RS, Nimmo D, Aw D, Jin L, Gray P, Berendonk TU, White-Cooper H, Scaife S, Kim Phuc H, Marinotti O, Jasinskiene N, James AA, Alphey L. Female-specific flightless phenotype for mosquito control. Proc Natl Acad Sci U S A 2010; 107:4550-4. [PMID: 20176967 PMCID: PMC2826341 DOI: 10.1073/pnas.1000251107] [Citation(s) in RCA: 215] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dengue and dengue hemorrhagic fever are increasing public health problems with an estimated 50-100 million new infections each year. Aedes aegypti is the major vector of dengue viruses in its range and control of this mosquito would reduce significantly human morbidity and mortality. Present mosquito control methods are not sufficiently effective and new approaches are needed urgently. A "sterile-male-release" strategy based on the release of mosquitoes carrying a conditional dominant lethal gene is an attractive new control methodology. Transgenic strains of Aedes aegypti were engineered to have a repressible female-specific flightless phenotype using either two separate transgenes or a single transgene, based on the use of a female-specific indirect flight muscle promoter from the Aedes aegypti Actin-4 gene. These strains eliminate the need for sterilization by irradiation, permit male-only release ("genetic sexing"), and enable the release of eggs instead of adults. Furthermore, these strains are expected to facilitate area-wide control or elimination of dengue if adopted as part of an integrated pest management strategy.
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Affiliation(s)
- Guoliang Fu
- Oxitec Limited, 71 Milton Park, Oxford OX14 4RX, United Kingdom
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - Rosemary S. Lees
- Oxitec Limited, 71 Milton Park, Oxford OX14 4RX, United Kingdom
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - Derric Nimmo
- Oxitec Limited, 71 Milton Park, Oxford OX14 4RX, United Kingdom
| | - Diane Aw
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900; and
| | - Li Jin
- Oxitec Limited, 71 Milton Park, Oxford OX14 4RX, United Kingdom
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - Pam Gray
- Oxitec Limited, 71 Milton Park, Oxford OX14 4RX, United Kingdom
| | - Thomas U. Berendonk
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - Helen White-Cooper
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - Sarah Scaife
- Oxitec Limited, 71 Milton Park, Oxford OX14 4RX, United Kingdom
| | - Hoang Kim Phuc
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - Osvaldo Marinotti
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900; and
| | - Nijole Jasinskiene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900; and
| | - Anthony A. James
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900; and
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697-3900
| | - Luke Alphey
- Oxitec Limited, 71 Milton Park, Oxford OX14 4RX, United Kingdom
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
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12
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Abstract
Germ-line transformation of a major agricultural pest, the Mexican fruit fly (Anastrepha ludens Loew, Mexfly), was achieved using composite piggyBac transposable elements marked with green, yellow and red fluorescent proteins (CopGreen, PhiYFP and J-Red). We also investigated the possibility of generating transposon-free insertions, in order to address potential concerns relating to proposed field use of transgenic Mexfly. We describe a highly efficient method for transforming Mexfly, compare efficiency of piggyBac terminal sequences for transformation and also describe the derivation of a transposon-free insertion line. The development of an efficient transformation system for Mexfly holds great promise for improved applications of the sterile insect technique, a major component of the present control measures for this economically important pest species.
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Affiliation(s)
- K C Condon
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
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13
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Gong P, Epton MJ, Fu G, Scaife S, Hiscox A, Condon KC, Condon GC, Morrison NI, Kelly DW, Dafa'alla T, Coleman PG, Alphey L. A dominant lethal genetic system for autocidal control of the Mediterranean fruitfly. Nat Biotechnol 2005; 23:453-6. [PMID: 15750586 DOI: 10.1038/nbt1071] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Accepted: 01/05/2005] [Indexed: 11/09/2022]
Abstract
The Sterile Insect Technique (SIT) used to control insect pests relies on the release of large numbers of radiation-sterilized insects. Irradiation can have a negative impact on the subsequent performance of the released insects and therefore on the cost and effectiveness of a control program. This and other problems associated with current SIT programs could be overcome by the use of recombinant DNA methods and molecular genetics. Here we describe the construction of strains of the Mediterranean fruit fly (medfly) harboring a tetracycline-repressible transactivator (tTA) that causes lethality in early developmental stages of the heterozygous progeny but has little effect on the survival of the parental transgenic tTA insects. We show that these properties should prove advantageous for the implementation of insect pest control programs.
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Affiliation(s)
- Peng Gong
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Scaife S, Brown R, Kellie S, Filer A, Martin S, Thomas AMC, Bradfield PF, Amft N, Salmon M, Buckley CD. Detection of differentially expressed genes in synovial fibroblasts by restriction fragment differential display. Rheumatology (Oxford) 2004; 43:1346-52. [PMID: 15292528 DOI: 10.1093/rheumatology/keh347] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE To identify differentially expressed genes in synovial fibroblasts and examine the effect on gene expression of exposure to TNF-alpha and IL-1beta. METHODS Restriction fragment differential display was used to isolate genes using degenerate primers complementary to the lysophosphatidic acid acyl transferase gene family. Differential gene expression was confirmed by reverse transcription-polymerase chain reaction and immunohistochemistry using a variety of synovial fibroblasts, including cells from patients with osteoarthritis and self-limiting parvovirus arthritis. RESULTS Irrespective of disease process, synovial fibroblasts constitutively produced higher levels of IL-6 and monocyte chemoattractant protein 1 (MCP-1) (CCL2) than skin fibroblasts. Seven genes were differentially expressed in synovial fibroblasts compared with skin fibroblasts. Of these genes, four [tissue factor pathway inhibitor 2 (TFPI2), growth regulatory oncogene beta (GRObeta), manganese superoxide dismutase (MnSOD) and granulocyte chemotactic protein 2 (GCP-2)] were all found to be constitutively overexpressed in synoviocytes derived from patients with osteoarthritis. These four genes were only weakly expressed in other synovial fibroblasts (rheumatoid and self-limiting parvovirus infection). However, expression in all types of fibroblasts was increased after stimulation with TNF-alpha and IL-1beta. Three other genes (aggrecan, biglycan and caldesmon) were expressed at higher levels in all types of synovial fibroblasts compared with skin fibroblasts even after stimulation with TNF-alpha and IL-1. CONCLUSIONS Seven genes have been identified with differential expression patterns in terms of disease process (osteoarthritis vs rheumatoid arthritis), state of activation (resting vs cytokine activation) and anatomical location (synovium vs skin). Four of these genes, TFPI2, GRObeta (CXCL2), MnSOD and GCP-2 (CXCL6), were selectively overexpressed in osteoarthritis fibroblasts rather than rheumatoid fibroblasts. While these differences may represent differential behaviour of synovial fibroblasts in in vitro culture, these observations suggest that TFPI2, GRObeta (CXCL2), MnSOD and GCP-2 (CXCL6) may represent new targets for treatments specifically tailored to osteoarthritis.
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Affiliation(s)
- S Scaife
- Yamanouchi Research Institute, Oxford, UK
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15
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Abstract
The eukaryotic pre-replication complex is assembled at replication origins in a reaction called licensing. Licensing involves the interactions of a variety of proteins including the origin recognition complex (ORC), Cdc6 and the Mcm2-7 helicase, homologues of which are also found in archaea. The euryarchaeote Archaeoglobus fulgidus encodes two genes with homology to Orc/Cdc6 and a single Mcm homologue. The A.fulgidus Mcm protein and one Orc/Cdc6 homologue have been purified and investigated in vitro. The Mcm protein is an ATP-dependent, hexameric helicase that can unwind between 200 and 400 bp of duplex DNA. Deletion of 112 amino acids from the N-terminus of A.f Mcm produced a protein, which was still capable of forming a hexamer, was competent in DNA binding and was able to unwind at least 1 kb of duplex DNA. The purified Orc/Cdc6 homologue was also able to bind DNA. Both Mcm and Orc/Cdc6 show a preference for specific DNA structures, namely molecules containing a single stranded bubble that mimics early replication intermediates. Nuclease protection showed that the binding sites for Mcm and Orc/Cdc6 overlap. The Orc/Cdc6 protein bound more tightly to these substrates and was able to displace pre-bound Mcm hexamer.
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Affiliation(s)
- Ian Grainge
- Cancer Research UK, Clare Hall Laboratories, The London Research Institute, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3LD, UK
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16
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Seybert A, Scott DJ, Scaife S, Singleton MR, Wigley DB. Biochemical characterisation of the clamp/clamp loader proteins from the euryarchaeon Archaeoglobus fulgidus. Nucleic Acids Res 2002; 30:4329-38. [PMID: 12384579 PMCID: PMC137147 DOI: 10.1093/nar/gkf584] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Replicative polymerases of eukaryotes, prokaryotes and archaea obtain processivity using ring-shaped DNA sliding clamps that are loaded onto DNA by clamp loaders [replication factor C (RFC) in eukaryotes]. In this study, we cloned the two genes for the subunits of the RFC homologue of the euryarchaeon Archaeoglobus fulgidus. The proteins were expressed and purified from Escherichia coli both individually and as a complex. The afRFC subunits form a heteropentameric complex consisting of one copy of the large subunit and four copies of the small subunits. To analyse the functionality of afRFC, we also expressed the A.fulgidus PCNA homologue and a type B polymerase (PolB1) in E.coli. In primer extension assays, afRFC stimulated the processivity of afPolB1 in afPCNA-dependent reactions. Although the afRFC complex showed significant DNA-dependent ATPase activity, which could be further stimulated by afPCNA, neither of the isolated afRFC subunits showed this activity. However, both the large and small afRFC subunits showed interaction with afPCNA. Furthermore, we demonstrate that ATP binding, but not hydrolysis, is needed to stimulate interactions of the afRFC complex with afPCNA and DNA.
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Affiliation(s)
- Anja Seybert
- Molecular Enzymology Laboratory, London Research Institute, Clare Hall Laboratories, Cancer Research UK
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17
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Singleton MR, Scaife S, Raven ND, Wigley DB. Crystallization and preliminary X-ray analysis of RecG, a replication-fork reversal helicase from Thermotoga maritima complexed with a three-way DNA junction. Acta Crystallogr D Biol Crystallogr 2001; 57:1695-6. [PMID: 11679748 DOI: 10.1107/s0907444901013105] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2001] [Accepted: 08/03/2001] [Indexed: 11/10/2022]
Abstract
The monomeric 3'-5' helicase RecG from the thermophilic bacterium Thermotoga maritima has been crystallized in complex with a three-way DNA junction, the preferred physiological substrate. The crystals were obtained by hanging-drop vapour diffusion. The crystals belong to space group C2, with unit-cell parameters a = 133.7, b = 144.6, c = 84.0 A, beta = 113.8 degrees. Native data to a resolution of 3.25 A were collected from crystals flash-cooled to 100 K.
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Affiliation(s)
- M R Singleton
- Imperial Cancer Research Fund, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, England
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18
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Abstract
The stalling of DNA replication forks that occurs as a consequence of encountering DNA damage is a critical problem for cells. RecG protein is involved in the processing of stalled replication forks, and acts by reversing the fork past the damage to create a four-way junction that allows template switching and lesion bypass. We have determined the crystal structure of RecG bound to a DNA substrate that mimics a stalled replication fork. The structure not only reveals the elegant mechanism used by the protein to recognize junctions but has also trapped the protein in the initial stage of fork reversal. We propose a mechanism for how forks are processed by RecG to facilitate replication fork restart. In addition, this structure suggests that the mechanism and function of the two largest helicase superfamilies are distinct.
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Affiliation(s)
- M R Singleton
- ICRF Clare Hall Laboratories, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3LD, United Kingdom
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20
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Scaife S, Kluson P, Quirke N. Characterization of Porous Materials by Gas Adsorption: Do Different Molecular Probes Give Different Pore Structures? J Phys Chem B 1999. [DOI: 10.1021/jp9930752] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. Scaife
- Department of Chemistry, University of Wales at Bangor, Bangor, Gywnedd, LL57 2DG, U.K
| | - P. Kluson
- Department of Chemistry, Imperial College, South Kensington, London, SW7 2AY, U.K
| | - N. Quirke
- Department of Chemistry, Imperial College, South Kensington, London, SW7 2AY, U.K
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