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Gómez-Palacio A, Cruz-Saavedra L, Van den Broeck F, Geerts M, Pita S, Vallejo GA, Carranza JC, Ramírez JD. High-throughput analysis of the Trypanosoma cruzi minicirculome (mcDNA) unveils structural variation and functional diversity. Sci Rep 2024; 14:5578. [PMID: 38448494 PMCID: PMC10917808 DOI: 10.1038/s41598-024-56076-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
Trypanosoma cruzi causes Chagas disease and has a unique extranuclear genome enclosed in a structure called the kinetoplast, which contains circular genomes known as maxi- and minicircles. While the structure and function of maxicircles are well-understood, many aspects of minicircles remain to be discovered. Here, we performed a high-throughput analysis of the minicirculome (mcDNA) in 50 clones isolated from Colombia's diverse T. cruzi I populations. Results indicate that mcDNA comprises four diverse subpopulations with different structures, lengths, and numbers of interspersed semi-conserved (previously termed ultra-conserved regions mHCV) and hypervariable (mHVPs) regions. Analysis of mcDNA ancestry and inter-clone differentiation indicates the interbreeding of minicircle sequence classes is placed along diverse strains and hosts. These results support evidence of the multiclonal dynamics and random bi-parental segregation. Finally, we disclosed the guide RNA repertoire encoded by mcDNA at a clonal scale, and several attributes of its abundance and function are discussed.
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Affiliation(s)
- Andrés Gómez-Palacio
- Laboratorio de Investigación en Genética Evolutiva, Universidad Pedagógica y Tecnológica de Colombia, Boyacá, Colombia
| | - Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Frederik Van den Broeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Manon Geerts
- Fish Eco-Evo-Devo and Conservation, KU Leuven, 3000, Leuven, Belgium
- Directorate Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, 1000, Brussels, Belgium
| | - Sebastián Pita
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
| | - Gustavo A Vallejo
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Julio C Carranza
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA.
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Alves CPA, Prazeres DMF, Monteiro GA. Real-Time PCR Method for Assessment of ParA-Mediated Recombination Efficiency in Minicircle Production. Methods Mol Biol 2023; 2967:117-131. [PMID: 37608107 DOI: 10.1007/978-1-0716-3358-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The in vivo intramolecular recombination of a parental plasmid allows excising prokaryotic backbone from the eukaryotic cassette of interest, leading to the formation of, respectively, a miniplasmid and a minicircle. Here we describe a real-time PCR protocol suitable for the determination of recombination efficiency of parental plasmids with multimer resolution sites (MRS). The protocol was successfully applied to purified DNA samples obtained from E. coli cultures, allowing a more reproducible determination of recombination efficiency than densitometry analysis of agarose gels.
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Affiliation(s)
- Cláudia P A Alves
- iBB- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Duarte Miguel F Prazeres
- iBB- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Gabriel A Monteiro
- iBB- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Associate Laboratory i4HB - Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
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Vetcher AA, Stanishevskiy YM. DNA microcircles - The promising tool for in vivo studies of the behavior of non-canonical DNA. Prog Biophys Mol Biol 2022; 169-170:84-88. [PMID: 35219771 DOI: 10.1016/j.pbiomolbio.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
The paper discusses the reasons for the resurrection of the term DNA microcircles through the change of its definition to "topologically closed DNA circles with the length less than 1 Kbp" from the entire population of circular DNA that holds the name of minicircles. The possible applications of such tool for in vivo studies of non-canonical DNA are also discussed. Prospective for in vivo and in vitro studies of non-canonical DNA cloned into microcircles are demonstrated. A method of stepwise elongation or shortening of plasmids is discussed.
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Affiliation(s)
- Alexandre A Vetcher
- IBCTN of the Peoples' Friendship University of Russia (RUDN), 6 Miklukho-Maklaya St, Moscow, 117198, Russian Federation; Complementary and Integrative Health Clinic of Dr. Shishonin, 5 Yasnogorskaya Str, Moscow, 117588, Russian Federation.
| | - Yaroslav M Stanishevskiy
- IBCTN of the Peoples' Friendship University of Russia (RUDN), 6 Miklukho-Maklaya St, Moscow, 117198, Russian Federation
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Geerts M, Schnaufer A, Van den Broeck F. rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects. BMC Bioinformatics 2021; 22:468. [PMID: 34583651 PMCID: PMC8479924 DOI: 10.1186/s12859-021-04384-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 09/20/2021] [Indexed: 12/28/2022] Open
Abstract
Background The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been generated and analyzed, information about the diversity, structure and evolution of their mitochondrial genomes remains fragmentary, mainly because of their extraordinary complexity. Indeed, unicellular flagellates of the order Kinetoplastida contain structurally the most complex mitochondrial genome of all eukaryotes, organized as a giant network of homogeneous maxicircles and heterogeneous minicircles. We recently developed KOMICS, an analysis toolkit that automates the assembly and circularization of the mitochondrial genomes of Kinetoplastid parasites. While this tool overcomes the limitation of extracting mitochondrial assemblies from Next-Generation Sequencing datasets, interpreting and visualizing the genetic (dis)similarity within and between samples remains a time-consuming process. Results Here, we present a new analysis toolkit—rKOMICS—to streamline the analyses of minicircle sequence diversity in population-scale genome projects. rKOMICS is a user-friendly R package that has simple installation requirements and that is applicable to all 27 trypanosomatid genera. Once minicircle sequence alignments are generated, rKOMICS allows to examine, summarize and visualize minicircle sequence diversity within and between samples through the analyses of minicircle sequence clusters. We showcase the functionalities of the (r)KOMICS tool suite using a whole-genome sequencing dataset from a recently published study on the history of diversification of the Leishmania braziliensis species complex in Peru. Analyses of population diversity and structure highlighted differences in minicircle sequence richness and composition between Leishmania subspecies, and between subpopulations within subspecies. Conclusion The rKOMICS package establishes a critical framework to manipulate, explore and extract biologically relevant information from mitochondrial minicircle assemblies in tens to hundreds of samples simultaneously and efficiently. This should facilitate research that aims to develop new molecular markers for identifying species-specific minicircles, or to study the ancestry of parasites for complementary insights into their evolutionary history.
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Affiliation(s)
- Manon Geerts
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Frederik Van den Broeck
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium. .,Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, 3000, Leuven, Belgium.
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Robinson ER, Gowrishankar G, D'Souza AL, Kheirolomoom A, Haywood T, Hori SS, Chuang HY, Zeng Y, Tumbale SK, Aalipour A, Beinat C, Alam IS, Sathirachinda A, Kanada M, Paulmurugan R, Ferrara KW, Gambhir SS. Minicircles for a two-step blood biomarker and PET imaging early cancer detection strategy. J Control Release 2021; 335:281-289. [PMID: 34029631 DOI: 10.1016/j.jconrel.2021.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/29/2021] [Accepted: 05/19/2021] [Indexed: 12/24/2022]
Abstract
Early cancer detection can dramatically increase treatment options and survival rates for patients, yet detection of early-stage tumors remains difficult. Here, we demonstrate a two-step strategy to detect and locate cancerous lesions by delivering tumor-activatable minicircle (MC) plasmids encoding a combination of blood-based and imaging reporter genes to tumor cells. We genetically engineered the MCs, under the control of the pan-tumor-specific Survivin promoter, to encode: 1) Gaussia Luciferase (GLuc), a secreted biomarker that can be easily assayed in blood samples; and 2) Herpes Simplex Virus Type 1 Thymidine Kinase mutant (HSV-1 sr39TK), a PET reporter gene that can be used for highly sensitive and quantitative imaging of the tumor location. We evaluated two methods of MC delivery, complexing the MCs with the chemical transfection reagent jetPEI or encapsulating the MCs in extracellular vesicles (EVs) derived from a human cervical cancer HeLa cell line. MCs delivered by EVs or jetPEI yielded significant expression of the reporter genes in cell culture versus MCs delivered without a transfection reagent. Secreted GLuc correlated with HSV-1 sr39TK expression with R2 = 0.9676. MC complexation with jetPEI delivered a larger mass of MC for enhanced transfection, which was crucial for in vivo animal studies, where delivery of MCs via jetPEI resulted in GLuc and HSV-1 sr39TK expression at significantly higher levels than controls. To the best of our knowledge, this is the first report of the PET reporter gene HSV-1 sr39TK delivered via a tumor-activatable MC to tumor cells for an early cancer detection strategy. This work explores solutions to endogenous blood-based biomarker and molecular imaging limitations of early cancer detection strategies and elucidates the delivery capabilities and limitations of EVs.
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Affiliation(s)
- Elise R Robinson
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gayatri Gowrishankar
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aloma L D'Souza
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Azadeh Kheirolomoom
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tom Haywood
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sharon S Hori
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA; Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Hui-Yen Chuang
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming University, Taipei, Taiwan
| | - Yitian Zeng
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Spencer K Tumbale
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amin Aalipour
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Corinne Beinat
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Israt S Alam
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ataya Sathirachinda
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Masamitsu Kanada
- Institute for Quantitative Health Science and Engineering (IQ), Michigan State University, East Lansing, MI 48824., USA
| | - Ramasamy Paulmurugan
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA; Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Katherine W Ferrara
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA; Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA.
| | - Sanjiv S Gambhir
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Stanford University School of Medicine, Stanford, CA 94305, USA; Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA 94304, USA
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Fayaz S, Fard-Esfahani P, Bahrami F, Parvizi P, Ajdary S. High resolution melting assay in discrimination of the main etiologic agents of leishmaniasis in Iran. Iran J Microbiol 2021; 13:137-144. [PMID: 33889373 PMCID: PMC8043822 DOI: 10.18502/ijm.v13i1.5505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background and Objectives: The three old world Leishmania species i.e., L. major, L. tropica, and L. infantum are considered as potential etiological agents of the various clinical forms of leishmaniasis in Iran. Different species co-exist in some areas. Accurate differentiation between the species is essential for choosing an appropriate therapy. Conventional and gold standard methods for the detection and characterization of parasites are time-consuming, laborious, and have low sensitivity. A polymerase chain reaction followed by high resolution melting (PCR-HRM) analysis has been employed for detection and species identification. Most of the studies suffer from the use of multiple targets and/or requiring more than one reaction to identify a single sample. The present study aimed to design a PCR method based on the amplification of kinetoplast DNA minicircles (kDNA) and HRM analysis of the amplicons for rapid discrimination of the three mentioned species. Materials and Methods: DNA from reference strains including L. major, L. tropica, and L. infantum and fifty-eight strains subjected to PCR-HRM analysis targeting kDNA. All the samples were also analyzed by conventional kDNA-PCR. Results: The PCR-HRM analysis allowed discrimination between the three Old World species. The normalized HRM curves for the amplicons of kDNA indicated a unique and repeatable melting plot for each species, even in combination with human and mouse genomic DNA. Conventional kDNA-PCR could not properly discriminate L. tropica from L. infantum. Conclusion: PCR-HRM analysis of kDNA proved to be fast and accurate for discrimination of L. major, L. tropica, and L. infantum.
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Affiliation(s)
- Shima Fayaz
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran.,Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Fariborz Bahrami
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | - Parviz Parvizi
- Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Soheila Ajdary
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
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Alcolea PJ, Alonso A, Larraga V. Guide RNA genes up-regulated in Leishmania infantum metacyclic promastigotes. Acta Trop 2018; 187:72-77. [PMID: 30055178 DOI: 10.1016/j.actatropica.2018.07.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 11/15/2017] [Revised: 07/16/2018] [Accepted: 07/24/2018] [Indexed: 02/01/2023]
Abstract
The kinetoplastid parasite Leishmania infantum is responsible for zoonotic visceral leishmaniasis in the mediterranean basin, where dogs are the reservoir. Differential gene expression analysis of metacyclic promastigotes in axenic culture by whole genome DNA microarray hybridization revealed up-regulation of two unidentified genes that are absent in the parasite's genome databases. Sequence analysis has revealed that these genes encode for guide RNAs (gRNAs), which are located in the kinetoplast and participate in the kinetoplastid-specific uridine insertion/deletion RNA editing process. Northern blot assays have confirmed that both gRNA genes are up-regulated in metacyclic promastigotes, thus suggesting that uridine insertion/deletion RNA editing contributes to metabolic shifts at this stage. A screening strategy described herein has revealed an uncharacterized 16S-like rRNA transcript as a target of one of the aforementioned gRNAs.
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Affiliation(s)
- Pedro J Alcolea
- Departamento de Biología Celular y Molecular, Centro de Investigaciones Biológicas (CSIC), calle Ramiro de Maeztu 9, 28034 Madrid, Spain.
| | - Ana Alonso
- Departamento de Biología Celular y Molecular, Centro de Investigaciones Biológicas (CSIC), calle Ramiro de Maeztu 9, 28034 Madrid, Spain
| | - Vicente Larraga
- Departamento de Biología Celular y Molecular, Centro de Investigaciones Biológicas (CSIC), calle Ramiro de Maeztu 9, 28034 Madrid, Spain
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Amodeo S, Jakob M, Ochsenreiter T. Characterization of the novel mitochondrial genome replication factor MiRF172 in Trypanosoma brucei. J Cell Sci 2018; 131:jcs211730. [PMID: 29626111 PMCID: PMC5963845 DOI: 10.1242/jcs.211730] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/20/2018] [Indexed: 01/07/2023] Open
Abstract
The unicellular parasite Trypanosoma brucei harbors one mitochondrial organelle with a singular genome called the kinetoplast DNA (kDNA). The kDNA consists of a network of concatenated minicircles and a few maxicircles that form the kDNA disc. More than 30 proteins involved in kDNA replication have been described. However, several mechanistic questions are only poorly understood. Here, we describe and characterize minicircle replication factor 172 (MiRF172), a novel mitochondrial genome replication factor that is essential for cell growth and kDNA maintenance. By performing super-resolution microscopy, we show that MiRF172 is localized to the kDNA disc, facing the region between the genome and the mitochondrial membranes. We demonstrate that depletion of MiRF172 leads to a loss of minicircles and maxicircles. Detailed analysis suggests that MiRF172 is involved in the reattachment of replicated minicircles to the kDNA disc. Furthermore, we provide evidence that the localization of the replication factor MiRF172 not only depends on the kDNA itself, but also on the mitochondrial genome segregation machinery, suggesting an interaction between the two essential entities.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Simona Amodeo
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern CH-3012, Switzerland
| | - Martin Jakob
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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Abstract
OBJECTIVE Agarose gel electrophoresis has been the mainstay technique for the analysis of DNA samples of moderate size. In addition to separating linear DNA molecules, it can also resolve different topological forms of plasmid DNAs, an application useful for the analysis of the reactions of DNA topoisomerases. However, gel electrophoresis is an intrinsically low-throughput technique and suffers from other potential disadvantages. We describe the application of the QIAxcel Advanced System, a high-throughput capillary electrophoresis system, to separate DNA topoisomers, and compare this technique with gel electrophoresis. RESULTS We prepared a range of topoisomers of plasmids pBR322 and pUC19, and a 339 bp DNA minicircle, and compared their separation by gel electrophoresis and the QIAxcel System. We found superior resolution with the QIAxcel System, and that quantitative analysis of topoisomer distributions was straightforward. We show that the QIAxcel system has advantages in terms of speed, resolution and cost, and can be applied to DNA circles of various sizes. It can readily be adapted for use in compound screening against topoisomerase targets.
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Affiliation(s)
- Lesley A. Mitchenall
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Rachel E. Hipkin
- Qiagen Ltd., Skelton House, Lloyd St. North, Manchester, M15 6SH UK
- Present Address: Fluidigm Ltd, 12 New Fetter Lane, London, EC4A 1JP UK
| | - Michael M. Piperakis
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: University Centre, Blackburn College, University Close, Blackburn, Lancashire BB2 1LH UK
| | - Nicolas P. Burton
- Inspiralis Ltd, Innovation Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
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Ceccarelli M, Galluzzi L, Diotallevi A, Andreoni F, Fowler H, Petersen C, Vitale F, Magnani M. The use of kDNA minicircle subclass relative abundance to differentiate between Leishmania (L.) infantum and Leishmania (L.) amazonensis. Parasit Vectors 2017; 10:239. [PMID: 28511704 DOI: 10.1186/s13071-017-2181-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leishmaniasis is a neglected disease caused by many Leishmania species, belonging to subgenera Leishmania (Leishmania) and Leishmania (Viannia). Several qPCR-based molecular diagnostic approaches have been reported for detection and quantification of Leishmania species. Many of these approaches use the kinetoplast DNA (kDNA) minicircles as the target sequence. These assays had potential cross-species amplification, due to sequence similarity between Leishmania species. Previous works demonstrated discrimination between L. (Leishmania) and L. (Viannia) by SYBR green-based qPCR assays designed on kDNA, followed by melting or high-resolution melt (HRM) analysis. Importantly, these approaches cannot fully distinguish L. (L.) infantum from L. (L.) amazonensis, which can coexist in the same geographical area. METHODS DNA from 18 strains/isolates of L. (L.) infantum, L. (L.) amazonensis, L. (V.) braziliensis, L. (V.) panamensis, L. (V.) guyanensis, and 62 clinical samples from L. (L.) infantum-infected dogs were amplified by a previously developed qPCR (qPCR-ML) and subjected to HRM analysis; selected PCR products were sequenced using an ABI PRISM 310 Genetic Analyzer. Based on the obtained sequences, a new SYBR-green qPCR assay (qPCR-ama) intended to amplify a minicircle subclass more abundant in L. (L.) amazonensis was designed. RESULTS The qPCR-ML followed by HRM analysis did not allow discrimination between L. (L.) amazonensis and L. (L.) infantum in 53.4% of cases. Hence, the novel SYBR green-based qPCR (qPCR-ama) has been tested. This assay achieved a detection limit of 0.1 pg of parasite DNA in samples spiked with host DNA and did not show cross amplification with Trypanosoma cruzi or host DNA. Although the qPCR-ama also amplified L. (L.) infantum strains, the Cq values were dramatically increased compared to qPCR-ML. Therefore, the combined analysis of Cq values from qPCR-ML and qPCR-ama allowed to distinguish L. (L.) infantum and L. (L.) amazonensis in 100% of tested samples. CONCLUSIONS A new and affordable SYBR-green qPCR-based approach to distinguish between L. (L.) infantum and L. (L.) amazonensis was developed exploiting the major abundance of a minicircle sequence rather than targeting a hypothetical species-specific sequence. The fast and accurate discrimination between these species can be useful to provide adequate prognosis and treatment.
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Brenciani A, Morroni G, Mingoia M, Varaldo PE, Giovanetti E. Stability of the cargo regions of the cfr-carrying, multiresistance plasmid pSP01 from Staphylococcus epidermidis. Int J Med Microbiol 2016; 306:717-21. [PMID: 27554790 DOI: 10.1016/j.ijmm.2016.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/20/2016] [Accepted: 08/14/2016] [Indexed: 11/20/2022] Open
Abstract
This study investigated the stability or instability - i.e. the ability or inability to undergo excision in circular form - of the four cargo regions (cr1 to cr4) of the novel cfr-carrying, multiresistance plasmid pSP01, arboured by a clinical Staphylococcus epidermidis isolate. Only cr4 proved unstable. The stability of cr1 and cr2 was substantially expected. Insertion sequences (ISs) played an important role in the stability of cr3 (the cfr gene context) and in the instability of cr4. Whereas the stability of cfr genetic contexts is associated with the presence of a single IS copy (istAS-istBS in cr3), their instability is associated with two identical, flanking ISs with the same orientation. cr4 is bracketed between two identical IS257 elements, and appears to behave as a composite transposon. Its instability is of interest because of the existence of a closely related cfr plasmid from S. epidermidis (pSP01.1) that differs from pSP01 only by the lack of cr4. An integration/recombination mechanism is suggested to explain how cr4 may have moved to pSP01.1 to form pSP01.
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Bazzani RP, Pringle IA, Connolly MM, Davies LA, Sumner-Jones SG, Schleef M, Hyde SC, Gill DR. Transgene sequences free of CG dinucleotides lead to high level, long-term expression in the lung independent of plasmid backbone design. Biomaterials 2016; 93:20-26. [PMID: 27061267 DOI: 10.1016/j.biomaterials.2016.03.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/17/2016] [Accepted: 03/17/2016] [Indexed: 12/13/2022]
Abstract
Non-viral aerosol gene therapy offers great potential for treating chronic lung diseases of the airways such as cystic fibrosis (CF). Early clinical trials showed that transgene expression in the airways was transient whereas maximal duration of transgene expression is essential in order to minimise the frequency of aerosol treatments. Improved vector design, such as careful selection of the promoter/enhancer, can lead to more persistent levels of transgene expression, but multiple factors affect expression in vivo. Following aerosol delivery to the lungs of mice, we measured reporter gene expression from a CpG-free luciferase transgene cassette in the context of both a plasmid and minicircle vector configuration and showed that the vector backbone had no effect on expression. Transgene activity was affected by the vector backbone however, when a similar, but sub-optimal CpG-containing transgene was used, suggesting that aspects of the plasmid backbone had a negative impact on transgene expression. Similar studies were performed in Toll-like receptor-9 (TLR9) knockout mice to investigate a potential role for the TLR9 signalling pathway in detecting CpGs in the vector sequence. Even in the absence of TLR9, persistent expression could only be achieved with a CpG-free transgene. Together, these data indicate that in order to achieve high levels of persistent expression in vivo, a CpG-free transgene cassette is required.
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Affiliation(s)
- Reto P Bazzani
- Gene Medicine Research Group, NDCLS, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DU, UK; The UK Cystic Fibrosis Gene Therapy Consortium, UK
| | - Ian A Pringle
- Gene Medicine Research Group, NDCLS, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DU, UK; The UK Cystic Fibrosis Gene Therapy Consortium, UK
| | - Mary M Connolly
- Gene Medicine Research Group, NDCLS, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DU, UK; The UK Cystic Fibrosis Gene Therapy Consortium, UK
| | - Lee A Davies
- Gene Medicine Research Group, NDCLS, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DU, UK; The UK Cystic Fibrosis Gene Therapy Consortium, UK
| | - Stephanie G Sumner-Jones
- Gene Medicine Research Group, NDCLS, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DU, UK; The UK Cystic Fibrosis Gene Therapy Consortium, UK
| | - Martin Schleef
- PlasmidFactory, Meisenstraße 96, D-33607 Bielefeld, Germany
| | - Stephen C Hyde
- Gene Medicine Research Group, NDCLS, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DU, UK; The UK Cystic Fibrosis Gene Therapy Consortium, UK
| | - Deborah R Gill
- Gene Medicine Research Group, NDCLS, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DU, UK; The UK Cystic Fibrosis Gene Therapy Consortium, UK.
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Abstract
DNA vectors have the potential to become powerful medical tools for treatment of human disease. The human body has, however, developed a range of defensive strategies to detect and silence foreign or misplaced DNA, which is more typically encountered during infection or chromosomal damage. A clinically relevant human gene therapy vector must overcome or avoid these protections whilst delivering sustained levels of therapeutic gene product without compromising the vitality of the recipient host. Many non-viral DNA vectors trigger these defense mechanisms and are subsequently destroyed or rendered silent. Thus, without modification or considered design, the clinical utility of a typical DNA vector is fundamentally limited due to the transient nature of its transgene expression. The development of safe and persistently expressing DNA vectors is a crucial prerequisite for its successful clinical application and subsequently remains, therefore, one of the main strategic tasks of non-viral gene therapy research. In this chapter we will describe our current understanding of the mechanisms that can destroy or silence DNA vectors and discuss strategies, which have been utilized to improve their sustenance and the level and duration of their transgene expression.
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Affiliation(s)
- Suet Ping Wong
- Leukocyte Biology Section, National Heart & Lung Institute, Imperial College London, London, UK
| | - Orestis Argyros
- Division of Pharmacology-Pharmacotechnology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Richard P Harbottle
- DNA Vector Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
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