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Sinha S, Medhi B, Sehgal R. Challenges of drug-resistant malaria. ACTA ACUST UNITED AC 2014; 21:61. [PMID: 25402734 PMCID: PMC4234044 DOI: 10.1051/parasite/2014059] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 10/23/2014] [Indexed: 01/09/2023]
Abstract
Over the past six decades, the drug resistance of Plasmodium falciparum has become an issue of utmost concern. Despite the remarkable progress that has been made in recent years in reducing the mortality rate to about 30% with the scaling-up of vector control, introduction of artemisinin-based combination therapies and other malaria control strategies, the confirmation of artemisinin resistance on the Cambodia–Thailand border threatened all the previous success. This review addresses the global scenario of antimalarial resistance and factors associated with it, with the main emphasis on futuristic approaches like nanotechnology and stem cell therapy that may impede resistant malaria, along with novel medications which are preparing to enter the global antimalarial market. These novel studies are likely to escalate over the coming years and will hopefully help to reduce the burden of malaria.
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Affiliation(s)
- Shweta Sinha
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Rakesh Sehgal
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
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Aditya N, Vathsala P, Vieira V, Murthy R, Souto E. Advances in nanomedicines for malaria treatment. Adv Colloid Interface Sci 2013; 201-202:1-17. [PMID: 24192063 DOI: 10.1016/j.cis.2013.10.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/10/2013] [Accepted: 10/13/2013] [Indexed: 01/28/2023]
Abstract
Malaria is an infectious disease that mainly affects children and pregnant women from tropical countries. The mortality rate of people infected with malaria per year is enormous and became a public health concern. The main factor that has contributed to the success of malaria proliferation is the increased number of drug resistant parasites. To counteract this trend, research has been done in nanotechnology and nanomedicine, for the development of new biocompatible systems capable of incorporating drugs, lowering the resistance progress, contributing for diagnosis, control and treatment of malaria by target delivery. In this review, we discussed the main problems associated with the spread of malaria and the most recent developments in nanomedicine for anti-malarial drug delivery.
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Pino P, Sebastian S, Kim E, Bush E, Brochet M, Volkmann K, Kozlowski E, Llinás M, Billker O, Soldati-Favre D. A Tetracycline-Repressible Transactivator System to Study Essential Genes in Malaria Parasites. Cell Host Microbe 2012; 12:824-34. [PMID: 23245327 PMCID: PMC3712325 DOI: 10.1016/j.chom.2012.10.016] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 09/10/2012] [Accepted: 10/12/2012] [Indexed: 11/25/2022]
Abstract
A major obstacle in analyzing gene function in apicomplexan parasites is the absence of a practical regulatable expression system. Here, we identified functional transcriptional activation domains within Apicomplexan AP2 (ApiAP2) family transcription factors. These ApiAP2 transactivation domains were validated in blood-, liver-, and mosquito-stage parasites and used to create a robust conditional expression system for stage-specific, tetracycline-dependent gene regulation in Toxoplasma gondii, Plasmodium berghei, and Plasmodium falciparum. To demonstrate the utility of this system, we created conditional knockdowns of two essential P. berghei genes: profilin (PRF), a protein implicated in parasite invasion, and N-myristoyltransferase (NMT), which catalyzes protein acylation. Tetracycline-induced repression of PRF and NMT expression resulted in a dramatic reduction in parasite viability. This efficient regulatable system will allow for the functional characterization of essential proteins that are found in these important parasites.
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Schwentke A, Krepstakies M, Mueller AK, Hammerschmidt-Kamper C, Motaal BA, Bernhard T, Hauber J, Kaiser A. In vitro and in vivo silencing of plasmodial dhs and eIf-5a genes in a putative, non-canonical RNAi-related pathway. BMC Microbiol 2012; 12:107. [PMID: 22694849 PMCID: PMC3438091 DOI: 10.1186/1471-2180-12-107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Accepted: 05/31/2012] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Deoxyhypusine synthase (DHS) catalyzes the first step in hypusine biosynthesis of eukaryotic initiation factor 5A (eIF-5A) in Plasmodium falciparum. Target evaluation of parasitic DHS has recently been performed with CNI-1493, a novel selective pro-inflammatory cytokine inhibitor used in clinical phase II for the treatment of Crohn's disease. CNI-1493 prevented infected mice from experimental cerebral malaria by decreasing the levels in hypusinated eIF-5A and serum TNF, implicating a link between cytokine signaling and the hypusine pathway.Therefore we addressed the question whether either DHS itself or eIF-5A is required for the outcome of severe malaria. In a first set of experiments we performed an in vitro knockdown of the plasmodial eIF-5A and DHS proteins by RNA interference (RNAi) in 293 T cells. Secondly, transfection of siRNA constructs into murine Plasmodium schizonts was performed which, in turn, were used for infection. RESULTS 293 T cells treated with plasmodial DHS- and eIF-5A specific siRNAs or control siRNAs were analyzed by RT-PCR to determine endogenous dhs -and eIF-5A mRNA levels. The expressed DHS-shRNA and EIF-5A-shRNA clearly downregulated the corresponding transcript in these cells. Interestingly, mice infected with transgenic schizonts expressing either the eIF-5A or dhs shRNA showed an elevated parasitemia within the first two days post infection which then decreased intermittently. These results were obtained without drug selection. Blood samples, which were taken from the infected mice at day 5 post infection with either the expressed EIF-5A-shRNA or the DHS-shRNA were analyzed by RT-PCR and Western blot techniques, demonstrating the absence of either the hypusinated form of eIF-5A or DHS. CONCLUSIONS Infection of NMRI mice with schizonts from the lethal P. berghei ANKA wildtype strain transgenic for plasmodial eIF-5A-specific shRNA or DHS-specific shRNA resulted in low parasitemia 2-9 days post infection before animals succumbed to hyperparasitemia similar to infections with the related but non-lethal phenotype P. berghei strain NK65. RT-PCR and Western blot experiments performed with blood from the transfected erythrocytic stages showed that both genes are important for the proliferation of the parasite. Moreover, these experiments clearly demonstrate that the hypusine pathway in Plasmodium is linked to human iNos induction.
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Affiliation(s)
- Andreas Schwentke
- University Duisburg-Essen, Medical Research Centre, Institute of Pharmacogenetics, Hufelandstrasse 55, 45147, Essen, Germany
| | - Marcel Krepstakies
- Heinrich Pette Institute - Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Ann-Kristin Mueller
- Department of Infectious Diseases, Parasitology Unit, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Christiane Hammerschmidt-Kamper
- Department of Infectious Diseases, Parasitology Unit, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Basma A Motaal
- Heinrich Pette Institute - Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Tina Bernhard
- University Duisburg-Essen, Medical Research Centre, Institute of Pharmacogenetics, Hufelandstrasse 55, 45147, Essen, Germany
| | - Joachim Hauber
- Heinrich Pette Institute - Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany
| | - Annette Kaiser
- University Duisburg-Essen, Medical Research Centre, Institute of Pharmacogenetics, Hufelandstrasse 55, 45147, Essen, Germany
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Abstract
Parasitic diseases cause important losses in public and veterinary health worldwide. Novel drugs, more reliable diagnostic techniques and vaccine candidates are urgently needed. Due to the complexity of parasites and the intricate relationship with their hosts, development of successful tools to fight parasites has been very limited to date. The growing information on individual parasite genomes is now allowing the use of a broader range of potential strategies to gain deeper insights into the host-parasite relationship and has increased the possibilities to develop molecular-based tools in the field of parasitology. Nevertheless, functional studies of respective genes are still scarce. The RNA interference phenomenon resulting in the regulation of protein expression through the specific degradation of defined mRNAs, and more specifically the possibility of artificially induce it, has shown to be a powerful tool for the investigation of proteins function in many organisms. Recent advances in the design and delivery of targeting molecules allow efficient and highly specific gene silencing in different types of parasites, pointing out this technology as a powerful tool for the identification of novel vaccine candidates or drug targets at the high-throughput level in the near future, and could enable researchers to functionally annotate parasite genomes. The aim of this review is to provide a comprehensive overview on the current advances and pitfalls in gene silencing mechanisms, techniques, applications and prospects in animal parasites.
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RNA interference in protozoan parasites: achievements and challenges. EUKARYOTIC CELL 2011; 10:1156-63. [PMID: 21764910 DOI: 10.1128/ec.05114-11] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protozoan parasites that profoundly affect mankind represent an exceptionally diverse group of organisms, including Plasmodium, Toxoplasma, Entamoeba, Giardia, trypanosomes, and Leishmania. Despite the overwhelming impact of these parasites, there remain many aspects to be discovered about mechanisms of pathogenesis and how these organisms survive in the host. Combined with the ever-increasing availability of sequenced genomes, RNA interference (RNAi), discovered a mere 13 years ago, has enormously facilitated the analysis of gene function, especially in organisms that are not amenable to classical genetic approaches. Here we review the current status of RNAi in studies of parasitic protozoa, with special emphasis on its use as a postgenomic tool.
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Batista TM, Marques JT. RNAi pathways in parasitic protists and worms. J Proteomics 2011; 74:1504-14. [PMID: 21385631 DOI: 10.1016/j.jprot.2011.02.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 02/24/2011] [Accepted: 02/26/2011] [Indexed: 12/15/2022]
Abstract
Tropical diseases caused by parasitic worms and protists are of major public health concern affecting millions of people worldwide. New therapeutic and diagnostic tools would be of great help in dealing with the public health and economic impact of these diseases. RNA interference (RNAi) pathways utilize small non-coding RNAs to regulate gene expression in a sequence-specific manner. In recent years, a wealth of data about the mechanisms and biological functions of RNAi pathways in distinct groups of eukaryotes has been described. Often, RNAi pathways have unique features that are restricted to groups of eukaryotes. The focus of this review will be on RNAi pathways in specific groups of parasitic eukaryotes that include Trypanosoma cruzi, Plasmodium and Schistosoma mansoni. These parasites are the causative agents of Chagas disease, Malaria, and Schistosomiasis, respectively, all of which are tropical diseases that would greatly benefit from the development of new diagnostic and therapeutic tools. In this context, we will describe specific features of RNAi pathways in each of these parasitic eukaryotic groups and discuss how they could be exploited for the treatment of tropical diseases.
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Affiliation(s)
- Thiago Mafra Batista
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Rosenthal PJ. Falcipains and other cysteine proteases of malaria parasites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 712:30-48. [PMID: 21660657 DOI: 10.1007/978-1-4419-8414-2_3] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A number of cysteine proteases of malaria parasites have been described and many more are suggested by analysis of the Plasmodium falciparum genome sequence. The best characterized of these proteases are the falcipains, a family of four papain-family enzymes. Falcipain-2 and falcipain-3 act in concert with other proteases to hydrolyze host erythrocyte hemoglobin in the parasite food vacuole. Disruption of the falcipain-2 gene led to a transient block in hemoglobin hydrolysis and parasites with increased sensitivity to protease inhibitors. Disruption of the falcipain-3 gene was not possible, strongly suggesting that this protease is essential for erythrocytic parasites. Disruption of the falcipain-1 gene did not alter development in erythrocytes, but led to decreased production of oocysts in mosquitoes. other papain-family proteases predicted by the genome sequence include dipeptidyl peptidases, a calpain homolog and serine-repeat antigens (SERAs). Dipeptidyl aminopeptidase 1 appears to be essential and localized to the food vacuole, suggesting a role in hemoglobin hydrolysis. Dipeptidyl aminopeptidase 3 appears to play a role in the rupture of erythrocytes by mature parasites. the P. falciparum calpain homolog gene could not be disrupted, suggesting that the protein is essential and a role in the parasite cell cycle has been suggested. Nine P. falciparum SERAs have cysteine protease motifs, but in some the active site cys is replaced by a Ser. Gene disruption studies suggested that SERA-5 and SERA-6 are essential. activation of SERA-5 by a serine protease seems to be required for merozoite egress from the erythrocyte. New drugs for malaria are greatly needed and cysteine proteases represent potential drug targets. cysteine protease inhibitors have demonstrated potent antimalarial effects and the optimization and testing of falcipain inhibitor antimalarials is underway.
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Affiliation(s)
- Philip J Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, California, USA.
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Matrajt M. Non-coding RNA in apicomplexan parasites. Mol Biochem Parasitol 2010; 174:1-7. [PMID: 20566348 DOI: 10.1016/j.molbiopara.2010.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Revised: 05/29/2010] [Accepted: 06/01/2010] [Indexed: 11/28/2022]
Abstract
In recent years it has became evident that the transcriptome of most species has little protein-coding capacity and that the abundance of non-coding RNA was previously overlooked. Non-coding RNAs were initially thought to be transcriptional noise, however, a growing number of studies is showing that many of these RNAs have important regulatory functions. Here, we review the progress done in apicomplexan parasites in this rapidly growing field.
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Affiliation(s)
- Mariana Matrajt
- Department of Microbiology and Molecular Genetics, University of Vermont, Stafford Hall, Room 306, 95 Carrigan Drive, Burlington, VT 05405, United States.
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Baum J, Papenfuss AT, Mair GR, Janse CJ, Vlachou D, Waters AP, Cowman AF, Crabb BS, de Koning-Ward TF. Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites. Nucleic Acids Res 2009; 37:3788-98. [PMID: 19380379 PMCID: PMC2699523 DOI: 10.1093/nar/gkp239] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 03/30/2009] [Accepted: 03/30/2009] [Indexed: 01/02/2023] Open
Abstract
Techniques for targeted genetic disruption in Plasmodium, the causative agent of malaria, are currently intractable for those genes that are essential for blood stage development. The ability to use RNA interference (RNAi) to silence gene expression would provide a powerful means to gain valuable insight into the pathogenic blood stages but its functionality in Plasmodium remains controversial. Here we have used various RNA-based gene silencing approaches to test the utility of RNAi in malaria parasites and have undertaken an extensive comparative genomics search using profile hidden Markov models to clarify whether RNAi machinery exists in malaria. These investigative approaches revealed that Plasmodium lacks the enzymology required for RNAi-based ablation of gene expression and indeed no experimental evidence for RNAi was observed. In its absence, the most likely explanations for previously reported RNAi-mediated knockdown are either the general toxicity of introduced RNA (with global down-regulation of gene expression) or a specific antisense effect mechanistically distinct from RNAi, which will need systematic analysis if it is to be of use as a molecular genetic tool for malaria parasites.
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Affiliation(s)
- Jake Baum
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal, Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands, Division of Infection and Immunity, Institute of Biomedical Life Sciences & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, G12 8TA, Scotland, UK, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004 and Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Anthony T. Papenfuss
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal, Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands, Division of Infection and Immunity, Institute of Biomedical Life Sciences & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, G12 8TA, Scotland, UK, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004 and Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Gunnar R. Mair
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal, Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands, Division of Infection and Immunity, Institute of Biomedical Life Sciences & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, G12 8TA, Scotland, UK, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004 and Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Chris J. Janse
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal, Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands, Division of Infection and Immunity, Institute of Biomedical Life Sciences & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, G12 8TA, Scotland, UK, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004 and Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Dina Vlachou
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal, Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands, Division of Infection and Immunity, Institute of Biomedical Life Sciences & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, G12 8TA, Scotland, UK, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004 and Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Andrew P. Waters
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal, Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands, Division of Infection and Immunity, Institute of Biomedical Life Sciences & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, G12 8TA, Scotland, UK, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004 and Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Alan F. Cowman
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal, Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands, Division of Infection and Immunity, Institute of Biomedical Life Sciences & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, G12 8TA, Scotland, UK, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004 and Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Brendan S. Crabb
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal, Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands, Division of Infection and Immunity, Institute of Biomedical Life Sciences & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, G12 8TA, Scotland, UK, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004 and Deakin University, Waurn Ponds, Victoria 3217, Australia
| | - Tania F. de Koning-Ward
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal, Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands, Division of Infection and Immunity, Institute of Biomedical Life Sciences & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, G12 8TA, Scotland, UK, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004 and Deakin University, Waurn Ponds, Victoria 3217, Australia
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11
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Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel. Genetica 2008; 136:189-209. [PMID: 19057851 DOI: 10.1007/s10709-008-9336-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 11/17/2008] [Indexed: 10/21/2022]
Abstract
The spread of drug resistance through malaria parasite populations calls for the development of new therapeutic strategies. However, the seemingly promising genomics-driven target identification paradigm is hampered by the weak annotation coverage. To identify potentially important yet uncharacterized proteins, we apply support vector machines using profile kernels, a supervised discriminative machine learning technique for remote homology detection, as a complement to the traditional alignment based algorithms. In this study, we focus on the prediction of proteases, which have long been considered attractive drug targets because of their indispensable roles in parasite development and infection. Our analysis demonstrates that an abundant and complex repertoire is conserved in five Plasmodium parasite species. Several putative proteases may be important components in networks that mediate cellular processes, including hemoglobin digestion, invasion, trafficking, cell cycle fate, and signal transduction. This catalog of proteases provides a short list of targets for functional characterization and rational inhibitor design.
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12
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Abstract
In this chapter, we outline the tools and techniques available to study the process of host cell invasion by apicomplexan parasites and we provide specific examples of how these methods have been used to further our understanding of apicomplexan invasive mechanisms. Throughout the chapter we focus our discussion on Toxoplasmagondii, because T. gondii is the most experimentally accessible model organism for studying apicomplexan invasion (discussed further in the section, "Toxoplasma as a Model Apicomplexan") and more is known about invasion in T. gondii than in any other apicomplexan.
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13
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Xue X, Zhang Q, Huang Y, Feng L, Pan W. No miRNA were found in Plasmodium and the ones identified in erythrocytes could not be correlated with infection. Malar J 2008; 7:47. [PMID: 18328111 PMCID: PMC2329658 DOI: 10.1186/1475-2875-7-47] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Accepted: 03/10/2008] [Indexed: 12/14/2022] Open
Abstract
Background The transcriptional regulation of Plasmodium during its complex life cycle requires sequential activation and/or repression of different genetic programmes. MicroRNAs (miRNAs) are a highly conserved class of non-coding RNAs that are important in regulating diverse cellular functions by sequence-specific inhibition of gene expression. What is know about double-stranded RNA-mediated gene silencing (RNAi) and posttranscriptional gene silencing (PTGS) in Plasmodium parasites entice us to speculate whether miRNAs can also function in Plasmodium-infected RBCs. Results Of 132 small RNA sequences, no Plasmodium-specific miRNAs have been found. However, a human miRNA, miR-451, was highly expressed, comprising approximately one third of the total identified miRNAs. Further analysis of miR-451 expression and malaria infection showed no association between the accumulation of miR-451 in Plasmodium falciparum-iRBCs, the life cycle stage of P. falciparum in the erythrocyte, or of P. berghei in mice. Moreover, treatment with an antisense oligonucleotide to miR-451 had no significant effect on the growth of the erythrocytic-stage P. falciparum. Methods Short RNAs from a mixed-stage of P. falciparum-iRBC were separated in a denaturing polyacrylamide gel and cloned into T vectors to create a cDNA library. Individual clones were then sequenced and further analysed by bioinformatics prediction to discover probable miRNAs in P. falciparum-iRBC. The association between miR-451 expression and the parasite were analysed by Northern blotting and antisense oligonucleotide (ASO) of miR-451. Conclusion These results contribute to eliminate the probability of miRNAs in P. falciparum. The absence of miRNA in P. falciparum could be correlated with absence of argonaute/dicer genes. In addition, the miR-451 accumulation in Plasmodium-infected RBCs is independent of parasite infection. Its accumulation might be only the residual of erythroid differentiation or a component to maintain the normal function of mature RBCs.
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Affiliation(s)
- Xiangyang Xue
- Institute for Infectious Diseases and Vaccine Development, Tongji University College of Medicine, 1239 Siping Road, Shanghai 200092, China.
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14
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Pereira TC, Pascoal VDB, Marchesini RB, Maia IG, Magalhães LA, Zanotti-Magalhães EM, Lopes-Cendes I. Schistosoma mansoni: evaluation of an RNAi-based treatment targeting HGPRTase gene. Exp Parasitol 2008; 118:619-23. [PMID: 18237732 DOI: 10.1016/j.exppara.2007.11.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 10/15/2007] [Accepted: 11/14/2007] [Indexed: 11/16/2022]
Abstract
Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase) is an essential gene of the parasite Schistosoma mansoni and it is well conserved in its hosts (mouse and human) at the protein but not at the RNA level. This feature prompted us to assess RNA interference (RNAi) to combat schistosomiasis. Small interfering RNAs (siRNAs) were produced against HGPRTase, injected in infected mice and the number of worms was counted six days after injection. The total number of parasites was reduced by approximately 27% after treatment. RT-PCR analyzes showed a significant reduction in parasite target mRNA but not in host's homologue. The use of low doses of molecules did not oversaturate si- or miRNA pathways as mice survival rates were not affected by siRNAs. This is the first successful in vivo demonstration of a RNAi-based treatment against schistosomiasis. We believe that improvements in molecule delivery and an increase on siRNA dose could rapidly eliminate parasite.
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Affiliation(s)
- T C Pereira
- Departamento de Genética Médica, Universidade Estadual de Campinas, Cidade Universitária Zeferino Vaz, FCM, Unicamp-Campinas, São Paulo, Brazil 13084-971
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15
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Yu L, Gao YF, Qiao ZP, Li CL, Li X, Shen JL. Toxoplasma gondii: siRNA can mediate the suppression of adenosine kinase expression. Exp Parasitol 2008; 118:96-102. [PMID: 17888425 DOI: 10.1016/j.exppara.2007.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 07/05/2007] [Accepted: 07/16/2007] [Indexed: 02/05/2023]
Abstract
Adenosine kinase (AK) is one of the most important enzymes in the Toxoplasma gondii purine salvage pathway. Three siRNAs specific to the AK gene were designed in the present study. At 24h following electroporation, two of them (siRNA786 and siRNA1200) significantly reduced the mRNA level compared with mock electroporation (P <0.05). The ability to incorporate [3H]-adenosine in the parasites electroporated with 4 microM siRNA786 or 4 microM siRNA1200 was decreased to 39+/-11% and 39+/-7% of the mock electroporation, respectively. At the 48th hour of electroporation, the enzyme's activity was still significantly lower than that of mock electroporation. The data show the siRNAs transfected into cells can work efficiently to regulate gene expression in T. gondii. The application of siRNA in interrupting gene expression in T. gondii would be useful for elucidating gene function as a step toward development of anti-toxoplasmasis vaccines and therapeutic reagents.
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Affiliation(s)
- Li Yu
- Institute of Clinical Pharmacology and Department of Pathobiology, Anhui Medical University, Hefei, Anhui 230032, PR China
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16
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Militello KT, Refour P, Comeaux CA, Duraisingh MT. Antisense RNA and RNAi in protozoan parasites: working hard or hardly working? Mol Biochem Parasitol 2007; 157:117-26. [PMID: 18053590 DOI: 10.1016/j.molbiopara.2007.10.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 10/11/2007] [Accepted: 10/12/2007] [Indexed: 10/22/2022]
Abstract
The complex life cycles of many protozoan parasites require the ability to respond to environmental and developmental cues through regulated gene expression. Traditionally, parasitologists have investigated these mechanisms by identifying and characterizing proteins that are necessary for the regulated expression of the genetic material. Although often successful, it is clear that protein-mediated gene regulation is only part of a complex story in which RNA itself is endowed with regulatory functions. Herein, we review both the known and potential regulatory roles of two types of RNA pathways within protozoan parasites: the RNA interference pathway and natural antisense transcripts. A better understanding of the native role of these pathways will not only enhance our understanding of the biology of these organisms but also aid in the development of more robust tools for reverse genetic analysis in this post-genomic era.
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Affiliation(s)
- Kevin T Militello
- Department of Biology, State University of New York at Geneseo, Geneseo, NY, USA
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17
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Meissner M, Agop-Nersesian C, Sullivan WJ. Molecular tools for analysis of gene function in parasitic microorganisms. Appl Microbiol Biotechnol 2007; 75:963-75. [PMID: 17401559 DOI: 10.1007/s00253-007-0946-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 03/12/2007] [Accepted: 03/12/2007] [Indexed: 01/01/2023]
Abstract
With the completion of several genome sequences for parasitic protozoa, research in molecular parasitology entered the "post-genomic" era. Accompanied by global transcriptome and proteome analysis, huge datasets have been generated that have added many novel candidates to the list of drug and vaccine targets. The challenge is now to validate these factors and to bring science back to the bench to perform a detailed characterization. In some parasites, like Trypanosoma brucei, high-throughput genetic screens have been established using RNA interference [for a detailed review, see Motyka and Englund (2004)]. In most protozoan parasites, however, more time-consuming approaches have to be employed to identify and characterize the function of promising candidates in detail. This review aims to summarize the status of molecular genetic tools available for a variety of protozoan pathogens and discuss how they can be implemented to advance our understanding of parasite biology.
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Affiliation(s)
- Markus Meissner
- Hygieneinstitut, Abteilung Parasitologie, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.
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18
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Akhtar S, Benter I. Toxicogenomics of non-viral drug delivery systems for RNAi: potential impact on siRNA-mediated gene silencing activity and specificity. Adv Drug Deliv Rev 2007; 59:164-82. [PMID: 17481774 DOI: 10.1016/j.addr.2007.03.010] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2007] [Accepted: 03/04/2007] [Indexed: 01/05/2023]
Abstract
RNA interference (RNAi) is an evolutionary conserved cellular process for the regulation of gene expression. In mammalian cells, RNAi is induced via short (21-23 nt) duplexes of RNA, termed small interfering RNA (siRNA), that can elicit highly sequence-specific gene silencing. However, synthetic siRNA duplexes are polyanionic macromolecules that do not readily enter cells and typically require the use of a delivery vector for effective gene silencing in vitro and in vivo. Choice of delivery system is usually made on its ability to enhance cellular uptake of siRNA. However, recent gene expression profiling (toxicogenomics) studies have shown that separate from their effects on cellular uptake, delivery systems can also elicit wide ranging gene changes in target cells that may impact on the 'off-target' effects of siRNA. Furthermore, if delivery systems also alter the expression of genes targeted for silencing, then siRNA activity may be compromised or enhanced depending on whether the target gene is up-regulated or down-regulated respectively. Citing recent examples from the literature, this article therefore reviews the toxicogenomics of non-viral delivery systems and highlights the importance of understanding the genomic signature of siRNA delivery reagents in terms of their impact on gene silencing activity and specificity. Such information will be essential in the selection of optimally acting siRNA-delivery system combinations for the many applications of RNA interference.
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Affiliation(s)
- Saghir Akhtar
- SA Pharma, Vesey Road 1, Sutton Coldfield, West Midlands, B73 5NP, United Kingdom.
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19
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Pereira TC, Bittencourt VDP, Secolin R, Rocha CDS, Maia IDG, Lopes-Cendes I. Strand Analysis, a free online program for the computational identification of the best RNA interference (RNAi) targets based on Gibbs free energy. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000600030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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20
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Rathjen T, Nicol C, McConkey G, Dalmay T. Analysis of short RNAs in the malaria parasite and its red blood cell host. FEBS Lett 2006; 580:5185-8. [PMID: 16963026 DOI: 10.1016/j.febslet.2006.08.063] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Revised: 07/14/2006] [Accepted: 08/11/2006] [Indexed: 02/01/2023]
Abstract
RNA interference (RNAi) is an RNA degradation process that involves short, double-stranded RNAs (dsRNA) as sequence specificity factors. The natural function of the RNAi machinery is to generate endogenous short double-stranded RNAs to regulate gene expression. It has been shown that treatment of Plasmodium falciparum, the etiologic agent of malaria, with dsRNA induces degradation of the corresponding microRNA (miRNA), yet typical RNAi-associated genes have not been identifiable in the parasite genome. To clarify this discrepancy we set out to clone short RNAs from P. falciparum-infected red blood cells and from purified parasites. We did not find any short RNA that was not a rRNA or tRNA fragment. Indeed, only known human miRNAs were isolated in parasite preparations indicating that very few if any short RNAs exist in P. falciparum. This suggests a different mechanism than classical RNAi in observations of dsRNA-mediated degradation. Of the human miRNAs identified, the human miRNA mir-451 accumulates at a very high level in both infected and healthy red blood cells. Interestingly, mir-451 was not detectable in a series of immortalised cell lines representing progenitor stages of all major blood lineages, suggesting that mir-451 may play a role in the differentiation of erythroid cells.
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MESH Headings
- Animals
- Cell Differentiation/drug effects
- Cell Differentiation/genetics
- Cloning, Molecular
- Erythrocytes/metabolism
- Erythrocytes/parasitology
- Gene Expression Regulation/drug effects
- Gene Expression Regulation/genetics
- Genome, Protozoan/drug effects
- Genome, Protozoan/genetics
- Humans
- Malaria/genetics
- Malaria/metabolism
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Plasmodium falciparum/genetics
- Plasmodium falciparum/metabolism
- RNA Stability/drug effects
- RNA Stability/genetics
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Double-Stranded/pharmacology
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Interfering
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
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Affiliation(s)
- Tina Rathjen
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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21
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Abstract
As soon as RNA interference (RNAi) was found to work in mammalian cells, research quickly focused on harnessing this powerful endogenous and specific mechanism of gene silencing for human therapy. RNAi uses small RNAs, less than 30 nucleotides in length, to suppress expression of genes with complementary sequences. Two strategies can introduce small RNAs into the cytoplasm of cells, where they are active - a drug approach where double-stranded RNAs are administered in complexes designed for intracellular delivery and a gene therapy approach to express precursor RNAs from viral vectors. Phase I clinical studies have already begun to test the therapeutic potential of small RNA drugs that silence disease-related genes by RNAi. This review will discuss progress in developing and testing small RNAi-based drugs and potential obstacles.
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Affiliation(s)
- D M Dykxhoorn
- CBR Institute for Biomedical Research and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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22
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Brown AE, Catteruccia F. Toward silencing the burden of malaria: progress and prospects for RNAi-based approaches. Biotechniques 2006; Suppl:38-44. [PMID: 16629386 DOI: 10.2144/000112117] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The discovery of RNA interference (RNAi) is one of the most significant of recent years, with potential for application beyond the laboratory to the clinic. As a tool for functional genomics, RNAi has permitted the characterization of genes in organisms that had previously remained recalcitrant to targeted gene manipulation. Efforts to understand its mode of action have revealed a central role in gene regulation and host defense. Finally, as a therapeutic tool, it has shown enormous promise in the control of a large array of diseases. Here we examine how RNAi is revolutionizing malaria research in an organism, the Anopheles mosquito, that until recently was essentially resistant to genetic study, and show how its application in both the mosquito vector and the Plasmodium parasite might ultimately lead to new ways of controlling and perhaps even eradicating this devastating disease.
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23
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Crooke A, Diez A, Mason PJ, Bautista JM. Transient silencing of Plasmodium falciparum bifunctional glucose-6-phosphate dehydrogenase- 6-phosphogluconolactonase. FEBS J 2006; 273:1537-46. [PMID: 16689939 DOI: 10.1111/j.1742-4658.2006.05174.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The bifunctional enzyme glucose-6-phosphate dehydrogenase-6-phosphogluconolactonase (G6PD-6PGL) found in Plasmodium falciparum has unique structural and functional characteristics restricted to this genus. This study was designed to examine the effects of RNA-mediated PfG6PD-6PGL gene silencing in cultures of P. falciparum on the expression of parasite antioxidant defense genes at the transcription level. The highest degree of G6PD-6PGL silencing achieved was 86% at the mRNA level, with a recovery to almost normal levels within 24 h, indicating only transient diminished expression of the PfG6PD-6PGL gene. PfG6PD-6PGL silencing caused arrest of the trophozoite stage and enhanced gametocyte formation. In addition, an immediate transcriptional response was shown by thioredoxin reductase suggesting that P. falciparum G6PD-6PGL plays a physiological role in the specific response of the parasite to intracellullar oxidative stress. P. falciparum transfection with an empty DNA vector also promoted intracellular stress, as determined by mRNA up-regulation of antioxidant genes. Collectively, our findings point to an important role for this enzyme in the parasite's infection cycle. The different characteristics of G6PD-6PGL with respect to its homologue in the host make it an ideal target for therapeutic strategies.
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Affiliation(s)
- Almudena Crooke
- Department of Biochemistry and Molecular Biology IV, Universidad Complutense de Madrid, Facultad de Veterinaria, Madrid, Spain
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24
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Behlke MA. Progress towards in vivo use of siRNAs. Mol Ther 2006; 13:644-70. [PMID: 16481219 PMCID: PMC7106286 DOI: 10.1016/j.ymthe.2006.01.001] [Citation(s) in RCA: 325] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Revised: 01/11/2006] [Accepted: 01/11/2006] [Indexed: 01/28/2023] Open
Abstract
RNA interference (RNAi) has become the method of choice to suppress gene expression in vitro. It is also emerging as a powerful tool for in vivo research with over 90 studies published using synthetic small interfering RNAs in mammals. These reports demonstrate the potential for use of synthetic small interfering RNAs (siRNAs) as therapeutic agents, especially in the areas of cancer and viral infection. The number of reports using siRNAs for functional genomics applications, for validation of targets for small-molecule drug development programs, and to address questions of basic biology will rapidly grow as methods and protocols for use in animals become more established. This review will first discuss aspects of RNAi biochemistry and biology that impact in vivo use, especially as relates to experimental design, and will then provide an overview of published work with a focus on methodology.
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Affiliation(s)
- Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA.
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25
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Kirk K, Martin RE, Bröer S, Howitt SM, Saliba KJ. Plasmodium permeomics: membrane transport proteins in the malaria parasite. Curr Top Microbiol Immunol 2005; 295:325-56. [PMID: 16265897 DOI: 10.1007/3-540-29088-5_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Membrane transport proteins are integral membrane proteins that mediate the passage across the membrane bilayer of specific molecules and/or ions. Such proteins serve a diverse range of physiological roles, mediating the uptake of nutrients into cells, the removal of metabolic wastes and xenobiotics (including drugs), and the generation and maintenance of transmembrane electrochemical gradients. In this chapter we review the present state of knowledge of the membrane transport mechanisms underlying the cell physiology of the intraerythrocytic malaria parasite and its host cell, considering in particular physiological measurements on the parasite and parasitized erythrocyte, the annotation of transport proteins in the Plasmodium genome, and molecular methods used to analyze transport protein function.
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Affiliation(s)
- K Kirk
- School of Biochemistry and Molecular Biology, The Australian National University, 0200 Canberra, ACT, Australia.
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26
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Torres JA, Rodriguez MH, Rodriguez MC, de la Cruz Hernandez-Hernandez F. Plasmodium berghei: effect of protease inhibitors during gametogenesis and early zygote development. Exp Parasitol 2005; 111:255-9. [PMID: 16198343 DOI: 10.1016/j.exppara.2005.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Revised: 08/11/2005] [Accepted: 08/13/2005] [Indexed: 11/18/2022]
Abstract
Plasmodium berghei: The effect of five protease inhibitors, TPCK, TLCK, PMSF, leupeptin, and 1,10-phenanthroline on in vitro gametogenesis and early zygote development of P. berghei was investigated. PMSF and leupeptin showed no effect. Cysteine/serine protease inhibitors TPCK/TLCK at concentrations of 75 and 100 microM were effective on inhibiting exflagellation center formation, and this effect was reversible with the addition of l-cysteine. Exflagellation center formation was most effectively blocked by 1,10-phenanthroline (1mM), and exflagellation center numbers were restored by the addition of Zn(2+). A reduction of ookinete production was observed when TPCK/TLCK (100 microM) was added at 2h after gametogenesis, but no effect was observed with 1,10-phenanthroline (1mM). Our results suggest that proteolysis is important in both gametocyte activation and sexual development of P. berghei.
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Affiliation(s)
- Jorge A Torres
- Department of Experimental Parasitology, CINVESTAV-IPN, Av. IPN 2508, Col. San Pedro Zacatenco Delegacion G.A. Madero, Mexico 07360 DF, Mexico
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27
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Dykxhoorn DM, Lieberman J. The silent revolution: RNA interference as basic biology, research tool, and therapeutic. Annu Rev Med 2005; 56:401-23. [PMID: 15660519 DOI: 10.1146/annurev.med.56.082103.104606] [Citation(s) in RCA: 225] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA interference (RNAi) is an evolutionarily conserved mechanism for silencing gene expression. In primitive organisms, RNAi protects the genome from viruses and other insertable genetic elements and regulates gene expression during development. The antisense (guide) strand of short double-stranded RNAs is incorporated into an RNA-induced silencing complex that can either suppress protein expression or direct degradation of messenger RNAs that contain homologous sequence(s). The discovery that RNAi works in mammalian cells has sparked intense investigation into its role in normal mammalian cell function, its use as a tool to understand or screen for genes functioning in cellular pathways in healthy and diseased cells and animals, and its potential for therapeutic gene silencing. RNAi may provide an important new therapeutic modality for treating infection, cancer, neurodegenerative disease, and other illnesses, although in vivo delivery of small interfering RNAs into cells remains a significant obstacle.
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Affiliation(s)
- Derek M Dykxhoorn
- CBR Institute for Biomedical Research and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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28
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Gilmore IR, Fox SP, Hollins AJ, Sohail M, Akhtar S. The design and exogenous delivery of siRNA for post-transcriptional gene silencing. J Drug Target 2005; 12:315-40. [PMID: 15545082 DOI: 10.1080/10611860400006257] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
RNA interference (RNAi) is a natural cellular process that effects post-transcriptional gene silencing in eukaryotic systems. Small interfering RNA (siRNA) molecules are the key intermediaries in this process which when exogenously administered can inhibit or "silence" the expression of any given target gene. Thus, siRNA molecules hold great promise as biological tools and as potential therapeutic agents for targeted inhibition of disease-causing genes. However, key challenges to the effective and widespread use of these polyanionic, macromolecular duplexes of RNA are their appropriate design and efficient delivery to cells in vitro and in vivo. This review highlights the current strategies used in the design of effective siRNA molecules and also summarises the main strategies being considered for the exogenous delivery of siRNA for both in vitro and in vivo applications.
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Affiliation(s)
- Ian R Gilmore
- Centre for Genome-based Therapeutics, The Welsh School of Pharmacy, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF10 3XF, UK
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29
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Militello KT, Patel V, Chessler AD, Fisher JK, Kasper JM, Gunasekera A, Wirth DF. RNA polymerase II synthesizes antisense RNA in Plasmodium falciparum. RNA (NEW YORK, N.Y.) 2005; 11:365-370. [PMID: 15703443 PMCID: PMC1370726 DOI: 10.1261/rna.7940705] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2004] [Accepted: 12/10/2004] [Indexed: 05/24/2023]
Abstract
The recent identification of antisense RNA in the transcriptomes of many eukaryotes has generated enormous interest. The presence of antisense RNA in Plasmodium falciparum, the causative agent of severe malaria, remains controversial. Elucidation of the mechanism of antisense RNA in P. falciparum synthesis is critical in order to demonstrate the origin and function of these transcripts. Therefore, a systematic analysis of antisense and sense RNA synthesis was performed using direct labeling experiments. Nuclear run on experiments with single-stranded DNA probes demonstrated that antisense RNA is synthesized in the nucleus at several genomic loci. Antisense RNA synthesis is sensitive to the potent RNA polymerase II inhibitor alpha-amanitin. Antisense and sense transcription was also detected in nuclei isolated from synchronized parasites, suggesting concurrent synthesis. In summary, our experiments directly demonstrate that antisense RNA synthesis is a common transcriptional phenomenon in P. falciparum, and is catalyzed by RNA polymerase II.
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Affiliation(s)
- Kevin T Militello
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, 665 Huntington Avenue, Building I, Room 705, Boston, MA 02115, USA
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30
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Abstract
The large number of candidate genes identified by modern high-throughput technologies require efficient methods for generating knockout phenotypes or gene silencing in order to study gene function. RNA interference (RNAi) is an efficient method that can be used for this purpose. Effective gene silencing by RNAi depends on a number of important parameters, including the dynamics of gene expression and the RNA dose. Using mouse hepatoma cells, we detail some of the principal characteristics of RNAi as a tool for gene silencing, such as the RNA dose level, RNA complex exposure time, and the time of transfection relative to gene induction, in the context of silencing a green fluorescent protein reporter gene. Our experiments demonstrate that different levels of silencing can be attained by modulating the dose level of RNA and the time of transfection and illustrate the importance of a dynamic analysis in designing robust silencing protocols. By quantifying the kinetics of RNAi-based gene silencing, we present a model that may be used to help determine key parameters in more complex silencing experiments and explore alternative gene silencing protocols.
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Affiliation(s)
- R Michael Raab
- Department of Chemical Engineering, Room 56-459, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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31
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Rosenthal PJ. Cysteine proteases of malaria parasites. Int J Parasitol 2004; 34:1489-99. [PMID: 15582526 DOI: 10.1016/j.ijpara.2004.10.003] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Revised: 10/07/2004] [Accepted: 10/07/2004] [Indexed: 11/23/2022]
Abstract
A number of cysteine proteases of malaria parasites have been described, and many more putative cysteine proteases are suggested by analysis of the Plasmodium falciparum genome sequence. Studies with protease inhibitors have suggested roles for cysteine proteases in hemoglobin hydrolysis, erythrocyte rupture, and erythrocyte invasion by erythrocytic malaria parasites. The best characterised Plasmodium cysteine proteases are the falcipains, a family of papain-family (clan CA) enzymes. Falcipain-2 and falcipain-3 are hemoglobinases that appear to hydrolyse host erythrocyte hemoglobin in the parasite food vacuole. This function was recently confirmed for falcipain-2, with the demonstration that disruption of the falcipain-2 gene led to a transient block in hemoglobin hydrolysis. A role for falcipain-1 in erythrocyte invasion was recently suggested, but disruption of the falcipain-1 gene did not alter parasite development. Other papain-family proteases predicted by the genome sequence include dipeptidyl peptidases, a calpain homolog, and serine-repeat antigens. The serine-repeat antigens have cysteine protease motifs, but in some the active site Cys is replaced by a Ser. One of these proteins, SERA-5, was recently shown to have serine protease activity. As SERA-5 and some other serine-repeat antigens localise to the parasitophorous vacuole in mature parasites, they may play a role in erythrocyte rupture. The P. falciparum genome sequence also predicts more distantly related (clan CD and CE) cysteine proteases, but biochemical characterisation of these proteins has not been done. New drugs for malaria are greatly needed, and cysteine proteases may provide useful new drug targets. Cysteine protease inhibitors have demonstrated potent antimalarial effects, and the optimisation and testing of falcipain inhibitor antimalarials is underway.
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Affiliation(s)
- Philip J Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, Box 0811, San Francisco, CA 94143, USA.
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32
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Osta WA, Chen Y, Mikhitarian K, Mitas M, Salem M, Hannun YA, Cole DJ, Gillanders WE. EpCAM is overexpressed in breast cancer and is a potential target for breast cancer gene therapy. Cancer Res 2004; 64:5818-24. [PMID: 15313925 DOI: 10.1158/0008-5472.can-04-0754] [Citation(s) in RCA: 391] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
EpCAM (epithelial cell adhesion molecule) is a cell surface molecule that is known to be highly expressed in colon and other epithelial carcinomas. EpCAM is involved in cell-to-cell adhesion and has been the target of antibody therapy in several clinical trials. To assess the value of EpCAM as a novel target for breast cancer gene therapy, we performed real-time reverse transcription-PCR to quantify the level of EpCAM mRNA expression in normal breast tissue and primary and metastatic breast cancers. We found that EpCAM is overexpressed 100- to 1000-fold in primary and metastatic breast cancer. Silencing EpCAM gene expression with EpCAM short interfering RNA (siRNA) resulted in a 35-80% decrease in the rate of cell proliferation in four different breast cancer cell lines. EpCAM siRNA treatment decreased cell migration by 91.8% and cell invasion by 96.4% in the breast cancer cell line MDA-MB-231 in vitro. EpCAM siRNA treatment was also associated with an increase in the detergent-insoluble protein fraction of E-cadherin, alpha-catenin, and beta-catenin, consistent with the known biology of EpCAM as a regulator of cell adhesion. Our hypothesis is that modulation of EpCAM expression can affect cell migration, invasion, and proliferation by enhancing E-cadherin-mediated cell-to-cell adhesion. These data provide compelling evidence that EpCAM is a potential novel target for breast cancer gene therapy and offer insights into the mechanisms associated with EpCAM gene silencing.
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Affiliation(s)
- Walid A Osta
- Department of Surgery, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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33
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Abstract
RNA interference or RNAi is defined as the mechanism through which gene-specific, double-stranded RNA (dsRNA) triggers degradation of homologous transcripts. Besides providing an invaluable tool to downregulate gene expression in a variety of organisms, it is now evident that RNAi extends its tentacles into both the nucleus and the cytoplasm and is involved in a variety of gene silencing phenomena. Here we review the current status of RNAi in protozoan parasites that cause diseases of considerable medical and veterinary importance throughout Africa, Asia and the Americas. RNAi was first discovered in Trypanosoma brucei, a species of the family Trypanosomatidae, and it rapidly became the method of choice to downregulate gene expression in these organisms. At the same time, mechanistic studies exposed a role for RNAi in the control of retroposon transcript abundance. Whereas RNAi is also present in T. congolense, other members of the same family of organisms, namely T. cruzi and Leishmania major, are RNAi-negative. In apicomplexan parasites, there is experimental evidence for RNAi in Plasmodium, but this is not supported by their genetic make up. In contrast, the genome of Toxoplasma gondii harbours gene candidates with convincing similarity to 'classical' RNAi genes. Thus, as previously shown in fungi, protozoan parasites are genetically heterogeneous as far as the RNAi pathway is concerned. Finally, database mining predicts that Entamoeba histolytica and Giardia intestinalis have an RNAi pathway and the presence of RNAi genes in Giardia supports the view that gene silencing by dsRNA appeared very early during evolution of the eukaryotic lineage.
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Affiliation(s)
- Elisabetta Ullu
- Department of Internal Medicine, Yale Medical School, BCMM 136D, 295 Congress Avenue, Box 9812, New Haven, CT, 06536-8012, USA.
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34
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Agrawal N, Malhotra P, Bhatnagar RK. siRNA-directed silencing of transgene expressed in cultured insect cells. Biochem Biophys Res Commun 2004; 320:428-34. [PMID: 15219846 DOI: 10.1016/j.bbrc.2004.05.184] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Indexed: 11/30/2022]
Abstract
RNA interference (RNAi) has emerged as a powerful tool to rapidly analyze gene functions in a wide variety of eukaryotic organisms as well as in cultured cell lines. We demonstrate here that RNAi can be applied to study the function of a transgene expressed in an insect cell line (Spodoptera frugiperda, Sf21). The aminopeptidase N gene (apn) targeted for silencing in the present study was isolated from the midgut of Spodoptera litura larvae and expressed in Sf21 cells using baculovirus expression system. The recombinant APN protein expressed at the surface of Sf21 cells was shown to interact with insecticidal crystal protein, Cry1C, by in vitro experiments. The exogenous addition/transfection of APN dsRNA or siRNA in the cultured cells resulted in partial/complete inhibition of expression of apn leading to the loss of toxin binding to the transgene expressing cells. These experiments highlighted the usefulness of RNAi as a tool to study the function of an expressed transgene in insect cell line and to study the specificity of receptor-ligand interaction.
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Affiliation(s)
- Neema Agrawal
- International Center for Genetic Engineering and Biotechnology, New Delhi 110 067, India
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