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Trajano-Silva LAM, Mule SN, Palmisano G. Molecular tools to regulate gene expression in Trypanosoma cruzi. Adv Clin Chem 2024; 120:169-190. [PMID: 38762241 DOI: 10.1016/bs.acc.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Developing molecular strategies to manipulate gene expression in trypanosomatids is challenging, particularly with respect to the unique gene expression mechanisms adopted by these unicellular parasites, such as polycistronic mRNA transcription and multi-gene families. In the case of Trypanosoma cruzi (T. cruzi), the causative agent of Chagas Disease, the lack of RNA interference machinery further complicated functional genetic studies important for understanding parasitic biology and developing biomarkers and potential therapeutic targets. Therefore, alternative methods of performing knockout and/or endogenous labelling experiments were developed to identify and understand the function of proteins for survival and interaction with the host. In this review, we present the main tools for the genetic manipulation of T. cruzi, focusing on the Clustered Regularly Interspaced Short Palindromic Repeats Cas9-associated system technique widely used in this organism. Moreover, we highlight the importance of using these tools to elucidate the function of uncharacterized and glycosylated proteins. Further developments of these technologies will allow the identification of new biomarkers, therapeutic targets and potential vaccines against Chagas disease with greater efficiency and speed.
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Affiliation(s)
- Lays Adrianne M Trajano-Silva
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil
| | - Simon Ngao Mule
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil
| | - Giuseppe Palmisano
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil; School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
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2
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Bustamante JM, White BE, Wilkerson GK, Hodo CL, Auckland LD, Wang W, McCain S, Hamer SA, Saunders AB, Tarleton RL. Frequency Variation and Dose Modification of Benznidazole Administration for the Treatment of Trypanosoma cruzi Infection in Mice, Dogs, and Nonhuman Primates. Antimicrob Agents Chemother 2023; 67:e0013223. [PMID: 37039666 PMCID: PMC10190575 DOI: 10.1128/aac.00132-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/22/2023] [Indexed: 04/12/2023] Open
Abstract
Trypanosoma cruzi naturally infects a broad range of mammalian species and frequently results in the pathology that has been most extensively characterized in human Chagas disease. Currently employed treatment regimens fail to achieve parasitological cure of T. cruzi infection in the majority of cases. In this study, we have extended our previous investigations of more effective, higher dose, intermittent administration protocols using the FDA-approved drug benznidazole (BNZ), in experimentally infected mice and in naturally infected dogs and nonhuman primates (NHP). Collectively, these studies demonstrate that twice-weekly administration of BNZ for more than 4 months at doses that are ~2.5-fold that of previously used daily dosing protocols, provided the best chance to obtain parasitological cure. Dosing less frequently or for shorter time periods was less dependable in all species. Prior treatment using an ineffective dosing regimen in NHPs did not prevent the attainment of parasitological cure with an intensified BNZ dosing protocol. Furthermore, parasites isolated after a failed BNZ treatment showed nearly identical susceptibility to BNZ as those obtained prior to treatment, confirming the low risk of induction of drug resistance with BNZ and the ability to adjust the treatment protocol when an initial regimen fails. These results provide guidance for the use of BNZ as an effective treatment for T. cruzi infection and encourage its wider use, minimally in high value dogs and at-risk NHP, but also potentially in humans, until better options are available.
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Affiliation(s)
- Juan M. Bustamante
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Brooke E. White
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Gregory K. Wilkerson
- MD Anderson Cancer Center, Michale E. Keeling Center for Comparative Medicine and Research, Bastrop, Texas, USA
| | - Carolyn L. Hodo
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, Texas, USA
| | - Lisa D. Auckland
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, Texas, USA
| | - Wei Wang
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | | | - Sarah A. Hamer
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, Texas, USA
| | - Ashley B. Saunders
- Department of Small Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Rick L. Tarleton
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
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3
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Bustamante JM, White BE, Wilkerson GK, Hodo CL, Auckland LD, Wang W, McCain S, Hamer SA, Saunders AB, Tarleton RL. Frequency variation and dose modification of benznidazole administration for the treatment of Trypanosoma cruzi infection in mice, dogs and non-human primates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526739. [PMID: 36778432 PMCID: PMC9915573 DOI: 10.1101/2023.02.01.526739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Trypanosoma cruzi naturally infects a broad range of mammalian species and frequently results in the pathology that has been most extensively characterized in human Chagas disease. Currently employed treatment regimens fail to achieve parasitological cure of T. cruzi infection in the majority of cases. In this study, we have extended our previous investigations of more effective, higher dose, intermittent administration protocols using the FDA-approved drug benznidazole (BNZ), in experimentally infected mice and in naturally infected dogs and non-human primates (NHP). Collectively these studies demonstrate that twice-weekly administration of BNZ for more than 4 months at doses that are ∼2.5-fold that of previously used daily dosing protocols, provided the best chance to obtain parasitological cure. Dosing less frequently or for shorter time periods was less dependable in all species. Prior treatment using an ineffective dosing regimen in NHPs did not prevent the attainment of parasitological cure with an intensified BNZ dosing protocol. Furthermore, parasites isolated after a failed BNZ treatment showed nearly identical susceptibility to BNZ as those obtained prior to treatment, confirming the low risk of induction of drug resistance with BNZ and the ability to adjust the treatment protocol when an initial regimen fails. These results provide guidance for the use of BNZ as an effective treatment for T. cruzi infection and encourage its wider use, minimally in high value dogs and at-risk NHP, but also potentially in humans, until better options are available.
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Affiliation(s)
- Juan M Bustamante
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Brooke E White
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Gregory K Wilkerson
- MD Anderson Cancer Center, Michale E. Keeling Center for Comparative Medicine and Research, Bastrop, Texas, USA
| | - Carolyn L Hodo
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, Texas, USA
| | - Lisa D Auckland
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, Texas, USA
| | - Wei Wang
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | | | - Sarah A Hamer
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, Texas, USA
| | - Ashley B Saunders
- Department of Small Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Rick L Tarleton
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
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4
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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
- *Correspondence: Mariana De Niz,
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5
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Bustamante JM, Sanchez-Valdez F, Padilla AM, White B, Wang W, Tarleton RL. A modified drug regimen clears active and dormant trypanosomes in mouse models of Chagas disease. Sci Transl Med 2021; 12:12/567/eabb7656. [PMID: 33115952 DOI: 10.1126/scitranslmed.abb7656] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/20/2020] [Accepted: 10/07/2020] [Indexed: 12/29/2022]
Abstract
A major contributor to treatment failure in Chagas disease, caused by infection with the protozoan parasite Trypanosoma cruzi, is that current treatment regimens do not address the drug insensitivity of transiently dormant T. cruzi amastigotes. Here, we demonstrated that use of a currently available drug in a modified treatment regimen of higher individual doses, given less frequently over an extended treatment period, could consistently extinguish T. cruzi infection in three mouse models of Chagas disease. Once per week administration of benznidazole at a dose 2.5 to 5 times the standard daily dose rapidly eliminated actively replicating parasites and ultimately eradicated the residual, transiently dormant parasite population in mice. This outcome was initially confirmed in "difficult to cure" mouse infection models using immunological, parasitological, and molecular biological approaches and ultimately corroborated by whole organ analysis of optically clarified tissues using light sheet fluorescence microscopy (LSFM). This tool was effective for monitoring pathogen load in intact organs, including detection of individual dormant parasites, and for assessing treatment outcomes. LSFM-based analysis also suggested that dormant amastigotes of T. cruzi may not be fully resistant to trypanocidal compounds such as benznidazole. Collectively, these studies provide important information on the phenomenon of dormancy in T. cruzi infection in mice, demonstrate methods to therapeutically override dormancy using a currently available drug, and provide methods to monitor alternative therapeutic approaches for this, and possibly other, low-density infectious agents.
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Affiliation(s)
- Juan M Bustamante
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Fernando Sanchez-Valdez
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA.,Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Argentina
| | - Angel M Padilla
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Brooke White
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Wei Wang
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
| | - Rick L Tarleton
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA. .,Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
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6
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Wang W, Peng D, Baptista RP, Li Y, Kissinger JC, Tarleton RL. Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease. PLoS Pathog 2021; 17:e1009254. [PMID: 33508020 PMCID: PMC7872254 DOI: 10.1371/journal.ppat.1009254] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/09/2021] [Accepted: 12/22/2020] [Indexed: 12/16/2022] Open
Abstract
The protozoan Trypanosoma cruzi almost invariably establishes life-long infections in humans and other mammals, despite the development of potent host immune responses that constrain parasite numbers. The consistent, decades-long persistence of T. cruzi in human hosts arises at least in part from the remarkable level of genetic diversity in multiple families of genes encoding the primary target antigens of anti-parasite immune responses. However, the highly repetitive nature of the genome-largely a result of these same extensive families of genes-have prevented a full understanding of the extent of gene diversity and its maintenance in T. cruzi. In this study, we have combined long-read sequencing and proximity ligation mapping to generate very high-quality assemblies of two T. cruzi strains representing the apparent ancestral lineages of the species. These assemblies reveal not only the full repertoire of the members of large gene families in the two strains, demonstrating extreme diversity within and between isolates, but also provide evidence of the processes that generate and maintain that diversity, including extensive gene amplification, dispersion of copies throughout the genome and diversification via recombination and in situ mutations. Gene amplification events also yield significant copy number variations in a substantial number of genes presumably not required for or involved in immune evasion, thus forming a second level of strain-dependent variation in this species. The extreme genome flexibility evident in T. cruzi also appears to create unique challenges with respect to preserving core genome functions and gene expression that sets this species apart from related kinetoplastids.
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Affiliation(s)
- Wei Wang
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Duo Peng
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Rodrigo P. Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Yiran Li
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Jessica C. Kissinger
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Rick L. Tarleton
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
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7
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Shapiro RS, Chavez A, Collins JJ. CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nat Rev Microbiol 2019; 16:333-339. [PMID: 29599458 DOI: 10.1038/s41579-018-0002-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genetic manipulation of microorganisms has been crucial in understanding their biology, yet for many microbial species, robust tools for comprehensive genetic analysis were lacking until the advent of CRISPR-Cas-based gene editing techniques. In this Progress article, we discuss advances in CRISPR-based techniques for the genetic analysis of genetically intractable microorganisms, with an emphasis on mycobacteria, fungi and parasites. We discuss how CRISPR-based analyses in these organisms have enabled the discovery of novel gene functions, the investigation of genetic interaction networks and the identification of virulence factors.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - James J Collins
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, MIT, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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8
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Al Doghaither H, Gull M. Plasmids as Genetic Tools and Their Applications in Ecology and Evolution. Plasmid 2019. [DOI: 10.5772/intechopen.85705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Berná L, Rodriguez M, Chiribao ML, Parodi-Talice A, Pita S, Rijo G, Alvarez-Valin F, Robello C. Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi. Microb Genom 2018; 4. [PMID: 29708484 PMCID: PMC5994713 DOI: 10.1099/mgen.0.000177] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (the abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degrees of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated with T. cruzi’s genome since they permit direct determination of the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, not only allows accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of two T. cruzi clones: the hybrid TCC (TcVI) and the non-hybrid Dm28c (TcI), determined by PacBio Single Molecular Real-Time (SMRT) technology. The improved assemblies herein obtained permitted us to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements). We found that the genome of T. cruzi is composed of a ‘core compartment’ and a ‘disruptive compartment’ which exhibit opposite GC content and gene composition. Novel tandem and dispersed repetitive sequences were identified, including some located inside coding sequences. Additionally, homologous chromosomes were separately assembled, allowing us to retrieve haplotypes as separate contigs instead of a unique mosaic sequence. Finally, manual annotation of surface multigene families, mucins and trans-sialidases allows now a better overview of these complex groups of genes.
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Affiliation(s)
- Luisa Berná
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Matias Rodriguez
- 2Sección Biomatemática - Unidad de Genómica Evolutiva, Facultad de Ciencias-UDELAR, Montevideo, Uruguay
| | - María Laura Chiribao
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.,3Departamento de Bioquímica, Facultad de Medicina-UDELAR, Montevideo, Uruguay
| | - Adriana Parodi-Talice
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.,4Sección Genética, Facultad de Ciencias-UDELAR, Montevideo, Uruguay
| | - Sebastián Pita
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.,4Sección Genética, Facultad de Ciencias-UDELAR, Montevideo, Uruguay
| | - Gastón Rijo
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Fernando Alvarez-Valin
- 2Sección Biomatemática - Unidad de Genómica Evolutiva, Facultad de Ciencias-UDELAR, Montevideo, Uruguay
| | - Carlos Robello
- 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.,3Departamento de Bioquímica, Facultad de Medicina-UDELAR, Montevideo, Uruguay
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Rapid, Selection-Free, High-Efficiency Genome Editing in Protozoan Parasites Using CRISPR-Cas9 Ribonucleoproteins. mBio 2017; 8:mBio.01788-17. [PMID: 29114029 PMCID: PMC5676044 DOI: 10.1128/mbio.01788-17] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Trypanosomatids (order Kinetoplastida), including the human pathogens Trypanosoma cruzi (agent of Chagas disease), Trypanosoma brucei, (African sleeping sickness), and Leishmania (leishmaniasis), affect millions of people and animals globally. T. cruzi is considered one of the least studied and most poorly understood tropical disease-causing parasites, in part because of the relative lack of facile genetic engineering tools. This situation has improved recently through the application of clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9 (CRISPR-Cas9) technology, but a number of limitations remain, including the toxicity of continuous Cas9 expression and the long drug marker selection times. In this study, we show that the delivery of ribonucleoprotein (RNP) complexes composed of recombinant Cas9 from Staphylococcus aureus (SaCas9), but not from the more routinely used Streptococcus pyogenes Cas9 (SpCas9), and in vitro-transcribed single guide RNAs (sgRNAs) results in rapid gene edits in T. cruzi and other kinetoplastids at frequencies approaching 100%. The highly efficient genome editing via SaCas9/sgRNA RNPs was obtained for both reporter and endogenous genes and observed in multiple parasite life cycle stages in various strains of T. cruzi, as well as in T. brucei and Leishmania major. RNP complex delivery was also used to successfully tag proteins at endogenous loci and to assess the biological functions of essential genes. Thus, the use of SaCas9 RNP complexes for gene editing in kinetoplastids provides a simple, rapid, and cloning- and selection-free method to assess gene function in these important human pathogens. Protozoan parasites remain some of the highest-impact human and animal pathogens, with very limited treatment and prevention options. The development of improved therapeutics and vaccines depends on a better understanding of the unique biology of these organisms, and understanding their biology, in turn, requires the ability to track and manipulate the products of genes. In this work, we describe new methods that are available to essentially any laboratory and applicable to any parasite isolate for easily and rapidly editing the genomes of kinetoplastid parasites. We demonstrate that these methods provide the means to quickly assess function, including that of the products of essential genes and potential targets of drugs, and to tag gene products at their endogenous loci. This is all achieved without gene cloning or drug selection. We expect this advance to enable investigations, especially in Trypanosoma cruzi and Leishmania spp., that have eluded investigators for decades.
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Pacheco-Lugo L, Díaz-Olmos Y, Sáenz-García J, Probst CM, DaRocha WD. Effective gene delivery to Trypanosoma cruzi epimastigotes through nucleofection. Parasitol Int 2017; 66:236-239. [DOI: 10.1016/j.parint.2017.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/27/2017] [Accepted: 01/27/2017] [Indexed: 12/21/2022]
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12
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CRISPR/Cas9-Induced Disruption of Paraflagellar Rod Protein 1 and 2 Genes in Trypanosoma cruzi Reveals Their Role in Flagellar Attachment. mBio 2015. [PMID: 26199333 PMCID: PMC4513075 DOI: 10.1128/mbio.01012-15] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Trypanosoma cruzi is the etiologic agent of Chagas disease, and current methods for its genetic manipulation have been highly inefficient. We report here the use of the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated gene 9) system for disrupting genes in the parasite by three different strategies. The utility of the method was established by silencing genes encoding the GP72 protein, which is required for flagellar attachment, and paraflagellar rod proteins 1 and 2 (PFR1, PFR2), key components of the parasite flagellum. We used either vectors containing single guide RNA (sgRNA) and Cas9, separately or together, or one vector containing sgRNA and Cas9 plus donor DNA for homologous recombination to rapidly generate mutant cell lines in which the PFR1, PFR2, and GP72 genes have been disrupted. We demonstrate that genome editing of these endogenous genes in T. cruzi is successful without detectable toxicity of Cas9. Our results indicate that PFR1, PFR2, and GP72 contribute to flagellar attachment to the cell body and motility of the parasites. Therefore, CRISPR/Cas9 allows efficient gene disruption in an almost genetically intractable parasite and suggest that this method will improve the functional analyses of its genome. Trypanosoma cruzi is the agent of Chagas disease, which affects millions of people worldwide. Vaccines to prevent this disease are not available, and drug treatments are not completely effective. The study of the biology of this parasite through genetic approaches will make possible the development of new preventive or treatment options. Previous attempts to use the CRISPR/Cas9 in T. cruzi found a detectable but low frequency of Cas9-facilitated homologous recombination and fluorescent marker swap between exogenous genes, while Cas9 was toxic to the cells. In this report, we describe new approaches that generate complete disruption of an endogenous gene without toxicity to the parasites and establish the relevance of several proteins for flagellar attachment and motility.
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13
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Abstract
Trypanosoma cruzi is a protozoan parasite of humans and animals, affecting 10 to 20 million people and innumerable animals, primarily in the Americas. Despite being the largest cause of infection-induced heart disease worldwide, even among the neglected tropical diseases (NTDs) T. cruzi is considered one of the least well understood and understudied. The genetic complexity of T. cruzi as well as the limited set of efficient techniques for genome engineering contribute significantly to the relative lack of progress in and understanding of this pathogen. Here, we adapted the CRISPR-Cas9 system for the genetic engineering of T. cruzi, demonstrating rapid and efficient knockout of multiple endogenous genes, including essential genes. We observed that in the absence of a template, repair of the Cas9-induced double-stranded breaks (DSBs) in T. cruzi occurs exclusively by microhomology-mediated end joining (MMEJ) with various-sized deletions. When a template for DNA repair is provided, DSB repair by homologous recombination is achieved at an efficiency several orders of magnitude higher than that in the absence of CRISPR-Cas9-induced DSBs. We also demonstrate the high multiplexing capacity of CRISPR-Cas9 in T. cruzi by knocking down expression of an enzyme gene family consisting of 65 members, resulting in a significant reduction of enzymatic product with no apparent off-target mutations. Lastly, we show that Cas9 can mediate disruption of its own coding sequence, rescuing a growth defect in stable Cas9-expressing parasites. These results establish a powerful new tool for the analysis of gene functions in T. cruzi, enabling the study of essential genes and their functions and analysis of the many large families of related genes that occupy a substantial portion of the T. cruzi genome. Trypanosoma cruzi, the causative agent of human Chagas disease, is the leading worldwide cause of infectious myocarditis. Diagnostics for the infection are relatively poor, treatment options are limited and of variable effectiveness, and suitable vaccines are nonexistent. The T. cruzi genome is replete with genes of unknown function and greatly expanded gene families with hundreds of members. The absence of facile genetic engineering tools, including RNA interference, for T. cruzi has prevented elucidation of gene and gene family function and the development of better infection prevention and control measures. In this study, we demonstrate that the CRISPR-Cas9 system is a versatile and powerful tool for genome manipulations in T. cruzi, bringing new opportunities for unraveling the functions of previously uncharacterized genes and how this human pathogen engages its large families of genes encoding surface proteins to interact with human and animal hosts.
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Sánchez-Valdéz FJ, Pérez Brandán C, Ferreira A, Basombrío MÁ. Gene-deleted live-attenuated Trypanosoma cruzi parasites as vaccines to protect against Chagas disease. Expert Rev Vaccines 2014; 14:681-97. [PMID: 25496192 DOI: 10.1586/14760584.2015.989989] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. This illness is now becoming global, mainly due to congenital transmission, and so far, there are no prophylactic or therapeutic vaccines available to either prevent or treat Chagas disease. Therefore, different approaches aimed at identifying new protective immunogens are urgently needed. Live vaccines are likely to be more efficient in inducing protection, but safety issues linked with their use have been raised. The development of improved protozoan genetic manipulation tools and genomic and biological information has helped to increase the safety of live vaccines. These advances have generated a renewed interest in the use of genetically attenuated parasites as vaccines against Chagas disease. This review discusses the protective capacity of genetically attenuated parasite vaccines and the challenges and perspectives for the development of an effective whole-parasite Chagas disease vaccine.
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Alonso VL, Ritagliati C, Cribb P, Serra EC. Construction of three new Gateway® expression plasmids for Trypanosoma cruzi. Mem Inst Oswaldo Cruz 2014; 109:1081-5. [PMID: 25424446 PMCID: PMC4325611 DOI: 10.1590/0074-0276140238] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/31/2014] [Indexed: 11/21/2022] Open
Abstract
We present here three expression plasmids for Trypanosoma cruzi
adapted to the Gateway® recombination cloning system. Two of
these plasmids were designed to express trypanosomal proteins fused to a double tag
for tandem affinity purification (TAPtag). The TAPtag and Gateway®
cassette were introduced into an episomal (pTEX) and an integrative (pTREX) plasmid.
Both plasmids were assayed by introducing green fluorescent protein (GFP) by
recombination and the integrity of the double-tagged protein was determined by
western blotting and immunofluorescence microscopy. The third Gateway adapted vector
assayed was the inducible pTcINDEX. When tested with GFP,
pTcINDEX-GW showed a good response to tetracycline, being less
leaky than its precursor (pTcINDEX).
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Affiliation(s)
- Victoria L Alonso
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carla Ritagliati
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Pamela Cribb
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Esteban C Serra
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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Alcantara MV, Fragoso SP, Picchi GFA. Knockout confirmation for Hurries: rapid genotype identification of Trypanosoma cruzi transfectants by polymerase chain reaction directly from liquid culture. Mem Inst Oswaldo Cruz 2014; 109:511-3. [PMID: 24936912 PMCID: PMC4155859 DOI: 10.1590/0074-0276140010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 03/18/2014] [Indexed: 11/24/2022] Open
Abstract
Gene knockout is a widely used approach to evaluate loss-of-function phenotypes
and it can be facilitated by the incorporation of a DNA cassette having a
drug-selectable marker. Confirmation of the correct knockout cassette insertion
is an important step in gene removal validation and has generally been performed
by polymerase chain reaction (PCR) assays following a time-consuming DNA
extraction step. Here, we show a rapid procedure for the identification of
Trypanosoma cruzi transfectants by PCR directly from liquid
culture - without prior DNA extraction. This simple approach enabled us to
generate PCR amplifications from different cultures varying from
106-108 cells/mL. We also show that it is possible to
combine different primer pairs in a multiplex detection reaction and even to
achieve knockout confirmation with an extremely simple interpretation of a
real-time PCR result. Using the “culture PCR” approach, we show for the first
time that we can assess different DNA sequence combinations by PCR directly from
liquid culture, saving time in several tasks for T. cruzi
genotype interrogation.
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Affiliation(s)
- Monica Visnieski Alcantara
- Laboratório de Biologia Molecular de Tripanossomatídeos, Instituto Carlos Chagas-Fiocruz, Curitiba, PR, Brasil
| | - Stenio Perdigão Fragoso
- Laboratório de Biologia Molecular de Tripanossomatídeos, Instituto Carlos Chagas-Fiocruz, Curitiba, PR, Brasil
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Roberts A, Torrie L, Wyllie S, Fairlamb A. Biochemical and genetic characterization of Trypanosoma cruzi N-myristoyltransferase. Biochem J 2014; 459:323-32. [PMID: 24444291 PMCID: PMC3969225 DOI: 10.1042/bj20131033] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 12/20/2022]
Abstract
Co- and post-translational N-myristoylation is known to play a role in the correct subcellular localization of specific proteins in eukaryotes. The enzyme that catalyses this reaction, NMT (N-myristoyltransferase), has been pharmacologically validated as a drug target in the African trypanosome, Trypanosoma brucei. In the present study, we evaluate NMT as a potential drug target in Trypanosoma cruzi, the causative agent of Chagas' disease, using chemical and genetic approaches. Replacement of both allelic copies of TcNMT (T. cruzi NMT) was only possible in the presence of a constitutively expressed ectopic copy of the gene, indicating that this gene is essential for survival of T. cruzi epimastigotes. The pyrazole sulphonamide NMT inhibitor DDD85646 is 13-23-fold less potent against recombinant TcNMT than TbNMT (T. brucei NMT), with Ki values of 12.7 and 22.8 nM respectively, by scintillation proximity or coupled assay methods. DDD85646 also inhibits growth of T. cruzi epimastigotes (EC50=6.9 μM), but is ~1000-fold less potent than that reported for T. brucei. On-target activity is demonstrated by shifts in cell potency in lines that over- and under-express NMT and by inhibition of intracellular N-myristoylation of several proteins in a dose-dependent manner. Collectively, our findings suggest that N-myristoylation is an essential and druggable target in T. cruzi.
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Key Words
- chagas’ disease
- click chemistry
- drug target
- n-myristoylation
- trypanosoma cruzi
- validation
- cap5.5, cytoskeleton-associated protein 5.5
- dig, digoxigenin
- dko, double knockout
- dmem, dulbecco’s modified eagle’s medium
- hyg, hygromycin phosphotransferase
- nmt, n-myristoyltransferase
- nmtoe, nmt overexpressor
- pac, puromycin n-acetyltransferase
- rth/fbs, rpmi 1640 medium supplemented with trypticase, haemin, hepes and 10% heat-inactivated fbs
- sko, single knockout
- tbnmt, trypanosoma brucei nmt
- tcep, tris-(2-carboxyethyl)phosphine
- tcnmt, trypanosoma cruzi nmt
- tctryr, trypanosoma cruzi trypanothione reductase
- wt, wild-type
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Affiliation(s)
- Adam J. Roberts
- *Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Leah S. Torrie
- *Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Susan Wyllie
- *Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Alan H. Fairlamb
- *Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
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Bouvier LA, Cámara MDLM, Canepa GE, Miranda MR, Pereira CA. Plasmid vectors and molecular building blocks for the development of genetic manipulation tools for Trypanosoma cruzi. PLoS One 2013; 8:e80217. [PMID: 24205392 PMCID: PMC3812015 DOI: 10.1371/journal.pone.0080217] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 06/24/2013] [Indexed: 11/24/2022] Open
Abstract
The post genomic era revealed the need for developing better performing, easier to use and more sophisticated genetic manipulation tools for the study of Trypanosoma cruzi, the etiological agent of Chagas disease. In this work a series of plasmids that allow genetic manipulation of this protozoan parasite were developed. First of all we focused on useful tools to establish selection strategies for different strains and which can be employed as expression vectors. On the other hand molecular building blocks in the form of diverse selectable markers, modifiable fluorescent protein and epitope-tag coding sequences were produced. Both types of modules were harboured in backbone molecules conceived to offer multiple construction and sub-cloning strategies. These can be used to confer new properties to already available genetic manipulation tools or as starting points for whole novel designs. The performance of each plasmid and building block was determined independently. For illustration purposes, some simple direct practical applications were conducted.
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Affiliation(s)
- León A. Bouvier
- Laboratorio de Biología Molecular de Trypanosoma cruzi (LBMTC), Instituto de Investigaciones Médicas “Alfredo Lanari”, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
- * E-mail:
| | - María de los Milagros Cámara
- Laboratorio de Biología Molecular de Trypanosoma cruzi (LBMTC), Instituto de Investigaciones Médicas “Alfredo Lanari”, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
| | - Gaspar E. Canepa
- Laboratorio de Biología Molecular de Trypanosoma cruzi (LBMTC), Instituto de Investigaciones Médicas “Alfredo Lanari”, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
| | - Mariana R. Miranda
- Laboratorio de Biología Molecular de Trypanosoma cruzi (LBMTC), Instituto de Investigaciones Médicas “Alfredo Lanari”, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
| | - Claudio A. Pereira
- Laboratorio de Biología Molecular de Trypanosoma cruzi (LBMTC), Instituto de Investigaciones Médicas “Alfredo Lanari”, Universidad de Buenos Aires and CONICET, Buenos Aires, Argentina
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Hashimoto M, Enomoto M, Morales J, Kurebayashi N, Sakurai T, Hashimoto T, Nara T, Mikoshiba K. Inositol 1,4,5-trisphosphate receptor regulates replication, differentiation, infectivity and virulence of the parasitic protist Trypanosoma cruzi. Mol Microbiol 2013; 87:1133-50. [PMID: 23320762 DOI: 10.1111/mmi.12155] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2013] [Indexed: 11/26/2022]
Abstract
In animals, inositol 1,4,5-trisphosphate receptors (IP3 Rs) are ion channels that play a pivotal role in many biological processes by mediating Ca(2+) release from the endoplasmic reticulum. Here, we report the identification and characterization of a novel IP3 R in the parasitic protist, Trypanosoma cruzi, the pathogen responsible for Chagas disease. DT40 cells lacking endogenous IP3 R genes expressing T. cruzi IP3 R (TcIP3 R) exhibited IP3 -mediated Ca(2+) release from the ER, and demonstrated receptor binding to IP3 . TcIP3 R was expressed throughout the parasite life cycle but the expression level was much lower in bloodstream trypomastigotes than in intracellular amastigotes or epimastigotes. Disruption of two of the three TcIP3 R gene loci led to the death of the parasite, suggesting that IP3 R is essential for T. cruzi. Parasites expressing reduced or increased levels of TcIP3 R displayed defects in growth, transformation and infectivity, indicating that TcIP3 R is an important regulator of the parasite's life cycle. Furthermore, mice infected with T. cruzi expressing reduced levels of TcIP3 R exhibited a reduction of disease symptoms, indicating that TcIP3 R is an important virulence factor. Combined with the fact that the primary structure of TcIP3 R has low similarity to that of mammalian IP3 Rs, TcIP3 R is a promising drug target for Chagas disease.
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Affiliation(s)
- Muneaki Hashimoto
- Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
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20
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Sánchez Valdéz FJ, Pérez Brandán C, Zago MP, Labriola C, Ferreira A, Basombrío MÁ. Trypanosoma cruzi carrying a monoallelic deletion of the calreticulin (TcCRT) gene are susceptible to complement mediated killing and defective in their metacyclogenesis. Mol Immunol 2012; 53:198-205. [PMID: 22954747 DOI: 10.1016/j.molimm.2012.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 06/25/2012] [Accepted: 08/07/2012] [Indexed: 11/17/2022]
Abstract
Trypanosoma cruzi calreticulin (TcCRT) can hijack complement C1, mannan-binding lectin and ficolins from serum thus inhibiting the classical and lectin complement pathway activation respectively. To understand the in vivo biological functions of TcCRT in T. cruzi we generated a clonal cell line lacking one TcCRT allele (TcCRT+/-) and another clone overexpressing it (TcCRT+). Both clones were derived from the TCC T. cruzi strain. As expected, TcCRT+/- epimastigotes showed impairment on TcCRT synthesis, whereas TcCRT+ ones showed increased protein levels. In correlation to this, monoallelic mutant parasites were significantly susceptible to killing by the complement machinery. On the contrary, TcCRT+ parasites showed higher levels of resistance to killing mediate by the classical and lectin but not the alternative pathway. The involvement of surface TcCRT in depleting C1 was demonstrated through restoration of serum killing activity by addition of exogenous C1. In axenic cultures, a reduced propagation rate of TcCRT+/- parasites was observed. Moreover, TcCRT+/- parasites presented a reduced rate of differentiation in in vitro assays. As shown by down- or upregulation of TcCRT expression this gene seems to play a major role in providing T. cruzi with the ability to resist complement system.
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21
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Pérez Brandan C, Basombrío MÁ. Genetically attenuated Trypanosoma cruzi parasites as a potential vaccination tool. Bioengineered 2012; 3:242-6. [PMID: 22705838 DOI: 10.4161/bioe.20680] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chagas disease is the clinical manifestation of the infection produced by the parasite Trypanosoma cruzi. Currently there is no vaccine to prevent this disease and the protection attained with vaccines containing non-replicating parasites is limited. Genetically attenuated trypanosomatid parasites can be obtained by deletion of selected genes. Gene deletion takes advantage of the fact that this parasite can undergo homologous recombination between endogenous and foreign DNA sequences artificially introduced in the cells. This approach facilitated the discovery of several unknown gene functions, as well as allowing us to speculate about the potential for genetically attenuated live organisms as experimental immunogens. Vaccination with live attenuated parasites has been used effectively in mice to reduce parasitemia and histological damage, and in dogs, to prevent vector-delivered infection in the field. However, the use of live parasites as immunogens is controversial due to the risk of reversion to a virulent phenotype. Herein, we present our results from experiments on genetic manipulation of two T. cruzi strains to produce parasites with impaired replication and infectivity, and using the mutation of the dhfr-ts gene as a safety device against reversion to virulence.
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Affiliation(s)
- Cecilia Pérez Brandan
- Instituto de Patología Experimental-CONICET, Universidad Nacional de Salta, Salta, Argentina.
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22
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Parikh PP, Minning TA, Nguyen V, Lalithsena S, Asiaee AH, Sahoo SS, Doshi P, Tarleton R, Sheth AP. A semantic problem solving environment for integrative parasite research: identification of intervention targets for Trypanosoma cruzi. PLoS Negl Trop Dis 2012; 6:e1458. [PMID: 22272365 PMCID: PMC3260319 DOI: 10.1371/journal.pntd.0001458] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 11/18/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Research on the biology of parasites requires a sophisticated and integrated computational platform to query and analyze large volumes of data, representing both unpublished (internal) and public (external) data sources. Effective analysis of an integrated data resource using knowledge discovery tools would significantly aid biologists in conducting their research, for example, through identifying various intervention targets in parasites and in deciding the future direction of ongoing as well as planned projects. A key challenge in achieving this objective is the heterogeneity between the internal lab data, usually stored as flat files, Excel spreadsheets or custom-built databases, and the external databases. Reconciling the different forms of heterogeneity and effectively integrating data from disparate sources is a nontrivial task for biologists and requires a dedicated informatics infrastructure. Thus, we developed an integrated environment using Semantic Web technologies that may provide biologists the tools for managing and analyzing their data, without the need for acquiring in-depth computer science knowledge. METHODOLOGY/PRINCIPAL FINDINGS We developed a semantic problem-solving environment (SPSE) that uses ontologies to integrate internal lab data with external resources in a Parasite Knowledge Base (PKB), which has the ability to query across these resources in a unified manner. The SPSE includes Web Ontology Language (OWL)-based ontologies, experimental data with its provenance information represented using the Resource Description Format (RDF), and a visual querying tool, Cuebee, that features integrated use of Web services. We demonstrate the use and benefit of SPSE using example queries for identifying gene knockout targets of Trypanosoma cruzi for vaccine development. Answers to these queries involve looking up multiple sources of data, linking them together and presenting the results. CONCLUSION/SIGNIFICANCE The SPSE facilitates parasitologists in leveraging the growing, but disparate, parasite data resources by offering an integrative platform that utilizes Semantic Web techniques, while keeping their workload increase minimal.
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Affiliation(s)
- Priti P. Parikh
- The Kno.e.sis Center, Department of Computer Science and Engineering, Wright State University, Dayton, Ohio, United States of America
| | - Todd A. Minning
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Vinh Nguyen
- The Kno.e.sis Center, Department of Computer Science and Engineering, Wright State University, Dayton, Ohio, United States of America
| | - Sarasi Lalithsena
- The Kno.e.sis Center, Department of Computer Science and Engineering, Wright State University, Dayton, Ohio, United States of America
| | - Amir H. Asiaee
- THINC Lab, Department of Computer Science, University of Georgia, Athens, Georgia, United States of America
| | - Satya S. Sahoo
- The Kno.e.sis Center, Department of Computer Science and Engineering, Wright State University, Dayton, Ohio, United States of America
- Division of Medical Informatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Prashant Doshi
- THINC Lab, Department of Computer Science, University of Georgia, Athens, Georgia, United States of America
| | - Rick Tarleton
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Amit P. Sheth
- The Kno.e.sis Center, Department of Computer Science and Engineering, Wright State University, Dayton, Ohio, United States of America
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Hashimoto M, Morales J, Fukai Y, Suzuki S, Takamiya S, Tsubouchi A, Inoue S, Inoue M, Kita K, Harada S, Tanaka A, Aoki T, Nara T. Critical importance of the de novo pyrimidine biosynthesis pathway for Trypanosoma cruzi growth in the mammalian host cell cytoplasm. Biochem Biophys Res Commun 2011; 417:1002-6. [PMID: 22209850 DOI: 10.1016/j.bbrc.2011.12.073] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 12/15/2011] [Indexed: 10/14/2022]
Abstract
The intracellular parasitic protist Trypanosoma cruzi is the causative agent of Chagas disease in Latin America. In general, pyrimidine nucleotides are supplied by both de novo biosynthesis and salvage pathways. While epimastigotes-an insect form-possess both activities, amastigotes-an intracellular replicating form of T. cruzi-are unable to mediate the uptake of pyrimidine. However, the requirement of de novo pyrimidine biosynthesis for parasite growth and survival has not yet been elucidated. Carbamoyl-phosphate synthetase II (CPSII) is the first and rate-limiting enzyme of the de novo biosynthetic pathway, and increased CPSII activity is associated with the rapid proliferation of tumor cells. In the present study, we showed that disruption of the T. cruzi cpsII gene significantly reduced parasite growth. In particular, the growth of amastigotes lacking the cpsII gene was severely suppressed. Thus, the de novo pyrimidine pathway is important for proliferation of T. cruzi in the host cell cytoplasm and represents a promising target for chemotherapy against Chagas disease.
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Affiliation(s)
- Muneaki Hashimoto
- Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan.
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24
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Knockout of the dhfr-ts gene in Trypanosoma cruzi generates attenuated parasites able to confer protection against a virulent challenge. PLoS Negl Trop Dis 2011; 5:e1418. [PMID: 22180798 PMCID: PMC3236718 DOI: 10.1371/journal.pntd.0001418] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/21/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Trypanosoma cruzi is a protozoan parasite that causes severe disease in millions of habitants of developing countries. Currently there is no vaccine to prevent this disease and the available drugs have the consequences of side effects. Live vaccines are likely to be more effective in inducing protection than recombinant proteins or DNA vaccines; however, safety problems associated to their use have been pointed out. In recent years, increasing knowledge on the molecular genetics of Trypanosomes has allowed the identification and elimination of genes that may be necessary for parasite infectivity and survival. In this sense, targeted deletion or disruption of specific genes in the parasite genome may protect against such reversion to virulent genotypes. METHODS AND FINDINGS By targeted gene disruption we generated monoallelic mutant parasites for the dhfr-ts gene in a T. cruzi strain that has been shown to be naturally attenuated. In comparison to T. cruzi wild type epimastigotes, impairment in growth of dhfr-ts(+/-) mutant parasites was observed and mutant clones displayed decreased virulence in mice. Also, a lower number of T. cruzi-specific CD8(+) T cells, in comparison to those induced by wild type parasites, was detected in mice infected with mutant parasites. However, no remarkable differences in the protective effect of TCC wild type versus TCC mutant parasites were observed. Mice challenged with virulent parasites a year after the original infection with the mutant parasites still displayed a significant control over the secondary infection. CONCLUSION This study indicates that it is possible to generate genetically attenuated T. cruzi parasites able to confer protection against further T. cruzi infections.
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Teixeira SM, El-Sayed NM, Araújo PR. The genome and its implications. ADVANCES IN PARASITOLOGY 2011; 75:209-30. [PMID: 21820558 DOI: 10.1016/b978-0-12-385863-4.00010-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Trypanosoma cruzi has a heterogeneous population composed of a pool of strains that circulate in the domestic and sylvatic cycles. Genome sequencing of the clone CL Brener revealed a highly repetitive genome of about 110Mb containing an estimated 22,570 genes. Because of its hybrid nature, sequences representing the two haplotypes have been generated. In addition, a repeat content close to 50% made the assembly of the estimated 41 pairs of chromosomes quite challenging. Similar to other trypanosomatids, the organization of T. cruzi chromosomes was found to be very peculiar, with protein-coding genes organized in long polycistronic transcription units encoding 20 or more proteins in one strand separated by strand switch regions. Another remarkable feature of the T. cruzi genome is the massive expansion of surface protein gene families. Because of the high genetic diversity of the T. cruzi population, sequencing of additional strains and comparative genomic and transcriptome analyses are in progress. Five years after its publication, the genome data have proven to be an essential tool for the study of T. cruzi and increasing efforts to translate this knowledge into the development of new modes of intervention to control Chagas disease are underway.
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Affiliation(s)
- Santuza M Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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26
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Oral exposure to Trypanosoma cruzi elicits a systemic CD8⁺ T cell response and protection against heterotopic challenge. Infect Immun 2011; 79:3397-406. [PMID: 21628516 DOI: 10.1128/iai.01080-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Trypanosoma cruzi infects millions of people in Latin America and often leads to the development of Chagas disease. T. cruzi infection can be acquired at or near the bite site of the triatomine vector, but per os infection is also a well-documented mode of transmission, as evidenced by recent microepidemics of acute Chagas disease attributed to the consumption of parasite-contaminated foods and liquids. It would also be convenient to deliver vaccines for T. cruzi by the oral route, particularly live parasite vaccines intended for the immunization of reservoir hosts. For these reasons, we were interested in better understanding immunity to T. cruzi following oral infection or oral vaccination, knowing that the route of infection and site of antigen encounter can have substantial effects on the ensuing immune response. Here, we show that the route of infection does not alter the ability of T. cruzi to establish infection in muscle tissue nor does it impair the generation of a robust CD8(+) T cell response. Importantly, oral vaccination with attenuated parasites provides protection against wild-type (WT) T. cruzi challenge. These results strongly support the development of whole-organism-based vaccines targeting reservoir species as a means to alleviate the burden of Chagas disease in affected regions.
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27
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Minning TA, Weatherly DB, Flibotte S, Tarleton RL. Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization. BMC Genomics 2011; 12:139. [PMID: 21385342 PMCID: PMC3060142 DOI: 10.1186/1471-2164-12-139] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 03/07/2011] [Indexed: 12/20/2022] Open
Abstract
Background Trypanosoma cruzi is a protozoan parasite and the etiologic agent of Chagas disease, an important public health problem in Latin America. T. cruzi is diploid, almost exclusively asexual, and displays an extraordinarily diverse population structure both genetically and phenotypically. Yet, to date the genotypic diversity of T. cruzi and its relationship, if any, to biological diversity have not been studied at the whole genome level. Results In this study, we used whole genome oligonucleotide tiling arrays to compare gene content in biologically disparate T. cruzi strains by comparative genomic hybridization (CGH). We observed that T. cruzi strains display widespread and focal copy number variations (CNV) and a substantially greater level of diversity than can be adequately defined by the current genetic typing methods. As expected, CNV were particularly frequent in gene family-rich regions containing mucins and trans-sialidases but were also evident in core genes. Gene groups that showed little variation in copy numbers among the strains tested included those encoding protein kinases and ribosomal proteins, suggesting these loci were less permissive to CNV. Moreover, frequent variation in chromosome copy numbers were observed, and chromosome-specific CNV signatures were shared by genetically divergent T. cruzi strains. Conclusions The large number of CNV, over 4,000, reported here uphold at a whole genome level the long held paradigm of extraordinary genome plasticity among T. cruzi strains. Moreover, the fact that these heritable markers do not parse T. cruzi strains along the same lines as traditional typing methods is strongly suggestive of genetic exchange playing a major role in T. cruzi population structure and biology.
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Affiliation(s)
- Todd A Minning
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA
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Abstract
It is almost 20 years since genetic manipulation of Trypanosoma cruzi was first reported. In this time, there have been steady improvements in the available vector systems, and the applications of the technology have been extended into new areas. Episomal vectors have been modified to enhance the level of expression of transfected genes and to facilitate the sub-cellular location of their products. Integrative vectors have been adapted to allow the development of inducible expression systems and the construction of vectors which enable genome modification through telomere-associated chromosome fragmentation. The uses of reverse genetic approaches to dissect peroxide metabolism and the mechanisms of drug activity and resistance in T. cruzi are illustrated in this chapter as examples of how the technology has been used to investigate biological function. Although there remains scope to improve the flexibility of these systems, they have made valuable contributions towards exploiting the genome sequence data and providing a greater understanding of parasite biology and the mechanisms of infection.
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Affiliation(s)
- Martin C Taylor
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Fulwiler AL, Soysa DR, Ullman B, Yates PA. A rapid, efficient and economical method for generating leishmanial gene targeting constructs. Mol Biochem Parasitol 2010; 175:209-12. [PMID: 21055426 DOI: 10.1016/j.molbiopara.2010.10.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 10/19/2010] [Accepted: 10/22/2010] [Indexed: 11/18/2022]
Abstract
Targeted gene replacement is a powerful tool in Leishmania genetics that can be time-consuming to implement. One tedious aspect that delays progress is the multi-step construction of gene targeting vectors. To accelerate this process, we developed a streamlined method that allows the assembly of a complete targeting vector from all its constituent parts in a single-step multi-fragment ligation. The individual components to be assembled are flanked by sites for the restriction endonuclease SfiI that generates non-identical, non-palindromic three base 3'-overhangs designed to allow annealing and ligation of the parts only in the proper order. The method was optimized by generating constructs for targeting the Leishmania donovani inosine monophosphate dehydrogenase gene (LdIMPDH) encoding six different drug resistance markers, and was found to be rapid and efficient. These constructs were successfully employed to generate heterozygous LdIMPDH gene replacement mutants. This method is adaptable for generating targeting vectors for a variety of species.
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Affiliation(s)
- Audrey L Fulwiler
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239-3098, USA
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Batista M, Marchini FK, Celedon PAF, Fragoso SP, Probst CM, Preti H, Ozaki LS, Buck GA, Goldenberg S, Krieger MA. A high-throughput cloning system for reverse genetics in Trypanosoma cruzi. BMC Microbiol 2010; 10:259. [PMID: 20942965 PMCID: PMC3020659 DOI: 10.1186/1471-2180-10-259] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 10/13/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The three trypanosomatids pathogenic to men, Trypanosoma cruzi, Trypanosoma brucei and Leishmania major, are etiological agents of Chagas disease, African sleeping sickness and cutaneous leishmaniasis, respectively. The complete sequencing of these trypanosomatid genomes represented a breakthrough in the understanding of these organisms. Genome sequencing is a step towards solving the parasite biology puzzle, as there are a high percentage of genes encoding proteins without functional annotation. Also, technical limitations in protein expression in heterologous systems reinforce the evident need for the development of a high-throughput reverse genetics platform. Ideally, such platform would lead to efficient cloning and compatibility with various approaches. Thus, we aimed to construct a highly efficient cloning platform compatible with plasmid vectors that are suitable for various approaches. RESULTS We constructed a platform with a flexible structure allowing the exchange of various elements, such as promoters, fusion tags, intergenic regions or resistance markers. This platform is based on Gateway® technology, to ensure a fast and efficient cloning system. We obtained plasmid vectors carrying genes for fluorescent proteins (green, cyan or yellow), and sequences for the c-myc epitope, and tandem affinity purification or polyhistidine tags. The vectors were verified by successful subcellular localization of two previously characterized proteins (TcRab7 and PAR 2) and a putative centrin. For the tandem affinity purification tag, the purification of two protein complexes (ribosome and proteasome) was performed. CONCLUSIONS We constructed plasmids with an efficient cloning system and suitable for use across various applications, such as protein localization and co-localization, protein partner identification and protein expression. This platform also allows vector customization, as the vectors were constructed to enable easy exchange of its elements. The development of this high-throughput platform is a step closer towards large-scale trypanosome applications and initiatives.
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Affiliation(s)
- Michel Batista
- Instituto Carlos Chagas, FIOCRUZ, Curitiba, Parana, Brazil
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In vitro and in vivo high-throughput assays for the testing of anti-Trypanosoma cruzi compounds. PLoS Negl Trop Dis 2010; 4:e740. [PMID: 20644616 PMCID: PMC2903469 DOI: 10.1371/journal.pntd.0000740] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 05/27/2010] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The two available drugs for treatment of T. cruzi infection, nifurtimox and benznidazole (BZ), have potential toxic side effects and variable efficacy, contributing to their low rate of use. With scant economic resources available for antiparasitic drug discovery and development, inexpensive, high-throughput and in vivo assays to screen potential new drugs and existing compound libraries are essential. METHODS In this work, we describe the development and validation of improved methods to test anti-T. cruzi compounds in vitro and in vivo using parasite lines expressing the firefly luciferase (luc) or the tandem tomato fluorescent protein (tdTomato). For in vitro assays, the change in fluorescence intensity of tdTomato-expressing lines was measured as an indicator of parasite replication daily for 4 days and this method was used to identify compounds with IC(50) lower than that of BZ. FINDINGS This method was highly reproducible and had the added advantage of requiring relatively low numbers of parasites and no additional indicator reagents, enzymatic post-processes or laborious visual counting. In vivo, mice were infected in the footpads with fluorescent or bioluminescent parasites and the signal intensity was measured as a surrogate of parasite load at the site of infection before and after initiation of drug treatment. Importantly, the efficacy of various drugs as determined in this short-term (<2 weeks) assay mirrored that of a 40 day treatment course. CONCLUSION These methods should make feasible broader and higher-throughput screening programs needed to identify potential new drugs for the treatment of T. cruzi infection and for their rapid validation in vivo.
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