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Fernández-García M, Mesquita I, Ferreira C, Araújo M, Saha B, Rey-Stolle MF, García A, Silvestre R, Barbas C. Leishmania donovani Induces Multiple Dynamic Responses in the Metabolome Associated with Amastigote Differentiation and Maturation Inside the Human Macrophage. J Proteome Res 2023. [PMID: 37339249 DOI: 10.1021/acs.jproteome.2c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Leishmania donovani infection of macrophages drives profound changes in the metabolism of both the host macrophage and the parasite, which undergoes different phases of development culminating in replication and propagation. However, the dynamics of this parasite-macrophage cometabolome are poorly understood. In this study, a multiplatform metabolomics pipeline combining untargeted, high-resolution CE-TOF/MS and LC-QTOF/MS with targeted LC-QqQ/MS was followed to characterize the metabolome alterations induced in L. donovani-infected human monocyte-derived macrophages from different donors at 12, 36, and 72 h post-infection. The set of alterations known to occur during Leishmania infection of macrophages, substantially expanded in this investigation, characterized the dynamics of the glycerophospholipid, sphingolipid, purine, pentose phosphate, glycolytic, TCA, and amino acid metabolism. Our results showed that only citrulline, arginine, and glutamine exhibited constant trends across all studied infection time points, while most metabolite alterations underwent a partial recovery during amastigote maturation. We determined a major metabolite response pointing to an early induction of sphingomyelinase and phospholipase activities and correlated with amino acid depletion. These data represent a comprehensive overview of the metabolome alterations occurring during promastigote-to-amastigote differentiation and maturation of L. donovani inside macrophages that contributes to our understanding of the relationship between L. donovani pathogenesis and metabolic dysregulation.
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Affiliation(s)
- Miguel Fernández-García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, España
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, España
| | - Inês Mesquita
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
| | - Carolina Ferreira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
| | - Marta Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
| | - Bhaskar Saha
- National Centre for Cell Science, 411007 Pune, India
| | - Ma Fernanda Rey-Stolle
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, España
| | - Antonia García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, España
| | - Ricardo Silvestre
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, España
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Transcriptome Analysis of Intracellular Amastigotes of Clinical Leishmania infantum Lines from Therapeutic Failure Patients after Infection of Human Macrophages. Microorganisms 2022; 10:microorganisms10071304. [PMID: 35889023 PMCID: PMC9324091 DOI: 10.3390/microorganisms10071304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is considered to be one of the most neglected tropical diseases affecting humans and animals around the world. Due to the absence of an effective vaccine, current treatment is based on chemotherapy. However, the continuous appearance of drug resistance and therapeutic failure (TF) lead to an early obsolescence of treatments. Identification of the factors that contribute to TF and drug resistance in leishmaniasis will constitute a useful tool for establishing future strategies to control this disease. In this manuscript, we evaluated the transcriptomic changes in the intracellular amastigotes of the Leishmania infantum parasites isolated from patients with leishmaniasis and TF at 96 h post-infection of THP-1 cells. The adaptation of the parasites to their new environment leads to expression alterations in the genes involved mainly in the transport through cell membranes, energy and redox metabolism, and detoxification. Specifically, the gene that codes for the prostaglandin f2α synthase seems to be relevant in the pathogenicity and TF since it appears substantially upregulated in all the L. infantum lines. Overall, our results show that at the late infection timepoint, the transcriptome of the parasites undergoes significant changes that probably improve the survival of the Leishmania lines in the host cells, contributing to the TF phenotype as well as drug therapy evasion.
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Glycosome heterogeneity in kinetoplastids. Biochem Soc Trans 2021; 49:29-39. [PMID: 33439256 PMCID: PMC7925000 DOI: 10.1042/bst20190517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/18/2020] [Accepted: 11/26/2020] [Indexed: 01/05/2023]
Abstract
Kinetoplastid parasites have essential organelles called glycosomes that are analogous to peroxisomes present in other eukaryotes. While many of the processes that regulate glycosomes are conserved, there are several unique aspects of their biology that are divergent from other systems and may be leveraged as therapeutic targets for the treatment of kinetoplastid diseases. Glycosomes are heterogeneous organelles that likely exist as sub-populations with different protein composition and function in a given cell, between individual cells, and between species. However, the limitations posed by the small size of these organelles makes the study of this heterogeneity difficult. Recent advances in the analysis of small vesicles by flow-cytometry provide an opportunity to overcome these limitations. In this review, we describe studies that document the diverse nature of glycosomes and propose an approach to using flow cytometry and organelle sorting to study the diverse composition and function of these organelles. Because the cellular machinery that regulates glycosome protein import and biogenesis is likely to contribute, at least in part, to glycosome heterogeneity we highlight some ways in which the glycosome protein import machinery differs from that of peroxisomes in other eukaryotes.
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Samarasinghe SR, Samaranayake N, Kariyawasam UL, Siriwardana YD, Imamura H, Karunaweera ND. Genomic insights into virulence mechanisms of Leishmania donovani: evidence from an atypical strain. BMC Genomics 2018; 19:843. [PMID: 30486770 PMCID: PMC6262978 DOI: 10.1186/s12864-018-5271-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 11/19/2018] [Indexed: 01/20/2023] Open
Abstract
Background Leishmaniasis is a neglected tropical disease with diverse clinical phenotypes, determined by parasite, host and vector interactions. Despite the advances in molecular biology and the availability of more Leishmania genome references in recent years, the association between parasite species and distinct clinical phenotypes remains poorly understood. We present a genomic comparison of an atypical variant of Leishmania donovani from a South Asian focus, where it mostly causes cutaneous form of leishmaniasis. Results Clinical isolates from six cutaneous leishmaniasis patients (CL-SL); 2 of whom were poor responders to antimony (CL-PR), and two visceral leishmaniasis patients (VL-SL) were sequenced on an Illumina MiSeq platform. Chromosome aneuploidy was observed in both groups but was more frequent in CL-SL. 248 genes differed by 2 fold or more in copy number among the two groups. Genes involved in amino acid use (LdBPK_271940) and energy metabolism (LdBPK_271950), predominated the VL-SL group with the same distribution pattern reflected in gene tandem arrays. Genes encoding amastins were present in higher copy numbers in VL-SL and CL-PR as well as being among predicted pseudogenes in CL-SL. Both chromosome and SNP profiles showed CL-SL and VL-SL to form two distinct groups. While expected heterozygosity was much higher in VL-SL, SNP allele frequency patterns did not suggest potential recent recombination breakpoints. The SNP/indel profile obtained using the more recently generated PacBio sequence did not vary markedly from that based on the standard LdBPK282A1 reference. Several genes previously associated with resistance to antimonials were observed in higher copy numbers in the analysis of CL-PR. H-locus amplification was seen in one cutaneous isolate which however did not belong to the CL-PR group. Conclusions The data presented suggests that intra species variations at chromosome and gene level are more likely to influence differences in tropism as well as response to treatment, and contributes to greater understanding of parasite molecular mechanisms underpinning these differences. These findings should be substantiated with a larger sample number and expression/functional studies. Electronic supplementary material The online version of this article (10.1186/s12864-018-5271-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sumudu R Samarasinghe
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Nilakshi Samaranayake
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Udeshika L Kariyawasam
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Yamuna D Siriwardana
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Hideo Imamura
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Nadira D Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka.
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Cuypers B, Berg M, Imamura H, Dumetz F, De Muylder G, Domagalska MA, Rijal S, Bhattarai NR, Maes I, Sanders M, Cotton JA, Meysman P, Laukens K, Dujardin JC. Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 62:170-178. [PMID: 29679745 PMCID: PMC6261844 DOI: 10.1016/j.meegid.2018.04.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 01/06/2023]
Abstract
Leishmania donovani is the responsible agent for visceral leishmaniasis (VL) in the Indian subcontinent (ISC). The disease is lethal without treatment and causes 0.2 to 0.4 million cases each year. Recently, reports of VL in Nepalese hilly districts have increased as well as VL cases caused by L. donovani from the ISC1 genetic group, a new and emerging genotype. In this study, we perform for the first time an integrated, untargeted genomics and metabolomics approach to characterize ISC1, in comparison with the Core Group (CG), main population that drove the most recent outbreak of VL in the ISC. We show that the ISC1 population is very different from the CG, both at genome and metabolome levels. The genomic differences include SNPs, CNV and small indels in genes coding for known virulence factors, immunogens and surface proteins. Both genomic and metabolic approaches highlighted dissimilarities related to membrane lipids, the nucleotide salvage pathway and the urea cycle in ISC1 versus CG. Many of these pathways and molecules are important for the interaction with the host/extracellular environment. Altogether, our data predict major functional differences in ISC1 versus CG parasites, including virulence. Therefore, particular attention is required to monitor the fate of this emerging ISC1 population in the ISC, especially in a post-VL elimination context.
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Affiliation(s)
- Bart Cuypers
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Maya Berg
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Hideo Imamura
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Franck Dumetz
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Géraldine De Muylder
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Suman Rijal
- BP Koirala Institute of Health Sciences, Dharan, Nepal
| | | | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - James A Cotton
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Pieter Meysman
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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Ahuja K, Beg MA, Sharma R, Saxena A, Naqvi N, Puri N, Rai PK, Chaudhury A, Duncan R, Salotra P, Nakhasi H, Selvapandiyan A. A novel signal sequence negative multimeric glycosomal protein required for cell cycle progression of Leishmania donovani parasites. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1148-1159. [DOI: 10.1016/j.bbamcr.2018.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/28/2018] [Accepted: 05/21/2018] [Indexed: 12/22/2022]
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Muxel SM, Aoki JI, Fernandes JCR, Laranjeira-Silva MF, Zampieri RA, Acuña SM, Müller KE, Vanderlinde RH, Floeter-Winter LM. Arginine and Polyamines Fate in Leishmania Infection. Front Microbiol 2018; 8:2682. [PMID: 29379478 PMCID: PMC5775291 DOI: 10.3389/fmicb.2017.02682] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 12/22/2017] [Indexed: 01/22/2023] Open
Abstract
Leishmania is a protozoan parasite that alternates its life cycle between the sand fly and the mammalian host macrophages, involving several environmental changes. The parasite responds to these changes by promoting a rapid metabolic adaptation through cellular signaling modifications that lead to transcriptional and post-transcriptional gene expression regulation and morphological modifications. Molecular approaches such as gene expression regulation, next-generation sequencing (NGS), microRNA (miRNA) expression profiling, in cell Western blot analyses and enzymatic activity profiling, have been used to characterize the infection of murine BALB/c and C57BL/6 macrophages, as well as the human monocytic cell-lineage THP-1, with Leishmania amazonensis wild type (La-WT) or arginase knockout (La-arg-). These models are being used to elucidate physiological roles of arginine and polyamines pathways and the importance of arginase for the establishment of the infection. In this review, we will describe the main aspects of Leishmania-host interaction, focusing on the arginine and polyamines pathways and pointing to possible targets to be used for prognosis and/or in the control of the infection. The parasite enzymes, arginase and nitric oxide synthase-like, have essential roles in the parasite survival and in the maintenance of infection. On the other hand, in mammalian macrophages, defense mechanisms are activated inducing alterations in the mRNA, miRNA and enzymatic profiles that lead to the control of infection. Furthermore, the genetic background of both parasite and host are also important to define the fate of infection.
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Affiliation(s)
- Sandra M Muxel
- Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana I Aoki
- Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliane C R Fernandes
- Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Ricardo A Zampieri
- Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Stephanie M Acuña
- Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Karl E Müller
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Rubia H Vanderlinde
- Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Lucile M Floeter-Winter
- Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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Zackay A, Cotton JA, Sanders M, Hailu A, Nasereddin A, Warburg A, Jaffe CL. Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival. PLoS Genet 2018; 14:e1007133. [PMID: 29315303 PMCID: PMC5777657 DOI: 10.1371/journal.pgen.1007133] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/22/2018] [Accepted: 11/28/2017] [Indexed: 12/22/2022] Open
Abstract
Leishmania donovani is the main cause of visceral leishmaniasis (VL) in East Africa. Differences between northern Ethiopia/Sudan (NE) and southern Ethiopia (SE) in ecology, vectors, and patient sensitivity to drug treatment have been described, however the relationship between differences in parasite genotype between these two foci and phenotype is unknown. Whole genomic sequencing (WGS) was carried out for 41 L. donovani strains and clones from VL and VL/HIV co-infected patients in NE (n = 28) and SE (n = 13). Chromosome aneuploidy was observed in all parasites examined with each isolate exhibiting a unique karyotype. Differences in chromosome ploidy or karyotype were not correlated with the geographic origin of the parasites. However, correlation between single nucleotide polymorphism (SNP) and geographic origin was seen for 38/41 isolates, separating the NE and SE parasites into two large groups. SNP restricted to NE and SE groups were associated with genes involved in viability and parasite resistance to drugs. Unique copy number variation (CNV) were also associated with NE and SE parasites, respectively. One striking example is the folate transporter (FT) family genes (LdBPK_100390, LdBPK_100400 and LdBPK_100410) on chromosome 10 that are single copy in all 13 SE isolates, but either double copy or higher in 39/41 NE isolates (copy number 2-4). High copy number (= 4) was also found for one Sudanese strain examined. This was confirmed by quantitative polymerase chain reaction for LdBPK_100400, the L. donovani FT1 transporter homolog. Good correlation (p = 0.005) between FT copy number and resistance to methotrexate (0.5 mg/ml MTX) was also observed with the haploid SE strains examined showing higher viability than the NE strains at this concentration. Our results emphasize the advantages of whole genome analysis to shed light on vital parasite processes in Leishmania.
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Affiliation(s)
- Arie Zackay
- Dept Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious & Tropical Diseases, IMRIC, Hebrew University–Hadassah Medical School, Jerusalem, Israel
| | - James A. Cotton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Asrat Hailu
- Dept Microbiology, Immunology & Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abedelmajeed Nasereddin
- Dept Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious & Tropical Diseases, IMRIC, Hebrew University–Hadassah Medical School, Jerusalem, Israel
| | - Alon Warburg
- Dept Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious & Tropical Diseases, IMRIC, Hebrew University–Hadassah Medical School, Jerusalem, Israel
| | - Charles L. Jaffe
- Dept Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious & Tropical Diseases, IMRIC, Hebrew University–Hadassah Medical School, Jerusalem, Israel
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9
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Singh J, Khan MI, Singh Yadav SP, Srivastava A, Sinha KK, Ashish, Das P, Kundu B. L-Asparaginase of Leishmania donovani: Metabolic target and its role in Amphotericin B resistance. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2017; 7:337-349. [PMID: 28988014 PMCID: PMC5633258 DOI: 10.1016/j.ijpddr.2017.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/22/2017] [Accepted: 09/21/2017] [Indexed: 01/12/2023]
Abstract
Emergence of Amphotericin B (AmB) resistant Leishmania donovani has posed major therapeutic challenge against the parasite. Consequently, combination therapy aimed at multiple molecular targets, based on proteome wise network analysis has been recommended. In this regard we had earlier identified and proposed L-asparaginase of Leishmania donovani (LdAI) as a crucial metabolic target. Here we report that both LdAI overexpressing axenic amastigote and promastigote forms of L. donovani survives better when challenged with AmB as compared to wild type strain. Conversely, qRT-PCR analysis showed an upregulation of LdAI in both forms upon AmB treatment. Our data demonstrates the importance of LdAI in imparting immediate protective response to the parasite upon AmB treatment. In the absence of structural and functional information, we modeled LdAI and validated its solution structure through small angle X-ray scattering (SAXS) analysis. We identified its specific inhibitors through ligand and structure-based approach and characterized their effects on enzymatic properties (Km, Vmax, Kcat) of LdAI. We show that in presence of two of the inhibitors L1 and L2, the survival of L. donovani is compromised whereas overexpression of LdAI in these cells restores viability. Taken together, our results conclusively prove that LdAI is a crucial metabolic enzyme conferring early counter measure against AmB treatment by Leishmania.
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Affiliation(s)
- Jasdeep Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Mohd Imran Khan
- National Institute of Pharmaceutical Education & Research, EPIP Complex, Hajipur, Vaishali 844102, India
| | - Shiv Pratap Singh Yadav
- The Council of Scientific and Industrial Research Institute of Microbial Technology, Chandigarh, India
| | - Ankit Srivastava
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Kislay K Sinha
- National Institute of Pharmaceutical Education & Research, EPIP Complex, Hajipur, Vaishali 844102, India
| | - Ashish
- The Council of Scientific and Industrial Research Institute of Microbial Technology, Chandigarh, India
| | - Pradeep Das
- Rajendra Memorial Research Institute of Medical Sciences, Patna 800007, India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India.
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10
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Herrera Sanchez MB, Previdi S, Bruno S, Fonsato V, Deregibus MC, Kholia S, Petrillo S, Tolosano E, Critelli R, Spada M, Romagnoli R, Salizzoni M, Tetta C, Camussi G. Extracellular vesicles from human liver stem cells restore argininosuccinate synthase deficiency. Stem Cell Res Ther 2017; 8:176. [PMID: 28750687 PMCID: PMC5531104 DOI: 10.1186/s13287-017-0628-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 06/16/2017] [Accepted: 07/10/2017] [Indexed: 11/25/2022] Open
Abstract
Background Argininosuccinate synthase (ASS)1 is a urea cycle enzyme that catalyzes the conversion of citrulline and aspartate to argininosuccinate. Mutations in the ASS1 gene cause citrullinemia type I, a rare autosomal recessive disorder characterized by neonatal hyperammonemia, elevated citrulline levels, and early neonatal death. Treatment for this disease is currently restricted to liver transplantation; however, due to limited organ availability, substitute therapies are required. Recently, extracellular vesicles (EVs) have been reported to act as intercellular transporters carrying genetic information responsible for cell reprogramming. In previous studies, we isolated a population of stem cell-like cells known as human liver stem cells (HLSCs) from healthy liver tissue. Moreover, EVs derived from HLSCs were reported to exhibit regenerative effects on the liver parenchyma in models of acute liver injury. The aim of this study was to evaluate whether EVs derived from normal HLSCs restored ASS1 enzymatic activity and urea production in hepatocytes differentiated from HLSCs derived from a patient with type I citrullinemia. Methods HLSCs were isolated from the liver of a patient with type I citrullinemia (ASS1-HLSCs) and characterized by fluorescence-activated cell sorting (FACS), immunofluorescence, and DNA sequencing analysis. Furthermore, their differentiation capabilities in vitro were also assessed. Hepatocytes differentiated from ASS1-HLSCs were evaluated by the production of urea and ASS enzymatic activity. EVs derived from normal HLSCs were purified by differential ultracentrifugation followed by floating density gradient. The EV content was analyzed to identify the presence of ASS1 protein, mRNA, and ASS1 gene. In order to obtain ASS1-depleted EVs, a knockdown of the ASS1 gene in HLSCs was performed followed by EV isolation from these cells. Results Treating ASS1-HLSCs with EVs from HLSCs restored both ASS1 activity and urea production mainly through the transfer of ASS1 enzyme and mRNA. In fact, EVs from ASS1-knockdown HLSCs contained low amounts of ASS1 mRNA and protein, and were unable to restore urea production in hepatocytes differentiated from ASS1-HLSCs. Conclusions Collectively, these results suggest that EVs derived from normal HLSCs may compensate the loss of ASS1 enzyme activity in hepatocytes differentiated from ASS1-HLSCs. Electronic supplementary material The online version of this article (doi:10.1186/s13287-017-0628-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Beatriz Herrera Sanchez
- 2i3T, Società per la gestione dell'incubatore di imprese e per il trasferimento tecnologico, Scarl University of Torino, Torino, Italy.,Molecular Biotechnology Center, University of Torino, Torino, Italy
| | | | - Stefania Bruno
- Department of Molecular Biotechnology and Health Science, University of Torino, Torino, Italy
| | - Valentina Fonsato
- 2i3T, Società per la gestione dell'incubatore di imprese e per il trasferimento tecnologico, Scarl University of Torino, Torino, Italy.,Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Maria Chiara Deregibus
- 2i3T, Società per la gestione dell'incubatore di imprese e per il trasferimento tecnologico, Scarl University of Torino, Torino, Italy.,Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Sharad Kholia
- Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Sara Petrillo
- Department of Molecular Biotechnology and Health Science, University of Torino, Torino, Italy
| | - Emanuela Tolosano
- Department of Molecular Biotechnology and Health Science, University of Torino, Torino, Italy
| | - Rossana Critelli
- Molecular and Genetic Epidemiology Unit, Human Genetics Foundation, Torino, Italy
| | - Marco Spada
- Department of Pediatrics, Regina Margherita Children's Hospital, University of Torino, Torino, Italy
| | - Renato Romagnoli
- Liver Transplantation Center, University of Torino, Torino, Italy
| | - Mauro Salizzoni
- Liver Transplantation Center, University of Torino, Torino, Italy
| | | | - Giovanni Camussi
- Department of Medical Sciences, University of Torino, Corso Dogliotti 14, I-10126, Torino, Italy.
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Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S, Sundar S, Mannaert A, Vanaerschot M, Berg M, De Muylder G, Dumetz F, Cuypers B, Maes I, Domagalska M, Decuypere S, Rai K, Uranw S, Bhattarai NR, Khanal B, Prajapati VK, Sharma S, Stark O, Schönian G, De Koning HP, Settimo L, Vanhollebeke B, Roy S, Ostyn B, Boelaert M, Maes L, Berriman M, Dujardin JC, Cotton JA. Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. eLife 2016; 5. [PMID: 27003289 PMCID: PMC4811772 DOI: 10.7554/elife.12613] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/15/2016] [Indexed: 12/25/2022] Open
Abstract
Leishmania donovani causes visceral leishmaniasis (VL), the second most deadly vector-borne parasitic disease. A recent epidemic in the Indian subcontinent (ISC) caused up to 80% of global VL and over 30,000 deaths per year. Resistance against antimonial drugs has probably been a contributing factor in the persistence of this epidemic. Here we use whole genome sequences from 204 clinical isolates to track the evolution and epidemiology of L. donovani from the ISC. We identify independent radiations that have emerged since a bottleneck coincident with 1960s DDT spraying campaigns. A genetically distinct population frequently resistant to antimonials has a two base-pair insertion in the aquaglyceroporin gene LdAQP1 that prevents the transport of trivalent antimonials. We find evidence of genetic exchange between ISC populations, and show that the mutation in LdAQP1 has spread by recombination. Our results reveal the complexity of L. donovani evolution in the ISC in response to drug treatment. DOI:http://dx.doi.org/10.7554/eLife.12613.001 The parasite Leishmania donovani causes a disease called visceral leishmaniasis that affects many of the world's poorest people. Around half a million new cases develop every year, but health authorities lack safe and effective drugs to treat them. Up to 80% of these cases occur in the Indian subcontinent, where devastating epidemics have occurred in the last decades. One reason these epidemics continue to occur is that the parasites develop genetic mutations allowing them to adapt to and resist the drugs used to kill them. As there are few existing drugs that can kill L. donovani, it is crucial to understand how drug resistance emerges and spreads among parasite populations. Imamura, Downing, Van den Broeck et al. have now investigated the history of visceral leishmaniasis epidemics by characterising the complete genetic sequence – or genome – of 204 L. donovani parasite samples. This revealed that the majority of parasites in the Indian subcontinent first appeared in the nineteenth century, matching the first historical records of visceral leishmaniasis epidemics. The genomes show that most of the parasites are genetically similar and can be clustered into several closely related groups. These groups first appeared in the 1960s following the end of a regional campaign to eradicate malaria. The most common parasite group is particularly resistant to drugs called antimonials, which were the main treatment for leishmaniasis until recently. These parasites have a small genetic change that scrambles most of a protein known to be involved in the uptake of antimonials. Parasites may also be able to develop resistance to drugs through additional mechanisms that allow them to produce many copies of the same gene. These mechanisms could allow the parasites to rapidly adapt to new drugs or changes in the populations it infects. The work of Imamura et al. looks only at parasites isolated from patients then grown in the laboratory, so further research is now needed to explore how variable the Leishmania genome is in both of the parasite’s hosts: humans and sandflies. Imamura et al.’s study reveals how L. donovani has spread throughout the Indian subcontinent in fine detail. The genome data can be used to create simple molecular tools that could form an "early warning system" to track the success of disease control programs and to determine how well the current drugs are working. DOI:http://dx.doi.org/10.7554/eLife.12613.002
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Affiliation(s)
- Hideo Imamura
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tim Downing
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,School of Maths, Applied Maths and Statistics, National University of Ireland Galway, Galway, Ireland
| | | | | | - Suman Rijal
- BP Koirala Institute of Health Sciences, Dharan, Nepal
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - An Mannaert
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Manu Vanaerschot
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Maya Berg
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Géraldine De Muylder
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Franck Dumetz
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bart Cuypers
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Saskia Decuypere
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Keshav Rai
- BP Koirala Institute of Health Sciences, Dharan, Nepal
| | | | | | | | - Vijay Kumar Prajapati
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Smriti Sharma
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Olivia Stark
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Gabriele Schönian
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Harry P De Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Luca Settimo
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
| | - Benoit Vanhollebeke
- Laboratory of Molecular Parasitology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Syamal Roy
- Department of Infectious Diseases and Immunology, Council of Scientific and Industrial Research, Indian Institute of Chemical Biology, Kolkata, India
| | - Bart Ostyn
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | - Marleen Boelaert
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | - Louis Maes
- Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - James A Cotton
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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Dong M, Fisher C, Añez G, Rios M, Nakhasi HL, Hobson JP, Beanan M, Hockman D, Grigorenko E, Duncan R. Standardized methods to generate mock (spiked) clinical specimens by spiking blood or plasma with cultured pathogens. J Appl Microbiol 2016; 120:1119-29. [PMID: 26835651 DOI: 10.1111/jam.13082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/11/2016] [Accepted: 01/20/2016] [Indexed: 11/29/2022]
Abstract
AIMS To demonstrate standardized methods for spiking pathogens into human matrices for evaluation and comparison among diagnostic platforms. METHODS AND RESULTS This study presents detailed methods for spiking bacteria or protozoan parasites into whole blood and virus into plasma. Proper methods must start with a documented, reproducible pathogen source followed by steps that include standardized culture, preparation of cryopreserved aliquots, quantification of the aliquots by molecular methods, production of sufficient numbers of individual specimens and testing of the platform with multiple mock specimens. Results are presented following the described procedures that showed acceptable reproducibility comparing in-house real-time PCR assays to a commercially available multiplex molecular assay. CONCLUSIONS A step by step procedure has been described that can be followed by assay developers who are targeting low prevalence pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY The development of diagnostic platforms for detection of low prevalence pathogens such as biothreat or emerging agents is challenged by the lack of clinical specimens for performance evaluation. This deficit can be overcome using mock clinical specimens made by spiking cultured pathogens into human matrices. To facilitate evaluation and comparison among platforms, standardized methods must be followed in the preparation and application of spiked specimens.
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Affiliation(s)
- M Dong
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - C Fisher
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - G Añez
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - M Rios
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - H L Nakhasi
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - J P Hobson
- Office of In Vitro Diagnostics and Radiological Health (OIR), Division of Microbiology Devices, Center for Devices and Radiological Health (CDRH), FDA, Silver Spring, MD, USA
| | - M Beanan
- Office of Biodefense, Research Resources, and Translational Research, Division of Microbiology and Infectious Diseases (DMID), National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD, USA
| | - D Hockman
- Diatherix Laboratory, Huntsville, AL, USA
| | | | - R Duncan
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD, USA
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Sardar AH, Jardim A, Ghosh AK, Mandal A, Das S, Saini S, Abhishek K, Singh R, Verma S, Kumar A, Das P. Genetic Manipulation of Leishmania donovani to Explore the Involvement of Argininosuccinate Synthase in Oxidative Stress Management. PLoS Negl Trop Dis 2016; 10:e0004308. [PMID: 26939071 PMCID: PMC4777552 DOI: 10.1371/journal.pntd.0004308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 11/25/2015] [Indexed: 11/20/2022] Open
Abstract
Reactive oxygen and nitrogen species (ROS and RNS) produced by the phagocytic cells are the most common arsenals used to kill the intracellular pathogens. However, Leishmania, an intracellular pathogen, has evolved mechanisms to survive by counterbalancing the toxic oxygen metabolites produced during infection. Polyamines, the major contributor in this anti-oxidant machinery, are largely dependent on the availability of L-arginine in the intracellular milieu. Argininosuccinate synthase (ASS) plays an important role as the rate-limiting step required for converting L-citrulline to argininosuccinate to provide arginine for an assortment of metabolic processes. Leishmania produce an active ASS enzyme, yet it has an incomplete urea cycle as it lacks an argininosuccinate lyase (ASL). There is no evidence for endogenous synthesis of L-arginine in Leishmania, which suggests that these parasites salvage L-arginine from extracellular milieu and makes the biological function of ASS and the production of argininosuccinate in Leishmania unclear. Our previous quantitative proteomic analysis of Leishmania promastigotes treated with sub-lethal doses of ROS, RNS, or a combination of both, led to the identification of several differentially expressed proteins which included ASS. To assess the involvement of ASS in stress management, a mutant cell line with greatly reduced ASS activity was created by a double-targeted gene replacement strategy in L. donovani promastigote. Interestingly, LdASS is encoded by three copies of allele, but Western blot analysis showed the third allele did not appear to express ASS. The free thiol levels in the mutant LdASS-/-/+ cell line were decreased. Furthermore, the cell viability in L-arginine depleted medium was greatly attenuated on exposure to different stress environments and was adversely impacted in its ability to infect mice. These findings suggest that ASS is important for Leishmania donovani to counterbalance the stressed environments encountered during infection and can be targeted for chemotherapeutic purpose to treat visceral leishmaniasis.
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Affiliation(s)
- Abul Hasan Sardar
- Division of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Bihar, India
| | - Armando Jardim
- Institute of Parasitology and Centre for Host-Parasite Interactions, Macdonald Campus, McGill University, Quebec, Canada
| | - Ayan Kumar Ghosh
- Division of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Bihar, India
| | - Abhishek Mandal
- Division of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Bihar, India
| | - Sushmita Das
- Department of Microbiology, All India Institute of Medical Sciences, Bihar, India
| | - Savita Saini
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Bihar, India
| | - Kumar Abhishek
- Division of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Bihar, India
| | - Ruby Singh
- Division of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Bihar, India
| | - Sudha Verma
- Division of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Bihar, India
| | - Ajay Kumar
- Division of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Bihar, India
| | - Pradeep Das
- Division of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Bihar, India
- * E-mail:
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Heterogeneity of molecular resistance patterns in antimony-resistant field isolates of Leishmania species from the western Mediterranean area. Antimicrob Agents Chemother 2014; 58:4866-74. [PMID: 24913173 DOI: 10.1128/aac.02521-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimonials remain the first-line treatment for the various manifestations of leishmaniasis in most areas where the disease is endemic, and increasing cases of therapeutic failure associated with parasite resistance have been reported. In this study, we assessed the molecular status of 47 clinical isolates of Leishmania causing visceral and cutaneous leishmaniasis from Algeria, Tunisia, and southern France. In total, we examined 14 genes that have been shown to exhibit significant variations in DNA amplification, mRNA levels, or protein expression with respect to resistance to antimonials. The gene status of each clinical isolate was assessed via qPCR and qRT-PCR. We then compared the molecular pattern against the phenotype determined via an in vitro sensitivity test of the clinical isolates against meglumine antimoniate, which is considered the reference technique. Our results demonstrate significant DNA amplification and/or RNA overexpression in 56% of the clinical isolates with the resistant phenotype. All clinical isolates that exhibited significant overexpression of at least 2 genes displayed a resistant phenotype. Among the 14 genes investigated, 10 genes displayed either significant amplification or overexpression in at least 1 clinical isolate; these genes are involved in several metabolic pathways. Moreover, various gene associations were observed depending on the clinical isolates, supporting the multifactorial nature of Leishmania resistance. Molecular resistance features were found in the 3 Leishmania species investigated (Leishmania infantum, Leishmania major, and Leishmania killicki). To our knowledge, this is the first report of the involvement of molecular resistance genes in field isolates of Leishmania major and Leishmania killicki with the resistance phenotype.
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Duncan R, Gannavaram S, Dey R, Debrabant A, Lakhal-Naouar I, Nakhasi HL. Identification and characterization of genes involved in leishmania pathogenesis: the potential for drug target selection. Mol Biol Int 2011; 2011:428486. [PMID: 22091403 PMCID: PMC3200065 DOI: 10.4061/2011/428486] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 03/26/2011] [Accepted: 04/28/2011] [Indexed: 12/14/2022] Open
Abstract
Identifying and characterizing Leishmania donovani genes and the proteins they encode for their role in pathogenesis can reveal the value of this approach for finding new drug targets. Effective drug targets are likely to be proteins differentially expressed or required in the amastigote life cycle stage found in the patient. Several examples and their potential for chemotherapeutic disruption are presented. A pathway nearly ubiquitous in living cells targeted by anticancer drugs, the ubiquitin system, is examined. New findings in ubiquitin and ubiquitin-like modifiers in Leishmania show how disruption of those pathways could point to additional drug targets. The programmed cell death pathway, now recognized among protozoan parasites, is reviewed for some of its components and evidence that suggests they could be targeted for antiparasitic drug therapy. Finally, the endoplasmic reticulum quality control system is involved in secretion of many virulence factors. How disruptions in this pathway reduce virulence as evidence for potential drug targets is presented.
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Affiliation(s)
- Robert Duncan
- Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, FDA, Bethesda, MD 20852, USA
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