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Tulloch LB, Tinti M, Wall RJ, Weidt SK, Corpas- Lopez V, Dey G, Smith TK, Fairlamb AH, Barrett MP, Wyllie S. Sterol 14-alpha demethylase (CYP51) activity in Leishmania donovani is likely dependent upon cytochrome P450 reductase 1. PLoS Pathog 2024; 20:e1012382. [PMID: 38991025 PMCID: PMC11265716 DOI: 10.1371/journal.ppat.1012382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 07/23/2024] [Accepted: 06/30/2024] [Indexed: 07/13/2024] Open
Abstract
Liposomal amphotericin B is an important frontline drug for the treatment of visceral leishmaniasis, a neglected disease of poverty. The mechanism of action of amphotericin B (AmB) is thought to involve interaction with ergosterol and other ergostane sterols, resulting in disruption of the integrity and key functions of the plasma membrane. Emergence of clinically refractory isolates of Leishmania donovani and L. infantum is an ongoing issue and knowledge of potential resistance mechanisms can help to alleviate this problem. Here we report the characterisation of four independently selected L. donovani clones that are resistant to AmB. Whole genome sequencing revealed that in three of the moderately resistant clones, resistance was due solely to the deletion of a gene encoding C24-sterol methyltransferase (SMT1). The fourth, hyper-resistant resistant clone (>60-fold) was found to have a 24 bp deletion in both alleles of a gene encoding a putative cytochrome P450 reductase (P450R1). Metabolic profiling indicated these parasites were virtually devoid of ergosterol (0.2% versus 18% of total sterols in wild-type) and had a marked accumulation of 14-methylfecosterol (75% versus 0.1% of total sterols in wild-type) and other 14-alpha methylcholestanes. These are substrates for sterol 14-alpha demethylase (CYP51) suggesting that this enzyme may be a bona fide P450R specifically involved in electron transfer from NADPH to CYP51 during catalysis. Deletion of P450R1 in wild-type cells phenocopied the metabolic changes observed in our AmB hyper-resistant clone as well as in CYP51 nulls. Likewise, addition of a wild type P450R1 gene restored sterol profiles to wild type. Our studies indicate that P450R1 is essential for L. donovani amastigote viability, thus loss of this gene is unlikely to be a driver of clinical resistance. Nevertheless, investigating the mechanisms underpinning AmB resistance in these cells provided insights that refine our understanding of the L. donovani sterol biosynthetic pathway.
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Affiliation(s)
- Lindsay B. Tulloch
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Michele Tinti
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Richard J. Wall
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Stefan K. Weidt
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Victoriano Corpas- Lopez
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Gourav Dey
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Terry K. Smith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Alan H. Fairlamb
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Michael P. Barrett
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
- School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
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Silva RVS, Uliana SRB, Yasunaka JKUY, Veloso CS, Sousa E, Ferreira MML, Carvalho VS, Ferreira GR, Costa DL, Costa CHN. Low Plasma Lipids Are Associated with Relapsing and Lethal Visceral Leishmaniasis in HIV-Infected Patients. Pathogens 2024; 13:450. [PMID: 38921748 PMCID: PMC11206293 DOI: 10.3390/pathogens13060450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
Visceral leishmaniasis (VL) results from protozoa Leishmania infantum and L. donovani infection. This study investigated whether host factors would explain the relapses. First, susceptibility to amphotericin B of L. infantum isolates was evaluated in vitro. Then, clinical data and the lipid profile of patients with relapsing and non-relapsing VL were assessed. Susceptibility to amphotericin B was similar between the isolates. CD4+ lymphocytes were reduced in both groups of patients in the first episode and with relapsing VL. Still, the strongest blood cell indicator associated with relapses was low total lymphocyte counts. Total plasma cholesterol, high-density lipoprotein, low-density lipoprotein, and, uniquely, triglycerides of the six individuals in the first episode and twenty-three with relapsing VL were lower in relapsing patients than those in the first episode. Deceased patients had extremely low low-density lipoprotein. After CD4+ decreases, lymphocyte CD8+ reduction is the final stage of immunological failure. The lower lipid concentrations appear to be secondary to the depletion of fat stores by inflammation-induced cachexia and fat exhaustion provoked by the co-occurrence of both diseases, which can finally lead to death.
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Affiliation(s)
- Renata V. S. Silva
- Laboratório de Leishmanioses, Departamento de Medicina Comunitária, Universidade Federal do Piauí, Teresina 64002-510, PI, Brazil;
| | - Silvia R. B. Uliana
- Laboratório de Leishmanioses, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil; (S.R.B.U.); (J.K.U.Y.Y.)
| | - Jenicer K. U. Y. Yasunaka
- Laboratório de Leishmanioses, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil; (S.R.B.U.); (J.K.U.Y.Y.)
| | - Cláudio S. Veloso
- Instituto de Doenças Tropicais “Natan Portella”, Teresina 64002-510, PI, Brazil; (C.S.V.); (D.L.C.)
| | - Emille Sousa
- Laboratório de Leishmanioses, Centro de Inteligência em Agravos Emergentes e Negligenciados, Teresina 64002-510, PI, Brazil; (E.S.); (M.M.L.F.)
| | - Maria M. L. Ferreira
- Laboratório de Leishmanioses, Centro de Inteligência em Agravos Emergentes e Negligenciados, Teresina 64002-510, PI, Brazil; (E.S.); (M.M.L.F.)
| | - Vivianne S. Carvalho
- Centro de Diagnóstico, “Dr. Raul Bacellar”, Fundação Municipal de Saúde, Teresina 64600-000, PI, Brazil;
| | - Gabriel R. Ferreira
- Department of Microbiology-Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 0A6, Canada;
| | - Dorcas L. Costa
- Instituto de Doenças Tropicais “Natan Portella”, Teresina 64002-510, PI, Brazil; (C.S.V.); (D.L.C.)
- Laboratório de Leishmanioses, Centro de Inteligência em Agravos Emergentes e Negligenciados, Teresina 64002-510, PI, Brazil; (E.S.); (M.M.L.F.)
- Departamento de Mãe e Filho, Universidade Federal do Piauí, Teresina 64002-510, PI, Brazil
| | - Carlos H. N. Costa
- Instituto de Doenças Tropicais “Natan Portella”, Teresina 64002-510, PI, Brazil; (C.S.V.); (D.L.C.)
- Laboratório de Leishmanioses, Centro de Inteligência em Agravos Emergentes e Negligenciados, Teresina 64002-510, PI, Brazil; (E.S.); (M.M.L.F.)
- Departamento de Medicina Comunitária, Universidade Federal do Piauí, Teresina 64002-510, PI, Brazil
- Laboratório de Pesquisas em Leishmanioses, Centro de Investigações em Agravos Tropicais Emergentes e Negligenciados, Instituto de Doenças Tropicais “Natan Portella”, Universidade Federal do Piauí, Rua Artur de Vasconcelos 151, Teresina 64002-510, PI, Brazil
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3
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Ferreira BA, Coser EM, de la Roca S, Aoki JI, Branco N, Soares GHC, Lima MIS, Coelho AC. Amphotericin B resistance in Leishmania amazonensis: In vitro and in vivo characterization of a Brazilian clinical isolate. PLoS Negl Trop Dis 2024; 18:e0012175. [PMID: 38768213 PMCID: PMC11142706 DOI: 10.1371/journal.pntd.0012175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/31/2024] [Accepted: 04/27/2024] [Indexed: 05/22/2024] Open
Abstract
In Brazil, Leishmania amazonensis is the etiological agent of cutaneous and diffuse cutaneous leishmaniasis. The state of Maranhão in the Northeast of Brazil is prevalent for these clinical forms of the disease and also has high rates of HIV infection. Here, we characterized the drug susceptibility of a L. amazonensis clinical isolate from a 46-year-old man with diffuse cutaneous leishmaniasis coinfected with HIV from this endemic area. This patient underwent several therapeutic regimens with meglumine antimoniate, liposomal amphotericin B, and pentamidine, without success. In vitro susceptibility assays against promastigotes and intracellular amastigotes demonstrated that this isolate had low susceptibility to amphotericin B, when compared with the reference strain of this species that is considered susceptible to antileishmanial drugs. Additionally, we investigated whether the low in vitro susceptibility would affect the in vivo response to amphotericin B treatment. The drug was effective in reducing the lesion size and parasite burden in mice infected with the reference strain, whereas those infected with the clinical isolate and a resistant line (generated experimentally by stepwise selection) were refractory to amphotericin B treatment. To evaluate whether the isolate was intrinsically resistant to amphotericin B in animals, infected mice were treated with other drugs that had not been used in the treatment of the patient (miltefosine, paromomycin, and a combination of both). Our findings demonstrated that all drug schemes were able to reduce lesion size and parasite burden in animals infected with the clinical isolate, confirming the amphotericin B-resistance phenotype. These findings indicate that the treatment failure observed in the patient may be associated with amphotericin B resistance, and demonstrate the potential emergence of amphotericin B-resistant L. amazonensis isolates in an area of Brazil endemic for cutaneous leishmaniasis.
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Affiliation(s)
- Bianca A. Ferreira
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Elizabeth M. Coser
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Stephane de la Roca
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Juliana I. Aoki
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Nilson Branco
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Gustavo H. C. Soares
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Mayara I. S. Lima
- Departamento de Biologia, Programas de Pós Graduação em Saúde e Ambiente e Ciências da Saúde, Universidade Federal do Maranhão, São Luís, Brazil
| | - Adriano C. Coelho
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
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Bharadava K, Upadhyay TK, Kaushal RS, Ahmad I, Alraey Y, Siddiqui S, Saeed M. Genomic Insight of Leishmania Parasite: In-Depth Review of Drug Resistance Mechanisms and Genetic Mutations. ACS OMEGA 2024; 9:12500-12514. [PMID: 38524425 PMCID: PMC10955595 DOI: 10.1021/acsomega.3c09400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 03/26/2024]
Abstract
Leishmaniasis, which is caused by a parasitic protozoan of the genus Leishmania, is still a major threat to global health, impacting millions of individuals worldwide in endemic areas. Chemotherapy has been the principal method for managing leishmaniasis; nevertheless, the evolution of drug resistance offers a significant obstacle to therapeutic success. Drug-resistant behavior in these parasites is a complex phenomenon including both innate and acquired mechanisms. Resistance is frequently related to changes in drug transportation, drug target alterations, and enhanced efflux of the drug from the pathogen. This review has revealed specific genetic mutations in Leishmania parasites that are associated with resistance to commonly used antileishmanial drugs such as pentavalent antimonials, miltefosine, amphotericin B, and paromomycin, resulting in changes in gene expression along with the functioning of various proteins involved in drug uptake, metabolism, and efflux. Understanding the genetic changes linked to drug resistance in Leishmania parasites is essential for creating approaches for tackling and avoiding the spread of drug-resistant variants. Based on which specific treatments focus on mutations and pathways could potentially improve treatment efficacy and help long-term leishmaniasis control. More study is needed to uncover the complete range of genetic changes generating medication resistance and to develop new therapies based on available information.
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Affiliation(s)
- Krupanshi Bharadava
- Biophysics
& Structural Biology, Research & Development Cell, Parul University, Vadodara, Gujarat 391760, India
| | - Tarun Kumar Upadhyay
- Department
of Life Sciences, Parul Institute of Applied Sciences & Research
and Development Cell, Parul University, Vadodara, Gujarat 391760, India
| | - Radhey Shyam Kaushal
- Biophysics
& Structural Biology, Research & Development Cell, Parul University, Vadodara, Gujarat 391760, India
- Department
of Life Sciences, Parul Institute of Applied Sciences & Research
and Development Cell, Parul University, Vadodara, Gujarat 391760, India
| | - Irfan Ahmad
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia
| | - Yasser Alraey
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia
| | - Samra Siddiqui
- Department
of Health Service Management, College of Public Health and Health
Informatics, University of Hail, Hail 55476, Saudi Arabia
| | - Mohd Saeed
- Department
of Biology, College of Science, University
of Hail, Hail 55476, Saudi Arabia
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5
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Bernardo L, Ibarra-Meneses AV, Douanne N, Corbeil A, Solana JC, Beaudry F, Carrillo E, Moreno J, Fernandez-Prada C. Potential selection of antimony and methotrexate cross-resistance in Leishmania infantum circulating strains. PLoS Negl Trop Dis 2024; 18:e0012015. [PMID: 38422164 DOI: 10.1371/journal.pntd.0012015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 03/12/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Visceral leishmaniasis (VL) resolution depends on a wide range of factors, including the instauration of an effective treatment coupled to a functional host immune system. Patients with a depressed immune system, like the ones receiving methotrexate (MTX), are at higher risk of developing VL and refusing antileishmanial drugs. Moreover, the alarmingly growing levels of antimicrobial resistance, especially in endemic areas, contribute to the increasing the burden of this complex zoonotic disease. PRINCIPAL FINDINGS To understand the potential links between immunosuppressants and antileishmanial drugs, we have studied the interaction of antimony (Sb) and MTX in a Leishmania infantum reference strain (LiWT) and in two L. infantum clinical strains (LiFS-A and LiFS-B) naturally circulating in non-treated VL dogs in Spain. The LiFS-A strain was isolated before Sb treatment in a case that responded positively to the treatment, while the LiFS-B strain was recovered from a dog before Sb treatment, with the dog later relapsing after the treatment. Our results show that, exposure to Sb or MTX leads to an increase in the production of reactive oxygen species (ROS) in LiWT which correlates with a sensitive phenotype against both drugs in promastigotes and intracellular amastigotes. LiFS-A was sensitive against Sb but resistant against MTX, displaying high levels of protection against ROS when exposed to MTX. LiFS-B was resistant to both drugs. Evaluation of the melting proteomes of the two LiFS, in the presence and absence of Sb and MTX, showed a differential enrichment of direct and indirect targets for both drugs, including common and unique pathways. CONCLUSION Our results show the potential selection of Sb-MTX cross-resistant parasites in the field, pointing to the possibility to undermine antileishmanial treatment of those patients being treated with immunosuppressant drugs in Leishmania endemic areas.
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Affiliation(s)
- Lorena Bernardo
- WHO Collaborating Centre for Leishmaniasis, Spanish National Center for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Ana Victoria Ibarra-Meneses
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Noelie Douanne
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Audrey Corbeil
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Jose Carlos Solana
- WHO Collaborating Centre for Leishmaniasis, Spanish National Center for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Francis Beaudry
- Département de Biomédecine, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Centre de recherche sur le cerveau et l'apprentissage (CIRCA), Université de Montréal, Montréal, Quebec, Canada
| | - Eugenia Carrillo
- WHO Collaborating Centre for Leishmaniasis, Spanish National Center for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Javier Moreno
- WHO Collaborating Centre for Leishmaniasis, Spanish National Center for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Christopher Fernandez-Prada
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
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Potvin JÉ, Fani F, Queffeulou M, Gazanion É, Leprohon P, Ouellette M. Increased copy number of the target gene squalene monooxygenase as the main resistance mechanism to terbinafine in Leishmania infantum. Int J Parasitol Drugs Drug Resist 2023; 23:37-43. [PMID: 37703646 PMCID: PMC10502319 DOI: 10.1016/j.ijpddr.2023.09.001] [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] [Received: 07/03/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023]
Abstract
We use here two genomic screens in an attempt to understand the mode of action and resistance mechanism of terbinafine, an antifungal contemplated as a potential drug against the parasite Leishmania. One screen consisted in in vitro drug evolution where 5 independent mutants were selected step-by-step for terbinafine resistance. Sequencing of the genome of the 5 mutants revealed no single nucleotide polymorphisms related to the resistance phenotype. However, the ERG1 gene was found amplified as part of a linear amplicon, and transfection of ERG1 fully recapitulated the terbinafine resistance phenotype of the mutants. The second screen, Cos-seq, consisted in selecting a gene overexpression library with terbinafine followed by the sequencing of the enriched cosmids. This screen identified two cosmids derived from loci on chromosomes 13 and 29 encoding the squalene monooxygenase (ERG1) and the C8 sterol isomerase (ERG2), respectively. Transfection of the ERG1-cosmid, but not the ERG2-cosmid, produced resistance to terbinafine. Our screens suggest that ERG1 is the main, if not only, target for terbinafine in Leishmania and amplification of its gene is the main resistance mechanism.
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Affiliation(s)
- Jade-Éva Potvin
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Quebec City, Québec, Canada
| | - Fereshteh Fani
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Quebec City, Québec, Canada
| | - Marine Queffeulou
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Quebec City, Québec, Canada
| | - Élodie Gazanion
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Quebec City, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Quebec City, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Quebec City, Québec, Canada.
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7
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Ferreira BA, Santos GDA, Coser EM, Sousa JM, Gama MEA, Júnior LLB, Pessoa FS, Lima MIS, Uliana SRB, Coelho AC. In Vitro Drug Susceptibility of a Leishmania (Leishmania) infantum Isolate from a Visceral Leishmaniasis Pediatric Patient after Multiple Relapses. Trop Med Infect Dis 2023; 8:354. [PMID: 37505650 PMCID: PMC10383904 DOI: 10.3390/tropicalmed8070354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/29/2023] Open
Abstract
The parasitic protozoan Leishmania (Leishmania) infantum is the etiological agent of human visceral leishmaniasis in South America, an infectious disease associated with malnutrition, anemia, and hepatosplenomegaly. In Brazil alone, around 2700 cases are reported each year. Treatment failure can occur as a result of drug, host, and/or parasite-related factors. Here, we isolated a Leishmania species from a pediatric patient with visceral leishmaniasis that did not respond to chemotherapy, experiencing a total of nine therapeutic relapses and undergoing a splenectomy. The parasite was confirmed as L. (L.) infantum after sequencing of the ribosomal DNA internal transcribed spacer, and the clinical isolate, in both promastigote and amastigote forms, was submitted to in vitro susceptibility assays with all the drugs currently used in the chemotherapy of leishmaniasis. The isolate was susceptible to meglumine antimoniate, amphotericin B, pentamidine, miltefosine, and paromomycin, similarly to another strain of this species that had previously been characterized. These findings indicate that the multiples relapses observed in this pediatric patient were not due to a decrease in the drug susceptibility of this isolate; therefore, immunophysiological aspects of the patient should be further investigated to understand the basis of treatment failure in this case.
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Affiliation(s)
- Bianca A Ferreira
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083-862, Brazil
| | - Gustavo de A Santos
- Departamento de Biologia, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, Brazil
- Programa de Pós-Graduação em Saúde e Ambiente, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, Brazil
| | - Elizabeth M Coser
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083-862, Brazil
| | - Juliana M Sousa
- Departamento de Biologia, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, Brazil
| | - Mônica E A Gama
- Programa de Pós-Graduação em Saúde e Ambiente, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, Brazil
| | - Leônidas L B Júnior
- Departamento de Medicina, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, Brazil
- Hospital Universitário, Universidade Federal do Maranhão, São Luís 65080-805, Brazil
| | - Fabrício S Pessoa
- Departamento de Medicina, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, Brazil
- Hospital Universitário, Universidade Federal do Maranhão, São Luís 65080-805, Brazil
| | - Mayara I S Lima
- Departamento de Biologia, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, Brazil
- Programa de Pós-Graduação em Saúde e Ambiente, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão, São Luís 65080-805, Brazil
| | - Silvia R B Uliana
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | - Adriano C Coelho
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083-862, Brazil
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8
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Gutierrez Guarnizo SA, Tikhonova EB, Karamyshev AL, Muskus CE, Karamysheva ZN. Translational reprogramming as a driver of antimony-drug resistance in Leishmania. Nat Commun 2023; 14:2605. [PMID: 37147291 PMCID: PMC10163012 DOI: 10.1038/s41467-023-38221-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
Leishmania is a unicellular protozoan that has a limited transcriptional control and mostly uses post-transcriptional regulation of gene expression, although the molecular mechanisms of the process are still poorly understood. Treatments of leishmaniasis, pathologies associated with Leishmania infections, are limited due to drug resistance. Here, we report dramatic differences in mRNA translation in antimony drug-resistant and sensitive strains at the full translatome level. The major differences (2431 differentially translated transcripts) were demonstrated in the absence of the drug pressure supporting that complex preemptive adaptations are needed to efficiently compensate for the loss of biological fitness once they are exposed to the antimony. In contrast, drug-resistant parasites exposed to antimony activated a highly selective translation of only 156 transcripts. This selective mRNA translation is associated with surface protein rearrangement, optimized energy metabolism, amastins upregulation, and improved antioxidant response. We propose a novel model that establishes translational control as a major driver of antimony-resistant phenotypes in Leishmania.
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Affiliation(s)
- Sneider Alexander Gutierrez Guarnizo
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
- Programa de Estudio y Control de Enfermedades Tropicales, Universidad de Antioquia. Medellín, Medellín, 050010, Colombia
| | - Elena B Tikhonova
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.
| | - Carlos E Muskus
- Programa de Estudio y Control de Enfermedades Tropicales, Universidad de Antioquia. Medellín, Medellín, 050010, Colombia.
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9
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Branched chain amino acids catabolism as a source of new drug targets in pathogenic protists. Exp Parasitol 2023; 249:108499. [PMID: 36898495 DOI: 10.1016/j.exppara.2023.108499] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 03/11/2023]
Abstract
Leucine, isoleucine, and valine, collectively termed Branched Chain Amino Acids (BCAA), are hydrophobic amino acids (AAs) and are essential for most eukaryotes since in these organisms they cannot be biosynthesized and must be supplied by the diet. These AAs are structurally relevant for muscle cells and, of course, important for the protein synthesis process. The metabolism of BCAA and its participation in different biological processes in mammals have been relatively well described. However, for other organisms as pathogenic parasites, the literature is really scarce. Here we review the BCAA catabolism, compile evidence on their relevance for pathogenic eukaryotes with special emphasis on kinetoplastids and highlight unique aspects of this underrated pathway.
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10
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Mano C, Kongkaew A, Tippawangkosol P, Somboon P, Roytrakul S, Pescher P, Späth GF, Uthaipibull C, Tantiworawit A, Siriyasatien P, Jariyapan N. Amphotericin B resistance correlates with increased fitness in vitro and in vivo in Leishmania ( Mundinia) martiniquensis. Front Microbiol 2023; 14:1156061. [PMID: 37089544 PMCID: PMC10116047 DOI: 10.3389/fmicb.2023.1156061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/15/2023] [Indexed: 04/25/2023] Open
Abstract
Amphotericin B (AmpB) deoxycholate is the available first-line drug used to treat visceral leishmaniasis caused by Leishmania (Mundinia) martiniquensis, however, some cases of AmpB treatment failure have been reported in Thailand. Resistance to drugs is known to affect parasite fitness with a potential impact on parasite transmission but still little is known about the effect of resistance to drugs on L. martiniquensis. Here we aimed to gain insight into the fitness changes occurring after treatment failure or in vitro-induced resistance to AmpB. L. martiniquensis parasites isolated from a patient before (LSCM1) and after relapse (LSCM1-6) were compared for in vitro and in vivo fitness changes together with an in vitro induced AmpB-resistant parasite generated from LSCM1 parasites (AmpBRP2i). Results revealed increased metacyclogenesis of the AmpBPR2i and LSCM1-6 strains (AmpB-resistant strains) compared to the LSCM1 strain and increased fitness with respect to growth and infectivity. The LSCM1-6 and AmpBRP2i strains were present in mice for longer periods compared to the LSCM1 strain, but no clinical signs of the disease were observed. These results suggest that the AmpB-resistant parasites could be more efficiently transmitted to humans and maintained in asymptomatic hosts longer than the susceptible strain. The asymptomatic hosts therefore may represent "reservoirs" for the resistant parasites enhancing transmission. The results in this study advocate an urgent need to search and monitor for AmpB-resistant L. martiniquensis in patients with relapsing leishmaniasis and in asymptomatic patients, especially, in HIV/Leishmania coinfected patients.
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Affiliation(s)
- Chonlada Mano
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Aphisek Kongkaew
- Animal House Unit, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pongsri Tippawangkosol
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pradya Somboon
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Pascale Pescher
- Institut Pasteur, INSERM U1201, Université Paris Cité, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Gerald F. Späth
- Institut Pasteur, INSERM U1201, Université Paris Cité, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | | | - Adisak Tantiworawit
- Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Padet Siriyasatien
- Center of Excellence in Vector Biology and Vector-Borne Disease, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Narissara Jariyapan
- Center of Excellence in Vector Biology and Vector-Borne Disease, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- *Correspondence: Narissara Jariyapan,
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11
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Martí-Carreras J, Carrasco M, Gómez-Ponce M, Noguera-Julián M, Fisa R, Riera C, Alcover MM, Roura X, Ferrer L, Francino O. Identification of Leishmania infantum Epidemiology, Drug Resistance and Pathogenicity Biomarkers with Nanopore Sequencing. Microorganisms 2022; 10:2256. [PMID: 36422326 PMCID: PMC9697816 DOI: 10.3390/microorganisms10112256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 12/31/2023] Open
Abstract
The emergence of drug-resistant strains of the parasite Leishmania infantum infecting dogs and humans represents an increasing threat. L. infantum genomes are complex and unstable with extensive structural variations, ranging from aneuploidies to multiple copy number variations (CNVs). These CNVs have recently been validated as biomarkers of Leishmania concerning virulence, tissue tropism, and drug resistance. As a proof-of-concept to develop a novel diagnosis platform (LeishGenApp), four L. infantum samples from humans and dogs were nanopore sequenced. Samples were epidemiologically typed within the Mediterranean L. infantum group, identifying members of the JCP5 and non-JCP5 subgroups, using the conserved region (CR) of the maxicircle kinetoplast. Aneuploidies were frequent and heterogenous between samples, yet only chromosome 31 tetrasomy was common between all the samples. A high frequency of aneuploidies was observed for samples with long passage history (MHOM/TN/80/IPT-1), whereas fewer were detected for samples maintained in vivo (MCRI/ES/2006/CATB033). Twenty-two genes were studied to generate a genetic pharmacoresistance profile against miltefosine, allopurinol, trivalent antimonials, amphotericin, and paromomycin. MHOM/TN/80/IPT-1 and MCRI/ES/2006/CATB033 displayed a genetic profile with potential resistance against miltefosine and allopurinol. Meanwhile, MHOM/ES/2016/CATB101 and LCAN/ES/2020/CATB102 were identified as potentially resistant against paromomycin. All four samples displayed a genetic profile for resistance against trivalent antimonials. Overall, this proof-of-concept revealed the potential of nanopore sequencing and LeishGenApp for the determination of epidemiological, drug resistance, and pathogenicity biomarkers in L. infantum.
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Affiliation(s)
- Joan Martí-Carreras
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Marina Carrasco
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Marcel Gómez-Ponce
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Marc Noguera-Julián
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Roser Fisa
- Laboratori de Parasitologia, Departament de Biologia Sanitat i Mediambient, Facultat de Farmàcia I Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
| | - Cristina Riera
- Laboratori de Parasitologia, Departament de Biologia Sanitat i Mediambient, Facultat de Farmàcia I Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
| | - Maria Magdalena Alcover
- Laboratori de Parasitologia, Departament de Biologia Sanitat i Mediambient, Facultat de Farmàcia I Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
| | - Xavier Roura
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
- Hospital Clínic Veterinari, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Lluís Ferrer
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
- Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Olga Francino
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
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12
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Alpizar-Sosa EA, Ithnin NRB, Wei W, Pountain AW, Weidt SK, Donachie AM, Ritchie R, Dickie EA, Burchmore RJS, Denny PW, Barrett MP. Amphotericin B resistance in Leishmania mexicana: Alterations to sterol metabolism and oxidative stress response. PLoS Negl Trop Dis 2022; 16:e0010779. [PMID: 36170238 PMCID: PMC9581426 DOI: 10.1371/journal.pntd.0010779] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/19/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Amphotericin B is increasingly used in treatment of leishmaniasis. Here, fourteen independent lines of Leishmania mexicana and one L. infantum line were selected for resistance to either amphotericin B or the related polyene antimicrobial, nystatin. Sterol profiling revealed that, in each resistant line, the predominant wild-type sterol, ergosta-5,7,24-trienol, was replaced by other sterol intermediates. Broadly, two different profiles emerged among the resistant lines. Whole genome sequencing then showed that these distinct profiles were due either to mutations in the sterol methyl transferase (C24SMT) gene locus or the sterol C5 desaturase (C5DS) gene. In three lines an additional deletion of the miltefosine transporter gene was found. Differences in sensitivity to amphotericin B were apparent, depending on whether cells were grown in HOMEM, supplemented with foetal bovine serum, or a serum free defined medium (DM). Metabolomic analysis after exposure to AmB showed that a large increase in glucose flux via the pentose phosphate pathway preceded cell death in cells sustained in HOMEM but not DM, indicating the oxidative stress was more significantly induced under HOMEM conditions. Several of the lines were tested for their ability to infect macrophages and replicate as amastigote forms, alongside their ability to establish infections in mice. While several AmB resistant lines showed reduced virulence, at least two lines displayed heightened virulence in mice whilst retaining their resistance phenotype, emphasising the risks of resistance emerging to this critical drug.
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Affiliation(s)
- Edubiel A. Alpizar-Sosa
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Nur Raihana Binti Ithnin
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Department of Medical Microbiology, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Wenbin Wei
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Andrew W. Pountain
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Institute for Computational Medicine, New York University Grossman School of Medicine, New York City, New York, United States of America
| | - Stefan K. Weidt
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Anne M. Donachie
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ryan Ritchie
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Emily A. Dickie
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Richard J. S. Burchmore
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Paul W. Denny
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Michael P. Barrett
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
- * E-mail:
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13
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Ghosh S, Kumar V, Verma A, Sharma T, Pradhan D, Selvapandiyan A, Salotra P, Singh R. Genome-wide analysis reveals allelic variation and chromosome copy number variation in paromomycin-resistant Leishmania donovani. Parasitol Res 2022; 121:3121-3132. [PMID: 36056959 DOI: 10.1007/s00436-022-07645-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022]
Abstract
In the absence of adequate diagnosis and treatment, leishmaniasis remains a major public health concern on a global scale. Drug resistance remains a key obstacle in controlling and eliminating visceral leishmaniasis. The therapeutic gap due to lack of target-specific medicine and vaccine can be minimized by obtaining parasite's genomic information. This study compared whole-genome sequence of paromomycin-resistant parasite (K133PMM) developed through in vitro adaptation and selection with sensitive Leishmania clinical isolate (K133WT). We found a large number of upstream and intergenic gene variations in K133PMM. There were 259 single nucleotide polymorphisms (SNPs), 187 insertion-deletion (InDels), and 546 copy number variations (CNVs) identified. Most of the genomic variations were found in the gene's upstream and non-coding regions. Ploidy estimation revealed chromosome 5 in tetrasomy and 6, 9, and 12 in trisomy, uniquely in K133PMM. These contain the genes for protein degradation, parasite motility, autophagy, cell cycle maintenance, and drug efflux membrane transporters. Furthermore, we also observed reduction in ploidy of chromosomes 15, 20, and 23, in the resistant parasite containing mostly the genes for hypothetical proteins and membrane transporters. We chronicled correlated genomic conversion and aneuploidy in parasites and hypothesize that this led to rapid evolutionary changes in response to drug induced pressure, which causes them to become resistant.
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Affiliation(s)
- Sushmita Ghosh
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.,Department of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Vinay Kumar
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Aditya Verma
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Tanya Sharma
- ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, New Delhi, 110029, India
| | - Dibyabhaba Pradhan
- ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, New Delhi, 110029, India
| | | | - Poonam Salotra
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Ruchi Singh
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.
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14
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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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15
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Boozhmehrani MJ, Eslami G, Khamesipour A, Jafari AA, Vakili M, Hosseini SS, Askari V. The role of ATP-binding cassette transporter genes expression in treatment failure cutaneous leishmaniasis. AMB Express 2022; 12:78. [PMID: 35710996 PMCID: PMC9203622 DOI: 10.1186/s13568-022-01419-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022] Open
Abstract
Leishmaniasis is one of the common diseases transmitted by sand flies in tropical and subtropical regions of the world. Currently, antimonial derivatives are the first line of treatment. Some of the members of the ATP-binding cassette (ABC) family of Leishmania are shown to be associated with no response to treatment. In this study, we evaluated ABCI4, ABCG2, ABCC7, ABCB4, and ABCC3 genes expression in Leishmania isolated from patients with non-healing cutaneous leishmaniasis and treatment response isolates. We selected 17 clinical isolates including 8 treatment failure and 9 treatment response samples from September 2020 to March 2021. The isolates were obtained from patients of Health Center Laboratory of Varzaneh, Isfahan, Iran with cutaneous leishmaniasis. The diagnosis was performed using microscopic observation. The samples were directly collected from the lesions. The expression profiling of genes was assessed using SYBR Green real-time PCR that was analyzed with delta-delta Ct. All treatment failure clinical isolates were L. major. Gene expression analysis in treatment failure isolates showed that the ABC transported genes had a different pattern in each isolate. Treatment failure has been reported for cutaneous leishmaniasis worldwide. Knowledge of the molecular mechanisms of treatment failure could solve this problem. ABC transporter genes are considered controversial over the mechanisms of treatment failure outcomes. In this study, we showed that ABC transporter genes could be considered one of the important mechanisms.
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Affiliation(s)
- Mohammad Javad Boozhmehrani
- Department of Parasitology and Mycology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Gilda Eslami
- Department of Parasitology and Mycology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Ali Khamesipour
- Center for Research and Training in Skin Diseases and Leprosy, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Ali Jafari
- Department of Parasitology and Mycology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mahmood Vakili
- Health Monitoring Research Center, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Saeedeh Sadat Hosseini
- Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Vahideh Askari
- Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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16
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The Astonishing Large Family of HSP40/DnaJ Proteins Existing in Leishmania. Genes (Basel) 2022; 13:genes13050742. [PMID: 35627127 PMCID: PMC9141911 DOI: 10.3390/genes13050742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 02/04/2023] Open
Abstract
Abrupt environmental changes are faced by Leishmania parasites during transmission from a poikilothermic insect vector to a warm-blooded host. Adaptation to harsh environmental conditions, such as nutrient deprivation, hypoxia, oxidative stress and heat shock needs to be accomplished by rapid reconfiguration of gene expression and remodeling of protein interaction networks. Chaperones play a central role in the maintenance of cellular homeostasis, and they are responsible for crucial tasks such as correct folding of nascent proteins, protein translocation across different subcellular compartments, avoiding protein aggregates and elimination of damaged proteins. Nearly one percent of the gene content in the Leishmania genome corresponds to members of the HSP40 family, a group of proteins that assist HSP70s in a variety of cellular functions. Despite their expected relevance in the parasite biology and infectivity, little is known about their functions or partnership with the different Leishmania HSP70s. Here, we summarize the structural features of the 72 HSP40 proteins encoded in the Leishmania infantum genome and their classification into four categories. A review of proteomic data, together with orthology analyses, allow us to postulate cellular locations and possible functional roles for some of them. A detailed study of the members of this family would provide valuable information and opportunities for drug discovery and improvement of current treatments against leishmaniasis.
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17
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Perea-Martínez A, García-Hernández R, Manzano JI, Gamarro F. Transcriptomic Analysis in Human Macrophages Infected with Therapeutic Failure Clinical Isolates of Leishmania infantum. ACS Infect Dis 2022; 8:800-810. [PMID: 35352952 PMCID: PMC9003231 DOI: 10.1021/acsinfecdis.1c00513] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Leishmaniasis is one of the neglected tropical diseases with a worldwide distribution, affecting humans and animals. In the absence of an effective vaccine, current treatment is through the use of chemotherapy; however, existing treatments have frequent appearance of drug resistance and therapeutic failure (TF). The identification of factors that contribute to TF in leishmaniasis will provide the basis for a future therapeutic strategy more efficient for the control of this disease. In this article, we have evaluated the transcriptomic changes in the host cells THP-1 after infection with clinical Leishmania infantum isolates from leishmaniasis patients with TF. Our results show that distinct L. infantum isolates differentially modulate host cell response, inducing phenotypic changes that probably may account for parasite survival and TF of patients. Analysis of differential expression genes (DEGs), with a statistical significance threshold of a fold change ≥ 2 and a false discovery rate value ≤ 0.05, revealed a different number of DEGs according to the Leishmanialine. Globally, there was a similar number of genes up- and downregulated in all the infected host THP-1 cells, with exception of Hi-L2221, which showed a higher number of downregulated DEGs. We observed a total of 58 DEGs commonly modulated in all infected host cells, including upregulated (log2FC ≥ 1) and downregulated (log2FC ≤ -1) genes. Based on the results obtained from the analysis of RNA-seq, volcano plot, and GO enrichment analysis, we identified the most significant transcripts of relevance for their possible contribution to the TF observed in patients with leishmaniasis.
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Affiliation(s)
- Ana Perea-Martínez
- Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Raquel García-Hernández
- Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - José Ignacio Manzano
- Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Francisco Gamarro
- Instituto de Parasitología y Biomedicina “López-Neyra”, IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda del Conocimiento 17, 18016 Armilla, Granada, Spain
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18
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In-Depth Quantitative Proteomics Characterization of In Vitro Selected Miltefosine Resistance in Leishmania infantum. Proteomes 2022; 10:proteomes10020010. [PMID: 35466238 PMCID: PMC9036279 DOI: 10.3390/proteomes10020010] [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: 02/28/2022] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
Visceral leishmaniasis (VL) is a neglected disease caused by Leishmania parasites. Although significant morbidity and mortality in tropical and subtropical regions of the world are associated with VL, the low investment for developing new treatment measures is chronic. Moreover, resistance and treatment failure are increasing for the main medications, but the emergence of resistance phenotypes is poorly understood at the protein level. Here, we analyzed the development of resistance to miltefosine upon experimental selection in a L. infantum strain. Time to miltefosine resistance emergence was ~six months and label-free quantitative mass-spectrometry-based proteomics analyses revealed that this process involves a remodeling of components of the membrane and mitochondrion, with significant increase in oxidative phosphorylation complexes, particularly on complex IV and ATP synthase, accompanied by increased energy metabolism mainly dependent on β-oxidation of fatty acids. Proteins canonically involved in ROS detoxification did not contribute to the resistant process whereas sterol biosynthesis enzymes could have a role in this development. Furthermore, changes in the abundance of proteins known to be involved in miltefosine resistance such as ABC transporters and phospholipid transport ATPase were detected. Together, our data show a more complete picture of the elements that make up the miltefosine resistance phenotype in L. infantum.
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Simvastatin Resistance of Leishmania amazonensis Induces Sterol Remodeling and Cross-Resistance to Sterol Pathway and Serine Protease Inhibitors. Microorganisms 2022; 10:microorganisms10020398. [PMID: 35208853 PMCID: PMC8877030 DOI: 10.3390/microorganisms10020398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 01/27/2023] Open
Abstract
The sterol biosynthesis pathway of Leishmania spp. is used as a pharmacological target; however, available information about the mechanisms of the regulation and remodeling of sterol-related genes is scarce. The present study investigated compensatory mechanisms of the sterol biosynthesis pathway using an inhibitor of HMG-CoA reductase (simvastatin) and by developing drug-resistant parasites to evaluate the impact on sterol remodeling, cross-resistance, and gene expression. Simvastatin-resistant L. amazonensis parasites (LaSimR) underwent reprogramming of sterol metabolism manifested as an increase in cholestane- and stigmastane-based sterols and a decrease in ergostane-based sterols. The levels of the transcripts of sterol 24-C-methyltransferase (SMT), sterol C14-α-demethylase (C14DM), and protease subtilisin (SUB) were increased in LaSimR. LaSimR was cross-resistance to ketoconazole (a C14DM inhibitor) and remained sensitive to terbinafine (an inhibitor of squalene monooxygenase). Sensitivity of the LaSimR mutant to other antileishmanial drugs unrelated to the sterol biosynthesis pathway, such as trivalent antimony and pentamidine, was similar to that of the wild-type strain; however, LaSimR was cross-resistant to miltefosine, general serine protease inhibitor N-p-tosyl-l-phenylalanine chloromethyl ketone (TPCK), subtilisin-specific inhibitor 4-[(diethylamino)methyl]-N-[2-(2-methoxyphenyl)ethyl]-N-(3R)-3-pyrrolidinyl-benzamide dihydrochloride (PF-429242), and tunicamycin. The findings on the regulation of the sterol pathway can support the development of drugs and protease inhibitors targeting this route in parasites.
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da Silva RB, Bertoldo WDR, Naves LL, de Vito FB, Damasceno JD, Tosi LRO, Machado CR, Pedrosa AL. Specific Human ATR and ATM Inhibitors Modulate Single Strand DNA Formation in Leishmania major Exposed to Oxidative Agent. Front Cell Infect Microbiol 2022; 11:802613. [PMID: 35059327 PMCID: PMC8763966 DOI: 10.3389/fcimb.2021.802613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/02/2021] [Indexed: 12/03/2022] Open
Abstract
Leishmania parasites are the causative agents of a group of neglected tropical diseases known as leishmaniasis. The molecular mechanisms employed by these parasites to adapt to the adverse conditions found in their hosts are not yet completely understood. DNA repair pathways can be used by Leishmania to enable survival in the interior of macrophages, where the parasite is constantly exposed to oxygen reactive species. In higher eukaryotes, DNA repair pathways are coordinated by the central protein kinases ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3 related (ATR). The enzyme Exonuclease-1 (EXO1) plays important roles in DNA replication, repair, and recombination, and it can be regulated by ATM- and ATR-mediated signaling pathways. In this study, the DNA damage response pathways in promastigote forms of L. major were investigated using bioinformatics tools, exposure of lineages to oxidizing agents and radiation damage, treatment of cells with ATM and ATR inhibitors, and flow cytometry analysis. We demonstrated high structural and important residue conservation for the catalytic activity of the putative LmjEXO1. The overexpression of putative LmjEXO1 made L. major cells more susceptible to genotoxic damage, most likely due to the nuclease activity of this enzyme and the occurrence of hyper-resection of DNA strands. These cells could be rescued by the addition of caffeine or a selective ATM inhibitor. In contrast, ATR-specific inhibition made the control cells more susceptible to oxidative damage in an LmjEXO1 overexpression-like manner. We demonstrated that ATR-specific inhibition results in the formation of extended single-stranded DNA, most likely due to EXO1 nucleasic activity. Antagonistically, ATM inhibition prevented single-strand DNA formation, which could explain the survival phenotype of lineages overexpressing LmjEXO1. These results suggest that an ATM homolog in Leishmania could act to promote end resection by putative LmjEXO1, and an ATR homologue could prevent hyper-resection, ensuring adequate repair of the parasite DNA.
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Affiliation(s)
- Raíssa Bernardes da Silva
- Departamento de Bioquímica, Farmacologia e Fisiologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Willian Dos Reis Bertoldo
- Departamento de Bioquímica, Farmacologia e Fisiologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil.,Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lucila Langoni Naves
- Departamento de Bioquímica, Farmacologia e Fisiologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Fernanda Bernadelli de Vito
- Departamento de Clínica Médica, Instituto de Ciências da Saúde, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Jeziel Dener Damasceno
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Luiz Ricardo Orsini Tosi
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Carlos Renato Machado
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - André Luiz Pedrosa
- Departamento de Bioquímica, Farmacologia e Fisiologia, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
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Nitric Oxide Resistance in Leishmania (Viannia) braziliensis Involves Regulation of Glucose Consumption, Glutathione Metabolism and Abundance of Pentose Phosphate Pathway Enzymes. Antioxidants (Basel) 2022; 11:antiox11020277. [PMID: 35204161 PMCID: PMC8868067 DOI: 10.3390/antiox11020277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 11/16/2022] Open
Abstract
In American Tegumentary Leishmaniasis production of cytokines, reactive oxygen species and nitric oxide (NO) by host macrophages normally lead to parasite death. However, some Leishmania braziliensis strains exhibit natural NO resistance. NO-resistant strains cause more lesions and are frequently more resistant to antimonial treatment than NO-susceptible ones, suggesting that NO-resistant parasites are endowed with specific mechanisms of survival and persistence. To tests this, we analyzed the effect of pro- and antioxidant molecules on the infectivity in vitro of L. braziliensis strains exhibiting polar phenotypes of resistance or susceptibility to NO. In addition, we conducted a comprehensive quantitative mass spectrometry-based proteomics analysis of those parasites. NO-resistant parasites were more infective to peritoneal macrophages, even in the presence of high levels of reactive species. Principal component analysis of protein concentration values clearly differentiated NO-resistant from NO-susceptible parasites, suggesting that there are natural intrinsic differences at molecular level among those strains. Upon NO exposure, NO-resistant parasites rapidly modulated their proteome, increasing their total protein content and glutathione (GSH) metabolism. Furthermore, NO-resistant parasites showed increased glucose analogue uptake, and increased abundance of phosphotransferase and G6PDH after nitrosative challenge, which can contribute to NADPH pool maintenance and fuel the reducing conditions for the recovery of GSH upon NO exposure. Thus, increased glucose consumption and GSH-mediated redox capability may explain the natural resistance of L. braziliensis against NO.
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Santi AMM, Murta SMF. Impact of Genetic Diversity and Genome Plasticity of Leishmania spp. in Treatment and the Search for Novel Chemotherapeutic Targets. Front Cell Infect Microbiol 2022; 12:826287. [PMID: 35141175 PMCID: PMC8819175 DOI: 10.3389/fcimb.2022.826287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/04/2022] [Indexed: 11/21/2022] Open
Abstract
Leishmaniasis is one of the major public health concerns in Latin America, Africa, Asia, and Europe. The absence of vaccines for human use and the lack of effective vector control programs make chemotherapy the main strategy to control all forms of the disease. However, the high toxicity of available drugs, limited choice of therapeutic agents, and occurrence of drug-resistant parasite strains are the main challenges related to chemotherapy. Currently, only a small number of drugs are available for leishmaniasis treatment, including pentavalent antimonials (SbV), amphotericin B and its formulations, miltefosine, paromomycin sulphate, and pentamidine isethionate. In addition to drug toxicity, therapeutic failure of leishmaniasis is a serious concern. The occurrence of drug-resistant parasites is one of the causes of therapeutic failure and is closely related to the diversity of parasites in this genus. Owing to the enormous plasticity of the genome, resistance can occur by altering different metabolic pathways, demonstrating that resistance mechanisms are multifactorial and extremely complex. Genetic variability and genome plasticity cause not only the available drugs to have limitations, but also make the search for new drugs challenging. Here, we examined the biological characteristics of parasites that hinder drug discovery.
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Salloum T, Tokajian S, Hirt RP. Advances in Understanding Leishmania Pathobiology: What Does RNA-Seq Tell Us? Front Cell Dev Biol 2021; 9:702240. [PMID: 34540827 PMCID: PMC8440825 DOI: 10.3389/fcell.2021.702240] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/30/2021] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is a vector-borne disease caused by a protozoa parasite from over 20 Leishmania species. The clinical manifestations and the outcome of the disease vary greatly. Global RNA sequencing (RNA-Seq) analyses emerged as a powerful technique to profile the changes in the transcriptome that occur in the Leishmania parasites and their infected host cells as the parasites progresses through their life cycle. Following the bite of a sandfly vector, Leishmania are transmitted to a mammalian host where neutrophils and macrophages are key cells mediating the interactions with the parasites and result in either the elimination the infection or contributing to its proliferation. This review focuses on RNA-Seq based transcriptomics analyses and summarizes the main findings derived from this technology. In doing so, we will highlight caveats in our understanding of the parasite's pathobiology and suggest novel directions for research, including integrating more recent data highlighting the role of the bacterial members of the sandfly gut microbiota and the mammalian host skin microbiota in their potential role in influencing the quantitative and qualitative aspects of leishmaniasis pathology.
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Affiliation(s)
- Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Robert P. Hirt
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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Medina J, Cruz-Saavedra L, Patiño LH, Muñoz M, Ramírez JD. Comparative analysis of the transcriptional responses of five Leishmania species to trivalent antimony. Parasit Vectors 2021; 14:419. [PMID: 34419127 PMCID: PMC8380399 DOI: 10.1186/s13071-021-04915-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leishmaniasis is a neglected tropical disease caused by several species of Leishmania. The resistance phenotype of these parasites depends on the characteristics of each species, which contributes to increased therapeutic failures. Understanding the mechanism used by the parasite to survive under treatment pressure in order to identify potential common and specific therapeutic targets is essential for the control of leishmaniasis. The aim of this study was to investigate the expression profiles and potential shared and specific resistance markers of the main Leishmania species of medical importance [subgenus L. (Leishmania): L. donovani, L. infantum and L. amazonensis; subgenus L. (Viannia): L. panamensis and L. braziliensis)] resistant and sensitive to trivalent stibogluconate (SbIII). METHODS We conducted comparative analysis of the transcriptomic profiles (only coding sequences) of lines with experimentally induced resistance to SbIII from biological replicates of five Leishmania species available in the databases of four articles based on ortholog attribution. Simultaneously, we carried out functional analysis of ontology and reconstruction of metabolic pathways of the resulting differentially expressed genes (DEGs). RESULTS Resistant lines for each species had differential responses in metabolic processes, compound binding, and membrane components concerning their sensitive counterpart. One hundred and thirty-nine metabolic pathways were found, with the three main pathways comprising cysteine and methionine metabolism, glycolysis, and the ribosome. Differentially expressed orthologous genes assigned to species-specific responses predominated, with 899 self-genes. No differentially expressed genes were found in common among the five species. Two common upregulated orthologous genes were found among four species (L. donovani, L. braziliensis, L. amazonensis, and L. panamensis) related to an RNA-binding protein and the NAD(P)H cytochrome-B5-oxidoreductase complex, associated with transcriptional control and de novo synthesis of linoleic acid, critical mechanisms in resistance to antimonials. CONCLUSION Herein, we identified potential species-specific genes related to resistance to SbIII. Therefore, we suggest that future studies consider a treatment scheme that is species-specific. Despite the limitations of our study, this is the first approach toward unraveling the pan-genus genetic mechanisms of resistance in leishmaniasis.
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Affiliation(s)
- Julián Medina
- Centro de Investigaciones en Microbiología y Biotecnología- UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología- UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología- UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología- UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología- UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
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Morelle C, Mukherjee A, Zhang J, Fani F, Khandelwal A, Gingras H, Trottier J, Barbier O, Leprohon P, Burke MD, Ouellette M. Well-Tolerated Amphotericin B Derivatives That Effectively Treat Visceral Leishmaniasis. ACS Infect Dis 2021; 7:2472-2482. [PMID: 34282886 DOI: 10.1021/acsinfecdis.1c00245] [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: 11/28/2022]
Abstract
Chemotherapy against the neglected tropical disease visceral leishmaniasis (VL) is suboptimal with only four licensed drugs. Amphotericin B (AmB), despite its toxicity, remained a second line drug for a long time. However, the demonstration that liposomal AmB is highly effective against VL propelled it, despite its cost, to a first line drug in many countries. While several ongoing efforts are aiming at finding cheaper and stable AmB-formulations, an alternative strategy is the development of less-toxic AmB derivatives. We show here that two less-toxic AmB derivatives with the carboxylate at position 16 of AmB derivatized to a methyl urea (AmB-MU) or amino urea (AmB-AU) are active in vitro against Leishmania donovani, both as free-living parasites as well as their intracellular form. Both less-toxic derivatives, similarly to AmB, target the ergosterol pathway of L. donovani. While the AmB-AU derivative showed female-specific liver toxicity in vivo, the AmB-MU derivative was well-tolerated and more effective than AmB against experimental VL. These studies are an important step for improving AmB-based therapy against a prevalent parasitic disease.
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Affiliation(s)
- Christelle Morelle
- Axe des Maladies Infectieuses et Immunitaires du Centre de Recherche du CHU de Québec, Centre de Recherche en Infectiologie, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec G1V 4G2,Canada
| | - Angana Mukherjee
- Axe des Maladies Infectieuses et Immunitaires du Centre de Recherche du CHU de Québec, Centre de Recherche en Infectiologie, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec G1V 4G2,Canada
| | - Jiabao Zhang
- Department of Chemistry, Department of Biochemistry, Arnold and Mabel Beckman Institute, Carle Illinois College of Medicine, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Fereshteh Fani
- Axe des Maladies Infectieuses et Immunitaires du Centre de Recherche du CHU de Québec, Centre de Recherche en Infectiologie, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec G1V 4G2,Canada
| | - Anuj Khandelwal
- Department of Chemistry, Department of Biochemistry, Arnold and Mabel Beckman Institute, Carle Illinois College of Medicine, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Hélène Gingras
- Axe des Maladies Infectieuses et Immunitaires du Centre de Recherche du CHU de Québec, Centre de Recherche en Infectiologie, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec G1V 4G2,Canada
| | - Jocelyn Trottier
- Laboratory of Molecular Pharmacology, Endocrinology-Nephrology Axis, Centre de Recherche du CHU de Québec, Faculty of Pharmacy, Université Laval, Québec City, Québec G1V 4G2,Canada
| | - Olivier Barbier
- Laboratory of Molecular Pharmacology, Endocrinology-Nephrology Axis, Centre de Recherche du CHU de Québec, Faculty of Pharmacy, Université Laval, Québec City, Québec G1V 4G2,Canada
| | - Philippe Leprohon
- Axe des Maladies Infectieuses et Immunitaires du Centre de Recherche du CHU de Québec, Centre de Recherche en Infectiologie, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec G1V 4G2,Canada
| | - Martin D. Burke
- Department of Chemistry, Department of Biochemistry, Arnold and Mabel Beckman Institute, Carle Illinois College of Medicine, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Marc Ouellette
- Axe des Maladies Infectieuses et Immunitaires du Centre de Recherche du CHU de Québec, Centre de Recherche en Infectiologie, and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec G1V 4G2,Canada
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Hendrickx S, Reis-Cunha JL, Forrester S, Jeffares DC, Caljon G. Experimental Selection of Paromomycin Resistance in Leishmania donovani Amastigotes Induces Variable Genomic Polymorphisms. Microorganisms 2021; 9:microorganisms9081546. [PMID: 34442625 PMCID: PMC8398221 DOI: 10.3390/microorganisms9081546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 01/07/2023] Open
Abstract
The relatively high post-treatment relapse rates of paromomycin (PMM) in visceral leishmaniasis treatment and the swift emergence of experimental drug resistance challenge its broad application and urge for rational use and monitoring of resistance. However, no causal molecular mechanisms to Leishmania PMM resistance have been identified so far. To gain insights into potential resistance mechanisms, twelve experimentally selected Leishmania donovani clonal lines and the non-cloned preselection population, with variable degrees of PMM resistance, were subjected to whole genome sequencing. To identify genomic variations potentially associated with resistance, SNPs, Indels, chromosomal somy and gene copy number variations were compared between the different parasite lines. A total of 11 short nucleotide variations and the copy number alterations in 39 genes were correlated to PMM resistance. Some of the identified genes are involved in transcription, translation and protein turn-over (transcription elongation factor-like protein, RNA-binding protein, ribosomal protein L1a, 60S ribosomal protein L6, eukaryotic translation initiation factor 4E-1, proteasome regulatory non-ATP-ase subunit 3), virulence (major surface protease gp63, protein-tyrosine phosphatase 1-like protein), mitochondrial function (ADP/ATP mitochondrial carrier-like protein), signaling (phosphatidylinositol 3-related kinase, protein kinase putative and protein-tyrosine phosphatase 1-like protein) and vesicular trafficking (ras-related protein RAB1). These results indicate that, in Leishmania, the aminoglycoside PMM affects protein translational processes and underlines the complex and probably multifactorial origin of resistance.
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Affiliation(s)
- Sarah Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Antwerp, Belgium;
| | - João Luís Reis-Cunha
- Department of Biology and York Biomedical Research Institute, University of York, York YO31 5DD, UK; (J.L.R.-C.); (S.F.)
| | - Sarah Forrester
- Department of Biology and York Biomedical Research Institute, University of York, York YO31 5DD, UK; (J.L.R.-C.); (S.F.)
| | - Daniel C. Jeffares
- Department of Biology and York Biomedical Research Institute, University of York, York YO31 5DD, UK; (J.L.R.-C.); (S.F.)
- Correspondence: (D.C.J.); (G.C.); Tel.: +32-3-265-26-01 (G.C.)
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Antwerp, Belgium;
- Correspondence: (D.C.J.); (G.C.); Tel.: +32-3-265-26-01 (G.C.)
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Coser EM, Ferreira BA, Yamashiro-Kanashiro EH, Lindoso JAL, Coelho AC. Susceptibility to paromomycin in clinical isolates and reference strains of Leishmania species responsible for tegumentary leishmaniasis in Brazil. Acta Trop 2021; 215:105806. [PMID: 33385363 DOI: 10.1016/j.actatropica.2020.105806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Treatment of tegumentary leishmaniasis in Brazil is limited to pentavalent antimonial, amphotericin B and pentamidine. These drugs, administered parenterally, cause several side effects and have a varied clinical response, depending on the species of Leishmania. Urgent expansion of the therapeutic arsenal against the disease is therefore necessary. Paromomycin is an aminoglycoside antibiotic that has already been approved for the treatment of visceral leishmaniasis in Southeast Asia. Here, we provide an in vitro evaluation of the activity of paromomycin in fifteen clinical isolates from patients with tegumentary leishmaniasis at a reference center for the treatment of the disease. Furthermore, the in vitro susceptibility to this drug in reference strains of Leishmania species that are endemic in Brazil has also been evaluated. Among the clinical isolates, nine were typed as Leishmania (Viannia) braziliensis, five as L. (Leishmania) amazonensis and one as L. (V.) guyanensis. Although never exposed to paromomycin, we found variable susceptibility among these isolates and reference strains in promastigotes and intracellular amastigotes, with the drug being more active in the amastigote form of the parasite. This study provides a preclinical dataset that is useful for the evaluation of paromomycin in the treatment of tegumentary leishmaniasis caused by species that are endemic in Brazil.
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Affiliation(s)
- Elizabeth M Coser
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Bianca A Ferreira
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Edite H Yamashiro-Kanashiro
- Laboratório de Soroepidemiologia e Imunobiologia, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil; Laboratório de Imunologia (LIM 48), Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - José Angelo L Lindoso
- Laboratório de Protozoologia, Instituto de Medicina Tropical de São Paulo, Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil; Instituto de Infectologia Emilio Ribas, São Paulo, Brazil
| | - Adriano C Coelho
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil.
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Schwabl P, Boité MC, Bussotti G, Jacobs A, Andersson B, Moreira O, Freitas-Mesquita AL, Meyer-Fernandes JR, Telleria EL, Traub-Csekö Y, Vaselek S, Leštinová T, Volf P, Morgado FN, Porrozzi R, Llewellyn M, Späth GF, Cupolillo E. Colonization and genetic diversification processes of Leishmania infantum in the Americas. Commun Biol 2021; 4:139. [PMID: 33514858 PMCID: PMC7846609 DOI: 10.1038/s42003-021-01658-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 01/04/2021] [Indexed: 12/30/2022] Open
Abstract
Leishmania infantum causes visceral leishmaniasis, a deadly vector-borne disease introduced to the Americas during the colonial era. This non-native trypanosomatid parasite has since established widespread transmission cycles using alternative vectors, and human infection has become a significant concern to public health, especially in Brazil. A multi-kilobase deletion was recently detected in Brazilian L. infantum genomes and is suggested to reduce susceptibility to the anti-leishmanial drug miltefosine. We show that deletion-carrying strains occur in at least 15 Brazilian states and describe diversity patterns suggesting that these derive from common ancestral mutants rather than from recurrent independent mutation events. We also show that the deleted locus and associated enzymatic activity is restored by hybridization with non-deletion type strains. Genetic exchange appears common in areas of secondary contact but also among closely related parasites. We examine demographic and ecological scenarios underlying this complex L. infantum population structure and discuss implications for disease control. Philipp Schwabl, Mariana Boité, and colleagues analyze 126 Leishmania infantum genomes to determine how demographic and selective consequences of the parasite’s invasive history have contributed to intricate population genetic heterogeneity across Brazil. Their data suggest a complex interplay of population expansion, secondary contact and genetic exchange events underlying diversity patterns at short and long-distance scales. These processes also appear pivotal to the proliferation of a drug resistance-associated multi-gene deletion on chromosome 31.
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Affiliation(s)
- Philipp Schwabl
- School of Life Sciences, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Mariana C Boité
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz, FIOCRUZ, 21040-365, Rio de Janeiro, Brazil.
| | - Giovanni Bussotti
- Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP CNRS, 75015, Paris, France.,Department of Parasites and Insect Vectors, Institut Pasteur, INSERM U1201, Unité de Parasitology moléculaire et Signalisation, 75015, Paris, France
| | - Arne Jacobs
- School of Life Sciences, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Bjorn Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, Biomedicum 9C, 171 77, Stockholm, Sweden
| | - Otacilio Moreira
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fiocruz, 21040-365, Rio de Janeiro, RJ, Brazil
| | - Anita L Freitas-Mesquita
- Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil
| | - Jose Roberto Meyer-Fernandes
- Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Universidade Federal do Rio de Janeiro (UFRJ), 21941-590, Rio de Janeiro, RJ, Brazil
| | - Erich L Telleria
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz, 21040-365, Rio de Janeiro, Brazil.,Faculty of Science, Department of Parasitology, Charles University, 128 44, Prague, Czech Republic
| | - Yara Traub-Csekö
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz, 21040-365, Rio de Janeiro, Brazil
| | - Slavica Vaselek
- Faculty of Science, Department of Parasitology, Charles University, 128 44, Prague, Czech Republic
| | - Tereza Leštinová
- Faculty of Science, Department of Parasitology, Charles University, 128 44, Prague, Czech Republic
| | - Petr Volf
- Faculty of Science, Department of Parasitology, Charles University, 128 44, Prague, Czech Republic
| | - Fernanda N Morgado
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz, FIOCRUZ, 21040-365, Rio de Janeiro, Brazil
| | - Renato Porrozzi
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz, FIOCRUZ, 21040-365, Rio de Janeiro, Brazil
| | - Martin Llewellyn
- School of Life Sciences, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, G12 8QQ, Glasgow, UK
| | - Gerald F Späth
- Department of Parasites and Insect Vectors, Institut Pasteur, INSERM U1201, Unité de Parasitology moléculaire et Signalisation, 75015, Paris, France
| | - Elisa Cupolillo
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz, FIOCRUZ, 21040-365, Rio de Janeiro, Brazil
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Zheng Z, Chen J, Ma G, Satoskar AR, Li J. Integrative genomic, proteomic and phenotypic studies of Leishmania donovani strains revealed genetic features associated with virulence and antimony-resistance. Parasit Vectors 2020; 13:510. [PMID: 33046138 PMCID: PMC7552375 DOI: 10.1186/s13071-020-04397-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/07/2020] [Indexed: 12/26/2022] Open
Abstract
Background Leishmaniasis is a neglected tropical disease affecting millions of people worldwide. Emerging drug resistance of Leishmania species poses threaten to the effective control and elimination programme of this neglected tropical disease. Methods In this work, we conducted drug-resistance testing, whole genome resequencing and proteome profiling for a recently reported clinical isolate with supposed drug resistance (HCZ), and two reference sensitive strains (DD8 and 9044) of Leishmania donovani, to explore molecular mechanisms underlying drug resistance in this parasite. Results With reference to DD8 and 9044 strains, HCZ isolate showed higher-level virulence and clear resistance to antimonials in promastigote culture, infected macrophages and animal experiment. Pairwise genomic comparisons revealed genetic variations (86 copy number variations, 271 frameshift mutations in protein-coding genes and two site mutations in non-coding genes) in HCZ isolate that were absent from the reference sensitive strains. Proteomic analysis indicated different protein expression between HCZ isolate and reference strains, including 69 exclusively detected proteins and 82 consistently down-/upregulated molecules in the HCZ isolate. Integrative analysis showed linkage of 12 genomic variations (gene duplication, insertion and deletion) and their protein expression changes in HCZ isolate, which might be associated with pathogenic and antimony-resistant phenotype. Functional annotation analyses further indicated that molecules involved in nucleotide-binding, fatty acid metabolism, oxidation-reduction and transport might play a role in host-parasite interaction and drug-resistance. Conclusions This comprehensive integrative work provided novel insights into the genetic basis underlying virulence and resistance, suggesting new aspects to be investigated for a better intervention against L. donovani and associated diseases.![]()
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Affiliation(s)
- Zhiwan Zheng
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jianping Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Guangxu Ma
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China.,Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Abhay R Satoskar
- Department of Pathology, Ohio State University Medical Center, Ohio State University, Columbus, USA.,Department of Microbiology, Ohio State University, Columbus, USA
| | - Jiao Li
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.
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30
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Bussotti G, Benkahla A, Jeddi F, Souiaï O, Aoun K, Späth GF, Bouratbine A. Nuclear and mitochondrial genome sequencing of North-African Leishmania infantum isolates from cured and relapsed visceral leishmaniasis patients reveals variations correlating with geography and phenotype. Microb Genom 2020; 6:mgen000444. [PMID: 32975503 PMCID: PMC7660250 DOI: 10.1099/mgen.0.000444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/13/2020] [Indexed: 12/19/2022] Open
Abstract
Although several studies have investigated genetic diversity of Leishmania infantum in North Africa, genome-wide analyses are lacking. Here, we conducted comparative analyses of nuclear and mitochondrial genomes of seven L. infantum isolates from Tunisia with the aim to gain insight into factors that drive genomic and phenotypic adaptation. Isolates were from cured (n=4) and recurrent (n=3) visceral leishmaniasis (VL) cases, originating from northern (n=2) and central (n=5) Tunisia, where respectively stable and emerging VL foci are observed. All isolates from relapsed patients were from Kairouan governorate (Centre); one showing resistance to the anti-leishmanial drug Meglumine antimoniate. Nuclear genome diversity of the isolates was analysed by comparison to the L. infantum JPCM5 reference genome. Kinetoplast maxi and minicircle sequences (1 and 59, respectively) were extracted from unmapped reads and identified by blast analysis against public data sets. The genome variation analysis grouped together isolates from the same geographical origins. Strains from the North were very different from the reference showing more than 34 587 specific single nucleotide variants, with one isolate representing a full genetic hybrid as judged by variant frequency. Composition of minicircle classes within isolates corroborated this geographical population structure. Read depth analysis revealed several significant gene copy number variations correlating with either geographical origin (amastin and Hsp33 genes) or relapse (CLN3 gene). However, no specific gene copy number variation was found in the drug-resistant isolate. In contrast, resistance was associated with a specific minicircle pattern suggesting Leishmania mitochondrial DNA as a potential novel source for biomarker discovery.
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Affiliation(s)
- Giovanni Bussotti
- Institut Pasteur, Hub Bioinformatique et biostatistique, 28 Rue du Dr Roux, 75015 Paris, France
- Institut Pasteur, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Département des Parasites et Insectes vecteurs, 25 Rue du Dr Roux, 75015 Paris, France
| | - Alia Benkahla
- Laboratoire de recherche, LR 16IPT09, Bioinformatique, Biomathématiques et Biostatistiques, Institut Pasteur de Tunis, Université Tunis El-Manar, 13 Place Pasteur, Tunis, Tunisie
| | - Fakhri Jeddi
- Laboratoire de Parasitologie, Hôpital de la Timone, Marseille, France
- Laboratoire de Parasitologie et Mycologie Médicale, CHU de Nantes, Nantes, France
| | - Oussama Souiaï
- Laboratoire de recherche, LR 16IPT09, Bioinformatique, Biomathématiques et Biostatistiques, Institut Pasteur de Tunis, Université Tunis El-Manar, 13 Place Pasteur, Tunis, Tunisie
| | - Karim Aoun
- Laboratoire de recherche, LR 16IPT06, Parasitoses médicales, Biotechnologies et Biomolécules, Institut Pasteur de Tunis, Université Tunis El-Manar, 13 Place Pasteur, Tunis, Tunisie
| | - Gerald F. Späth
- Institut Pasteur, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Département des Parasites et Insectes vecteurs, 25 Rue du Dr Roux, 75015 Paris, France
| | - Aïda Bouratbine
- Laboratoire de recherche, LR 16IPT06, Parasitoses médicales, Biotechnologies et Biomolécules, Institut Pasteur de Tunis, Université Tunis El-Manar, 13 Place Pasteur, Tunis, Tunisie
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31
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Assessing the composition of the plasma membrane of Leishmania (Leishmania) infantum and L. (L.) amazonensis using label-free proteomics. Exp Parasitol 2020; 218:107964. [PMID: 32822697 DOI: 10.1016/j.exppara.2020.107964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 02/03/2023]
Abstract
Protozoan parasites of the genus Leishmania are causative agents of leishmaniasis, a wide range of diseases affecting 12 million people worldwide. The species L. infantum and L. amazonensis are etiologic agents of visceral and cutaneous leishmaniasis, respectively. Most proteome analyses of Leishmania have been carried out on whole-cell extracts, but such an approach tends to underrepresent membrane-associated proteins due to their high hydrophobicity and low solubility. Considering the relevance of this category of proteins in virulence, invasiveness and the host-parasite interface, this study applied label-free proteomics to assess the plasma membrane sub-proteome of L. infantum and L. amazonensis. The number of proteins identified in L. infantum and L. amazonensis promastigotes was 1168 and 1455, respectively. After rigorous data processing and mining, 157 proteins were classified as putative plasma membrane-associated proteins, of which 56 proteins were detected in both species, six proteins were detected only in L. infantum and 39 proteins were exclusive to L. amazonensis. The quantitative analysis revealed that two proteins were more abundant in L. infantum, including the glucose transporter 2, and five proteins were more abundant in L. amazonensis. The identified proteins associated with distinct processes and functions. In this regard, proteins of L. infantum were linked to metabolic processes whereas L. amazonensis proteins were involved in signal transduction. Moreover, transmembrane transport was a significant process among the group of proteins detected in both species and members of the superfamily of ABC transporters were highly represented. Interestingly, some proteins of this family were solely detected in L. amazonensis, such as ABCA9. GP63, a well-known virulence factor, was the only GPI-anchored protein identified in the membrane preparations of both species. Finally, we found several proteins with uncharacterized functions, including differentially abundant ones, highlighting a gap in the study of Leishmania proteins. Proteins characterization could provide a better biological understanding of these parasites and deliver new possibilities regarding the discovery of therapeutic targets, drug resistance and vaccine candidates.
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32
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Coser EM, Ferreira BA, Branco N, Yamashiro-Kanashiro EH, Lindoso JAL, Coelho AC. Activity of paromomycin against Leishmania amazonensis: Direct correlation between susceptibility in vitro and the treatment outcome in vivo. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2020; 14:91-98. [PMID: 33011651 PMCID: PMC7548989 DOI: 10.1016/j.ijpddr.2020.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 11/10/2022]
Abstract
Paromomycin is an aminoglycoside antibiotic approved in 2006 for the treatment of visceral leishmaniasis caused by Leishmania donovani in Southeast Asia. Although this drug is not approved for the treatment of visceral and cutaneous leishmaniasis in Brazil, it is urgent and necessary to evaluate the potential of this drug as alternative for the treatment against species responsible for these clinical forms of the disease. In Brazil, Leishmania amazonensis is responsible for cutaneous and diffuse cutaneous leishmaniasis. The diffuse cutaneous form of the disease is difficult to treat and frequent relapses are reported, mainly when the treatment is interrupted. Here, we evaluated paromomycin susceptibility in vitro of a L. amazonensis clinical isolate from a patient with cutaneous leishmaniasis and the reference strain L. amazonensis M2269, as well as its in vivo efficacy in a murine experimental model. Although never exposed to paromomycin, a significant differential susceptibility between these two lines was found. Paromomycin was highly active in vitro against the clinical isolate in both forms of the parasite, while its activity against the reference strain was less active. In vivo studies in mice infected with each one of these lines demonstrated that paromomycin reduces lesion size and parasite burden and a direct correlation between the susceptibility in vitro and the effectiveness of this drug in vivo was found. Our findings indicate that paromomycin efficacy in vivo is dependent on intrinsic susceptibility of the parasite. Beyond that, this study contributes for the evaluation of the potential use of paromomycin in chemotherapy of cutaneous leishmaniasis in Brazil caused by L. amazonensis.
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Affiliation(s)
- Elizabeth M Coser
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Bianca A Ferreira
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Nilson Branco
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Edite H Yamashiro-Kanashiro
- Laboratório de Soroepidemiologia e Imunobiologia, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil; Laboratório de Imunologia (LIM 48), Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - José Angelo L Lindoso
- Laboratório de Protozoologia, Instituto de Medicina Tropical de São Paulo, Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil; Instituto de Infectologia Emilio Ribas, São Paulo, Brazil
| | - Adriano C Coelho
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil.
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Rogozin IB, Charyyeva A, Sidorenko IA, Babenko VN, Yurchenko V. Frequent Recombination Events in Leishmania donovani: Mining Population Data. Pathogens 2020; 9:pathogens9070572. [PMID: 32679679 PMCID: PMC7400496 DOI: 10.3390/pathogens9070572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/24/2020] [Accepted: 07/13/2020] [Indexed: 11/21/2022] Open
Abstract
The Leishmania donovani species complex consists of all L. donovani and L. infantum strains mainly responsible for visceral leishmaniasis (VL). It was suggested that genome rearrangements in Leishmania spp. occur very often, thus enabling parasites to adapt to the different environmental conditions. Some of these rearrangements may be directly linked to the virulence or explain the reduced efficacy of antimonial drugs in some isolates. In the current study, we focused on a large-scale analysis of putative gene conversion events using publicly available datasets. Previous population study of L. donovani suggested that population variability of L. donovani is relatively low, however the authors used masking procedures and strict read selection criteria. We decided to re-analyze DNA-seq data without masking sequences, because we were interested in the most dynamic fraction of the genome. The majority of samples have an excess of putative gene conversion/recombination events in the noncoding regions, however we found an overall excess of putative intrachromosomal gene conversion/recombination in the protein coding genes, compared to putative interchromosomal gene conversion/recombination events.
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Affiliation(s)
- Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA;
| | - Arzuv Charyyeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Ivan A. Sidorenko
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (I.A.S.); (V.N.B.)
| | - Vladimir N. Babenko
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (I.A.S.); (V.N.B.)
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia
- Correspondence:
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Van den Kerkhof M, Sterckx YGJ, Leprohon P, Maes L, Caljon G. Experimental Strategies to Explore Drug Action and Resistance in Kinetoplastid Parasites. Microorganisms 2020; 8:E950. [PMID: 32599761 PMCID: PMC7356981 DOI: 10.3390/microorganisms8060950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Kinetoplastids are the causative agents of leishmaniasis, human African trypanosomiasis, and American trypanosomiasis. They are responsible for high mortality and morbidity in (sub)tropical regions. Adequate treatment options are limited and have several drawbacks, such as toxicity, need for parenteral administration, and occurrence of treatment failure and drug resistance. Therefore, there is an urgency for the development of new drugs. Phenotypic screening already allowed the identification of promising new chemical entities with anti-kinetoplastid activity potential, but knowledge on their mode-of-action (MoA) is lacking due to the generally applied whole-cell based approach. However, identification of the drug target is essential to steer further drug discovery and development. Multiple complementary techniques have indeed been used for MoA elucidation. In this review, the different 'omics' approaches employed to define the MoA or mode-of-resistance of current reference drugs and some new anti-kinetoplastid compounds are discussed.
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Affiliation(s)
- Magali Van den Kerkhof
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB), University of Antwerp, 2610 Wilrijk, Belgium;
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du Centre Hospitalier Universitaire de Québec, Université Laval, Québec, QC G1V 0A6, Canada;
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
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Ballesteros N, Vásquez NM, Patiño LH, Cruz-Saavedra L, Ramírez JD. Minor temperature shifts do not affect chromosomal ploidy but cause transcriptomic changes in Leishmania braziliensis promastigotes in vitro. Mem Inst Oswaldo Cruz 2020; 115:e190413. [PMID: 32348407 PMCID: PMC7184772 DOI: 10.1590/0074-02760190413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/03/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The leishmaniases are complex neglected diseases caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the main etiological agent of cutaneous leishmaniasis in the New World. In recent studies, genomic changes such as chromosome and gene copy number variations (CNVs), as well as transcriptomic changes have been highlighted as mechanisms used by Leishmania species to adapt to stress situations. OBJECTIVES The aim of this study was to determine the effect of short-term minor temperature shifts in the genomic and transcriptomic responses of L. braziliensis promastigotes in vitro. METHODS Growth curves, genome and transcriptome sequencing of L. braziliensis promastigotes were conducted from cultures exposed to three different temperatures (24ºC, 28ºC and 30ºC) compared with the control temperature (26ºC). FINDINGS Our results showed a decrease in L. braziliensis proliferation at 30ºC, with around 3% of the genes showing CNVs at each temperature, and transcriptomic changes in genes encoding amastin surface-like proteins, heat shock proteins and transport proteins, which may indicate a direct response to temperature stress. MAIN CONCLUSIONS This study provides evidence that L. braziliensis promastigotes exhibit a decrease in cell density, and noticeable changes in the transcriptomic profiles. However, there were not perceptible changes at chromosome CNVs and only ~3% of the genes changed their copies in each treatment.
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Affiliation(s)
- Nathalia Ballesteros
- Universidad del Rosario, Facultad de Ciencias Naturales, Departamento de Biología, Grupo de Investigaciones Microbiológicas, Bogotá, Colombia
| | - Nubia M Vásquez
- Universidad del Rosario, Facultad de Ciencias Naturales, Departamento de Biología, Grupo de Investigaciones Microbiológicas, Bogotá, Colombia
| | - Luz H Patiño
- Universidad del Rosario, Facultad de Ciencias Naturales, Departamento de Biología, Grupo de Investigaciones Microbiológicas, Bogotá, Colombia
| | - Lissa Cruz-Saavedra
- Universidad del Rosario, Facultad de Ciencias Naturales, Departamento de Biología, Grupo de Investigaciones Microbiológicas, Bogotá, Colombia
| | - Juan David Ramírez
- Universidad del Rosario, Facultad de Ciencias Naturales, Departamento de Biología, Grupo de Investigaciones Microbiológicas, Bogotá, Colombia
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Regulation of Translation in the Protozoan Parasite Leishmania. Int J Mol Sci 2020; 21:ijms21082981. [PMID: 32340274 PMCID: PMC7215931 DOI: 10.3390/ijms21082981] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 01/31/2023] Open
Abstract
Leishmaniasis represents a serious health problem worldwide and drug resistance is a growing concern. Leishmania parasites use unusual mechanisms to control their gene expression. In contrast to many other species, they do not have transcriptional regulation. The lack of transcriptional control is mainly compensated by post-transcriptional mechanisms, including tight translational control and regulation of mRNA stability/translatability by RNA-binding proteins. Modulation of translation plays a major role in parasite survival and adaptation to dramatically different environments during change of host; however, our knowledge of fine molecular mechanisms of translation in Leishmania remains limited. Here, we review the current progress in our understanding of how changes in the translational machinery promote parasite differentiation during transmission from a sand fly to a mammalian host, and discuss how translational reprogramming can contribute to the development of drug resistance.
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37
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Pountain AW, Barrett MP. Untargeted metabolomics to understand the basis of phenotypic differences in amphotericin B-resistant Leishmania parasites. Wellcome Open Res 2020; 4:176. [PMID: 32133420 PMCID: PMC7041363 DOI: 10.12688/wellcomeopenres.15452.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2019] [Indexed: 11/20/2022] Open
Abstract
Background: Protozoan
Leishmania parasites are responsible for a range of clinical infections that represent a substantial challenge for global health. Amphotericin B (AmB) is increasingly used to treat
Leishmania infection, so understanding the potential for resistance to this drug is an important priority. Previously we described four independently-derived AmB-resistant
L. mexicana lines that exhibited resistance-associated genetic lesions resulting in altered sterol content. However, substantial phenotypic variation between these lines, including differences in virulence attributes, were not fully explained by these changes. Methods: To identify alterations in cellular metabolism potentially related to phenotypic differences between wild-type and AmB-resistant lines, we extracted metabolites and performed untargeted metabolomics by liquid chromatography-mass spectrometry. Results: We observed substantial differences in metabolite abundance between lines, arising in an apparently stochastic manner. Concerted remodeling of central carbon metabolism was not observed; however, in three lines, decreased abundance of several oligohexoses was observed. Given that the oligomannose mannogen is an important virulence factor in
Leishmania, this could relate to loss of virulence in these lines. Increased abundance of the reduced forms of the oxidative stress-protective thiols trypanothione and glutathione was also observed in multiple lines. Conclusions: This dataset will provide a useful resource for understanding the molecular basis of drug resistance in
Leishmania, and suggests a role for metabolic changes separate from the primary mechanism of drug resistance in determining the phenotypic profile of parasite lines subjected to experimental selection of resistance.
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Affiliation(s)
- Andrew W Pountain
- Wellcome Center for Integrative Parasitology, University of Glasgow, Glasgow, G12 8TA, UK.,Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, 77030, USA
| | - Michael P Barrett
- Wellcome Center for Integrative Parasitology, University of Glasgow, Glasgow, G12 8TA, UK.,Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Bearsden, Glasgow, G61 1QH, UK
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Genomic and Metabolomic Polymorphism among Experimentally Selected Paromomycin-Resistant Leishmania donovani Strains. Antimicrob Agents Chemother 2019; 64:AAC.00904-19. [PMID: 31658971 PMCID: PMC7187574 DOI: 10.1128/aac.00904-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/23/2019] [Indexed: 12/22/2022] Open
Abstract
Understanding the mechanism(s) underpinning drug resistance could lead to novel treatments to reverse the increased tolerance of a pathogen. In this study, paromomycin (PMM) resistance (PMMr) was induced in three Nepalese clinical strains of Leishmania donovani with different inherent susceptibilities to antimony (Sb) drugs by stepwise exposure of promastigotes to PMM. Understanding the mechanism(s) underpinning drug resistance could lead to novel treatments to reverse the increased tolerance of a pathogen. In this study, paromomycin (PMM) resistance (PMMr) was induced in three Nepalese clinical strains of Leishmania donovani with different inherent susceptibilities to antimony (Sb) drugs by stepwise exposure of promastigotes to PMM. Exposure to PMM resulted in the production of mixed populations of parasites, even though a single cloned population was used at the start of selection. PMM 50% inhibitory concentration (IC50) values for PMMr parasites varied between 104 and 481 μM at the promastigote stage and 32 and 195 μM at the intracellular amastigote stage. PMM resistance was associated with increased resistance to nitric oxide at the amastigote stage but not the promastigote stage (P < 0.05). This effect was most marked in the Sb-resistant (Sbr) PMMr clone, in which PMM resistance was associated with a significant upregulation of glutathione compared to that in its wild type (P < 0.05), although there was no change in the regulation of trypanothione (detected in its oxidized form). Interestingly, PMMr strains showed an increase in either the keto acid derivative of isoleucine (Sb intermediate PMMr) or the 2-hydroxy acids derived from arginine and tyrosine (Sb susceptible PMMr and Sbr PMMr). These results are consistent with the recent finding that the upregulation of the branched-chain amino acid aminotransferase and d-lactate dehydrogenase is linked to PMMr. In addition, we found that PMMr is associated with a significant increase in aneuploidy during PMM selection in all the strains, which could allow the rapid selection of genetic changes that confer a survival advantage.
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Conceição-Silva F, Morgado FN. Leishmania Spp-Host Interaction: There Is Always an Onset, but Is There an End? Front Cell Infect Microbiol 2019; 9:330. [PMID: 31608245 PMCID: PMC6761226 DOI: 10.3389/fcimb.2019.00330] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/04/2019] [Indexed: 01/09/2023] Open
Abstract
For a long time Leishmaniasis had been considered as a neglected tropical disease. Recently, it has become a priority in public health all over the world for different aspects such as geographic spread, number of population living at risk of infection as well as the potential lethality and/or the development of disfiguring lesions in the, respectively, visceral and tegumentary forms of the disease. As a result, several groups have been bending over this issue and many valuable data have been published. Nevertheless, parasite-host interactions are still not fully known and, consequently, we do not entirely understand the infection dynamics and parasite persistence. This knowledge may point targets for modulation or blockage, being very useful in the development of measures to interfere in the course of infection/ disease and to minimize the risks and morbidity. In the present review we will discuss some aspects of the Leishmania spp-mammalian host interaction in the onset of infection and after the clinical cure of the lesions. We will also examine the information already available concerning the parasite strategy to evade immune response mainly at the beginning of the infection, as well as during the parasite persistence. This knowledge can improve the conditions of treatment, follow-up and cure control of patients, minimizing the potential damages this protozoosis can cause to infected individuals.
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Affiliation(s)
- Fatima Conceição-Silva
- Laboratory of Immunoparasitology, Oswaldo Cruz Institute, IOC/Fiocruz, Rio de Janeiro, Brazil
| | - Fernanda N Morgado
- Laboratory of Leishmaniasis Research, Oswaldo Cruz Institute, IOC/Fiocruz, Rio de Janeiro, Brazil
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Garg G, Ali V, Singh K, Gupta P, Ganguly A, Sahasrabuddhe AA, Das P. Quantitative secretome analysis unravels new secreted proteins in Amphotericin B resistant Leishmania donovani. J Proteomics 2019; 207:103464. [PMID: 31357030 DOI: 10.1016/j.jprot.2019.103464] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/24/2022]
Abstract
Leishmaniasis is second most neglected disease after malaria and seems to be a worldwide concern because of increased drug resistance and non-availability of approved vaccine. The underlying molecular mechanism of drug resistance (Amp B) in Leishmania parasites still remains elusive. Herein, the present study investigated differentially expressed secreted proteins of Amphotericin B sensitive (S) and resistant (R) isolate of Leishmania donovani by using label free quantitative LC-MS/MS approach. A total of 406 differentially expressed secreted proteins were found between sensitive (S) and resistant (R) isolate. Among 406 proteins, 32 were significantly up regulated (>2.0 fold) while 22 were down regulated (<0.5 fold) in resistant isolate of L. donovani. Further, differentially expressed proteins were classified into 11 various biological processes. Interestingly, identified up regulated proteins in resistant parasites were dominated in carbohydrate metabolism, stress response, transporters and proteolysis. Western blot and enzymatic activity of identified proteins validate our proteomic findings. Finally, our study demonstrated some new secreted proteins associated with Amp B resistance which provides a basis for further investigations to understand the role of proteins in L. donovani. BIOLOGICAL SIGNIFICANCE: Although great advances have been achieved in the diagnosis and treatment of leishmaniasis, still drug resistance is major hurdle in control of disease. Present study will enhance the deeper understanding of altered metabolic pathways involved in Amp B resistance mechanism and provide possible new proteins which can be potential candidate either for exploring as new drug target or vaccine. Protein-protein interactions highlighted the up-regulated metabolic pathways in resistant parasites which further unravel the adaptive mechanism of parasites.
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Affiliation(s)
- Gaurav Garg
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, India; Department of Biotechnology, National Institute of Pharmaceutical Education and Research, EPIP Complex, Hajipur 844102, India
| | - Vahab Ali
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, India; Department of Biotechnology, National Institute of Pharmaceutical Education and Research, EPIP Complex, Hajipur 844102, India.
| | - Kuljit Singh
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, India; Department of Biotechnology, National Institute of Pharmaceutical Education and Research, EPIP Complex, Hajipur 844102, India
| | - Parool Gupta
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, India
| | - Ashish Ganguly
- CSIR- Institute of Microbial Technology, Chandigarh, India
| | - Amogh A Sahasrabuddhe
- Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Pradeep Das
- Division of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, India
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Chemogenomic Profiling of Antileishmanial Efficacy and Resistance in the Related Kinetoplastid Parasite Trypanosoma brucei. Antimicrob Agents Chemother 2019; 63:AAC.00795-19. [PMID: 31160283 PMCID: PMC6658743 DOI: 10.1128/aac.00795-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 05/23/2019] [Indexed: 01/01/2023] Open
Abstract
The arsenal of drugs used to treat leishmaniasis, caused by Leishmania spp., is limited and beset by toxicity and emergent resistance. Furthermore, our understanding of drug mode of action and potential routes to resistance is limited. Forward genetic approaches have revolutionized our understanding of drug mode of action in the related kinetoplastid parasite Trypanosoma brucei. The arsenal of drugs used to treat leishmaniasis, caused by Leishmania spp., is limited and beset by toxicity and emergent resistance. Furthermore, our understanding of drug mode of action and potential routes to resistance is limited. Forward genetic approaches have revolutionized our understanding of drug mode of action in the related kinetoplastid parasite Trypanosoma brucei. Therefore, we screened our genome-scale T. brucei RNA interference (RNAi) library against the current antileishmanial drugs sodium stibogluconate (antimonial), paromomycin, miltefosine, and amphotericin B. Identification of T. brucei orthologues of the known Leishmania antimonial and miltefosine plasma membrane transporters effectively validated our approach, while a cohort of 42 novel drug efficacy determinants provides new insights and serves as a resource. Follow-up analyses revealed the antimonial selectivity of the aquaglyceroporin TbAQP3. A lysosomal major facilitator superfamily transporter contributes to paromomycin-aminoglycoside efficacy. The vesicle-associated membrane protein TbVAMP7B and a flippase contribute to amphotericin B and miltefosine action and are potential cross-resistance determinants. Finally, multiple phospholipid-transporting flippases, including the T. brucei orthologue of the Leishmania miltefosine transporter, a putative β-subunit/CDC50 cofactor, and additional membrane-associated hits, affect amphotericin B efficacy, providing new insights into mechanisms of drug uptake and action. The findings from this orthology-based chemogenomic profiling approach substantially advance our understanding of antileishmanial drug action and potential resistance mechanisms and should facilitate the development of improved therapies as well as surveillance for drug-resistant parasites.
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Patino LH, Muskus C, Ramírez JD. Transcriptional responses of Leishmania (Leishmania) amazonensis in the presence of trivalent sodium stibogluconate. Parasit Vectors 2019; 12:348. [PMID: 31300064 PMCID: PMC6626383 DOI: 10.1186/s13071-019-3603-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/06/2019] [Indexed: 12/13/2022] Open
Abstract
Background In the last decade, resistance to antimonials has become a serious problem due to the emergence of drug-resistant strains. Therefore, understanding the mechanisms used by Leishmania parasites to survive under drug pressure is essential, particularly for species of medical-veterinary importance such as L. amazonensis. Methods Here, we used RNA-seq technology to analyse transcriptome profiles and identify global changes in gene expression between antimony-resistant and -sensitive L. amazonensis promastigotes. Results A total of 723 differentially expressed genes were identified between resistant and sensitive lines. Comparative transcriptomic analysis revealed that genes encoding proteins involved in metabolism (fatty acids) and stress response, as well as those associated with antimony resistance in other Leishmania species, were upregulated in the antimony-resistant line. Most importantly, we observed upregulation of genes encoding autophagy proteins, suggesting that in the presence of trivalent stibogluconate (SbIII) L. amazonensis can activate these genes either as a survival strategy or to induce cell death, as has been observed in other parasites. Conclusions This work identified global transcriptomic changes in an in vitro-adapted strain in response to SbIII. Our results provide relevant information to continue understanding the mechanism used by parasites of the subgenus Leishmania (L. amazonensis) to generate an antimony-resistant phenotype. Electronic supplementary material The online version of this article (10.1186/s13071-019-3603-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luz H Patino
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Carlos Muskus
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia.
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Major changes in chromosomal somy, gene expression and gene dosage driven by Sb III in Leishmania braziliensis and Leishmania panamensis. Sci Rep 2019; 9:9485. [PMID: 31263131 PMCID: PMC6603004 DOI: 10.1038/s41598-019-45538-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/06/2019] [Indexed: 12/17/2022] Open
Abstract
Leishmania braziliensis and Leishmania panamensis are two species clinically and epidemiologically important, among others because of their relative resistance to first-line drugs (antimonials). The precise mechanism underlying the ability of these species to survive antimony treatment remains unknown. Therefore, elucidating the pathways mediating drug resistance is essential. We herein experimentally selected resistance to trivalent antimony (SbIII) in the reference strains of L. braziliensis (MHOM/BR75/M2904) and L. panamensis (MHOM/COL/81L13) and compared whole genome and transcriptome alterations in the culture promastigote stage. The results allowed us to identify differences in somy, copy number variations in some genes related to antimony resistance and large-scale copy number variations (deletions and duplications) in chromosomes with no somy changes. We found mainly in L. braziliensis, a direct relation between the chromosomal/local copy number variation and the gene expression. We identified differentially expressed genes in the resistant lines that are involved in antimony resistance, virulence, and vital biological processes in parasites. The results of this study may be useful for characterizing the genetic mechanisms of these Leishmania species under antimonial pressure, and for clarifying why the parasites are resistant to first-line drug treatments.
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Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation. Sci Rep 2019; 9:6127. [PMID: 30992521 PMCID: PMC6467909 DOI: 10.1038/s41598-019-42511-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/02/2019] [Indexed: 01/05/2023] Open
Abstract
Leishmania donovani is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of L. donovani is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an L. donovani genome attained to date. The use of a combination of sequencing platforms enabled to assemble, without any sequence gap, the 36 chromosomes for this species. Additionally, based on this assembly and using RNA-seq reads derived from poly-A + RNA, the transcriptome for this species, not yet available, was delineated. Alternative SL addition sites and heterogeneity in the poly-A addition sites were commonly observed for most of the genes. After a complete annotation of the transcriptome, 2,410 novel transcripts were defined. Additionally, the relative expression for all transcripts present in the promastigote stage was determined. Events of cis-splicing have been documented to occur during the maturation of the transcripts derived from genes LDHU3_07.0430 and LDHU3_29.3990. The complete genome assembly and the availability of the gene models (including annotation of untranslated regions) are important pieces to understand how differential gene expression occurs in this pathogen, and to decipher phenotypic peculiarities like tissue tropism, clinical disease, and drug susceptibility.
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Pountain AW, Weidt SK, Regnault C, Bates PA, Donachie AM, Dickens NJ, Barrett MP. Genomic instability at the locus of sterol C24-methyltransferase promotes amphotericin B resistance in Leishmania parasites. PLoS Negl Trop Dis 2019; 13:e0007052. [PMID: 30716073 PMCID: PMC6375703 DOI: 10.1371/journal.pntd.0007052] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/14/2019] [Accepted: 12/04/2018] [Indexed: 01/24/2023] Open
Abstract
Amphotericin B is an increasingly important tool in efforts to reduce the global disease burden posed by Leishmania parasites. With few other chemotherapeutic options available for the treatment of leishmaniasis, the potential for emergent resistance to this drug is a considerable threat. Here we characterised four novel amphotericin B-resistant Leishmania mexicana lines. All lines exhibited altered sterol biosynthesis, and hypersensitivity to pentamidine. Whole genome sequencing demonstrated resistance-associated mutation of the sterol biosynthesis gene sterol C5-desaturase in one line. However, in three out of four lines, RNA-seq revealed loss of expression of sterol C24-methyltransferase (SMT) responsible for drug resistance and altered sterol biosynthesis. Additional loss of the miltefosine transporter was associated with one of those lines. SMT is encoded by two tandem gene copies, which we found to have very different expression levels. In all cases, reduced overall expression was associated with loss of the 3' untranslated region of the dominant gene copy, resulting from structural variations at this locus. Local regions of sequence homology, between the gene copies themselves, and also due to the presence of SIDER1 retrotransposon elements that promote multi-gene amplification, correlate to these structural variations. Moreover, in at least one case loss of SMT expression was not associated with loss of virulence in primary macrophages or in vivo. Whilst such repeat sequence-mediated instability is known in Leishmania genomes, its presence associated with resistance to a major antileishmanial drug, with no evidence of associated fitness costs, is a significant concern.
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Affiliation(s)
- Andrew W. Pountain
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, United Kingdom
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Stefan K. Weidt
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Clément Regnault
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Paul A. Bates
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, United Kingdom
| | - Anne M. Donachie
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Nicholas J. Dickens
- Marine Biomedical & Biotechnology Research Program, Florida Atlantic University Harbor Branch Oceanographic Institute, Fort Pierce, Florida, United States of America
| | - Michael P. Barrett
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, United Kingdom
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Imamura H, Dujardin JC. A Guide to Next Generation Sequence Analysis of Leishmania Genomes. Methods Mol Biol 2019; 1971:69-94. [PMID: 30980298 DOI: 10.1007/978-1-4939-9210-2_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Next generation sequencing (NGS) technology transformed Leishmania genome studies and became an indispensable tool for Leishmania researchers. Recent Leishmania genomics analyses facilitated the discovery of various genetic diversities including single nucleotide polymorphisms (SNPs), copy number variations (CNVs), somy variations, and structural variations in detail and provided valuable insights into the complexity of the genome and gene regulation. Many aspects of Leishmania NGS analyses are similar to those of related pathogens like trypanosomes. However, the analyses of Leishmania genomes face a unique challenge because of the presence of frequent aneuploidy. This makes characterization and interpretation of read depth and somy a key part of Leishmania NGS analyses because read depth affects the accuracy of detection of all genetic variations. However, there are no general guidelines on how to explore and interpret the impact of aneuploidy, and this has made it difficult for biologists and bioinformaticians, especially for beginners, to perform their own analyses and interpret results across different analyses. In this guide we discuss a wide range of topics essential for Leishmania NGS analyses, ranging from how to set up a computational environment for genome analyses, to how to characterize genetic variations among Leishmania samples, and we will particularly focus on chromosomal copy number variation and its impact on genome analyses.
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Affiliation(s)
- Hideo Imamura
- Department of Biomedical Sciences, Institute of Tropical Medicine, 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
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Borsari C, Quotadamo A, Ferrari S, Venturelli A, Cordeiro-da-Silva A, Santarem N, Costi MP. Scaffolds and Biological Targets Avenue to Fight Against Drug Resistance in Leishmaniasis. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2018. [DOI: 10.1016/bs.armc.2018.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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