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Bruno F, Castelli G, Li B, Reale S, Carra E, Vitale F, Scibetta S, Calzolari M, Varani S, Ortalli M, Franceschini E, Gennari W, Rugna G, Späth GF. Genomic and epidemiological evidence for the emergence of a L. infantum/L. donovani hybrid with unusual epidemiology in northern Italy. mBio 2024:e0099524. [PMID: 38832792 DOI: 10.1128/mbio.00995-24] [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: 04/04/2024] [Accepted: 04/30/2024] [Indexed: 06/05/2024] Open
Abstract
Leishmania (L.) infantum is one of the main causative agents of animal and human leishmaniasis across many endemic areas in South America, Europe, North Africa, and Asia. Despite its clinical significance, little is known about the genetic diversity of L. infantum circulating in a given endemic area. Here, we investigate this important open question by applying a comparative genomics approach to seven L. infantum isolates from different hosts and Italian regions, including the northern part of the country (Emilia-Romagna, RER), Sicily, and Sardinia, as an initial attempt to explore the breadth of parasite genetic heterogeneity in Italy. Additionally, microsatellite analysis was carried out to compare the isolates from RER with other 70 L. infantum strains from the same region as well as 65 strains belonging to the L. donovani complex from other countries. We revealed important karyotypic instability and identified strain-specific changes in gene dosage, which affected important virulence factors such as amastins and surface antigen-like proteins. Single nucleotide polymorphism-based clustering analysis of these genomes together with over 80 publicly available L. infantum and L. donovani genomes placed the Italian isolates into three geographically distinct clusters within the Mediterranean basin and uncovered three isolates clustering with putative L. infantum/L. donovani hybrids isolated in Cyprus. As judged by microsatellite profiling, these hybrid isolates are representative of a sub-population of parasites circulating in northern Italy that preferentially infect humans but not dogs. Our results place Italy at the crossroads of L. infantum infection in the Mediterranean and call attention to the public health risk represented by the introduction of non-European Leishmania species.IMPORTANCEThis study closes important knowledge gaps with respect to Leishmania (L.) infantum genetic heterogeneity in a given endemic country, as exemplified here for Italy, and reveals genetic hybridization as a main cause for re-emerging human leishmaniasis in northern Italy. The observed high diversity of Leishmania parasites on the Italian peninsula suggests different geographical origins, with genomic adaptation to various ecologies affecting both pathogenicity and transmission potential. This is documented by the discovery of a putative L. infantum/L. donovani hybrid strain, which has been shown to preferentially infect humans but not dogs. Our results provide important information to health authorities, which need to consider the public health risk represented by the introduction of new Leishmania species into EU countries due to population displacement or travel from countries where exotic/allochthonous parasite species are endemic.
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Affiliation(s)
- F Bruno
- WOAH Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia, Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), Palermo, Italy
| | - G Castelli
- WOAH Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia, Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), Palermo, Italy
| | - B Li
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - S Reale
- WOAH Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia, Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), Palermo, Italy
| | - E Carra
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "B. Ubertini", Brescia, Italy
| | - F Vitale
- WOAH Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia, Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), Palermo, Italy
| | - S Scibetta
- WOAH Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia, Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), Palermo, Italy
| | - M Calzolari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "B. Ubertini", Brescia, Italy
| | - S Varani
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - M Ortalli
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - E Franceschini
- Infectious Disease Unit, Azienda Ospedaliera Universitaria di Modena, Modena, Italy
| | - W Gennari
- Virology and Molecular Microbiology Unit, University Hospital of Modena, Modena, Italy
| | - G Rugna
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "B. Ubertini", Brescia, Italy
| | - G F Späth
- Unité de Parasitologie moléculaire et Signalisation, INSERM U1201, Institut Pasteur, Université Paris Cité, Paris, France
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Matiz-González JM, Pardo-Rodriguez D, Puerta CJ, Requena JM, Martinez PAN, Cuervo C. Exploring the functionality and conservation of Alba proteins in Trypanosoma cruzi: A focus on biological diversity and RNA binding ability. Int J Biol Macromol 2024:132705. [PMID: 38810850 DOI: 10.1016/j.ijbiomac.2024.132705] [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: 11/07/2023] [Revised: 05/07/2024] [Accepted: 05/26/2024] [Indexed: 05/31/2024]
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, as well as a trypanosomatid parasite with a complex biological cycle that requires precise mechanisms for regulating gene expression. In Trypanosomatidae, gene regulation occurs mainly at the mRNA level through the recognition of cis elements by RNA-binding proteins (RBPs). Alba family members are ubiquitous DNA/RNA-binding proteins with representatives in trypanosomatid parasites functionally related to gene expression regulation. Although T. cruzi possesses two groups of Alba proteins (Alba1/2 and Alba30/40), their functional role remains poorly understood. Thus, herein, a characterization of T. cruzi Alba (TcAlba) proteins was undertaken. Physicochemical, structural, and phylogenetic analysis of TcAlba showed features compatible with RBPs, such as hydrophilicity, RBP domains/motifs, and evolutionary conservation of the Alba-domain, mainly regarding other trypanosomatid Alba. However, in silico RNA interaction analysis of T. cruzi Alba proteins showed that TcAlba30/40 proteins, but not TcAlba1/2, would directly interact with the assayed RNA molecules, suggesting that these two groups of TcAlba proteins have different targets. Given the marked differences existing between both T. cruzi Alba groups (TcAlba1/2 and TcAlba30/40), regarding sequence divergence, RNA binding potential, and life-cycle expression patterns, we suggest that they would be involved in different biological processes.
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Affiliation(s)
- J Manuel Matiz-González
- Grupo de Enfermedades Infecciosas, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231 Bogotá, Colombia
| | - Daniel Pardo-Rodriguez
- Grupo de Fitoquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231 Bogotá, Colombia; Metabolomics Core Facility, Vice-Presidency for Research, Universidad de los Andes, 111711 Bogotá, Colombia
| | - Concepcion J Puerta
- Grupo de Enfermedades Infecciosas, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231 Bogotá, Colombia
| | - José M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Paola Andrea Nocua Martinez
- Grupo de Enfermedades Infecciosas, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231 Bogotá, Colombia.
| | - Claudia Cuervo
- Grupo de Enfermedades Infecciosas, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231 Bogotá, Colombia.
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3
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Barbero-Moyano J, Castro-Scholten S, Gonzálvez M, Moreno I, Domínguez M, Cano-Terriza D, Jiménez-Martín D, Camacho-Sillero L, Martínez R, García-Bocanegra I. Epidemiological surveillance of Leishmania infantum in wild lagomorphs in Spanish Mediterranean ecosystems. Prev Vet Med 2024; 228:106231. [PMID: 38788301 DOI: 10.1016/j.prevetmed.2024.106231] [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: 01/11/2024] [Revised: 04/30/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Wild lagomorphs play a key epidemiological role as reservoirs of Leishmania infantum, causative agent of the largest outbreak of human leishmaniosis in Europe to date. A large-scale survey study was conducted on wild rabbit (Oryctolagus cuniculus) and Iberian hare (Lepus granatensis) populations in Spanish Mediterranean ecosystems to evaluate the exposure of L. infantum and investigate potential risk factors associated with exposure to this zoonotic parasite. Between 2018 and 2021, a total of 631 wild lagomorphs (471 wild rabbits and 160 Iberian hares) were collected in Andalusia (southern Spain) and tested for antibodies against L. infantum using the indirect fluorescent antibody test (IFAT). Spleen samples from 563 of the wild lagomorphs sampled (441 wild rabbits and 122 Iberian hares) were also evaluated by real-time quantitative PCR (qPCR) for detection of Leishmania kDNA. Exposure to L. infantum (positive by IFAT and/or qPCR) was detected in 56.4 % (356/631; 95 %CI: 52.3-60.3) of the lagomorphs analyzed. Anti-Leishmania antibodies were found in 12.8 % (81/631; 95 %CI: 10.2-15.5) of the animals, and L. infantum kDNA was detected in 59.0 % (332/563; 95 %CI: 54.9-63.0) of the spleen samples tested. Phylogenetic analysis revealed high homology (99.9-100 %) between L. infantum sequences obtained and strains previously isolated from humans in Spain. While apparent seroprevalence was significantly higher in Iberian hares (19.4 %; 95 %CI: 13.3-25.5) compared to wild rabbits (10.6 %; 95 %CI: 7.9-13.4), no significant differences in prevalence were found between wild rabbits (61.0 %; 95 %CI: 56.5-65.6) and Iberian hares (51.6 %; 95 %CI: 42.8-60.5). At least one positive animal was found on 64.8 % (70/108) of the hunting grounds sampled, and a high-risk spatial cluster (P < 0.001) was also identified in central Andalusia. The multivariable analysis identified bioclimatic level (meso-Mediterranean climate) and the presence of goats on hunting grounds as risk factors potentially associated with L. infantum exposure in wild lagomorphs. This study shows high, widespread exposure, but heterogeneous distribution of L. infantum in wild lagomorph populations in Mediterranean ecosystems in southern Spain. The results point to the need to promote integrated surveillance programs for the detection of Leishmania spp. in wild lagomorphs in order to establish effective control measures against human leishmaniosis under a One Health approach.
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Affiliation(s)
- Jesús Barbero-Moyano
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba 14014, Spain
| | - Sabrina Castro-Scholten
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba 14014, Spain
| | - Moisés Gonzálvez
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba 14014, Spain; Departamento de Sanidad Animal, Facultad de Veterinaria, Campus de Excelencia Internacional Regional "Campus Mare Nostrum", Universidad de Murcia, Murcia 30100, Spain
| | - Inmaculada Moreno
- Unidad de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
| | - Mercedes Domínguez
- Unidad de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
| | - David Cano-Terriza
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba 14014, Spain; CIBERINFEC, ISCIII CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Débora Jiménez-Martín
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba 14014, Spain
| | - Leonor Camacho-Sillero
- Programa de Vigilancia Epidemiológica de la Fauna Silvestre (PVE), Consejería de Sostenibilidad, Medio Ambiente y Economía Azul, Junta de Andalucía, Málaga 29002, Spain
| | - Remigio Martínez
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba 14014, Spain; Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres 10003, Spain.
| | - Ignacio García-Bocanegra
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba 14014, Spain; CIBERINFEC, ISCIII CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid 28029, Spain
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Roberts AJ, Ong HB, Clare S, Brandt C, Harcourt K, Takele Y, Ghosh P, Toepp A, Waugh M, Matano D, Färnert A, Adams E, Moreno J, Mbuchi M, Petersen C, Mondal D, Kropf P, Wright GJ. A panel of recombinant Leishmania donovani cell surface and secreted proteins identifies LdBPK_323600.1 as a serological marker of symptomatic infection. mBio 2024; 15:e0085924. [PMID: 38639536 PMCID: PMC11077996 DOI: 10.1128/mbio.00859-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
Visceral leishmaniasis is a deadly infectious disease and is one of the world's major neglected health problems. Because the symptoms of infection are similar to other endemic diseases, accurate diagnosis is crucial for appropriate treatment. Definitive diagnosis using splenic or bone marrow aspirates is highly invasive, and so, serological assays are preferred, including the direct agglutination test (DAT) or rK39 strip test. These tests, however, are either difficult to perform in the field (DAT) or lack specificity in some endemic regions (rK39), making the development of new tests a research priority. The availability of Leishmania spp. genomes presents an opportunity to identify new diagnostic targets. Here, we use genome data and a mammalian protein expression system to create a panel of 93 proteins consisting of the extracellular ectodomains of the Leishmania donovani cell surface and secreted proteins. We use these panel and sera from murine experimental infection models and natural human and canine infections to identify new candidates for serological diagnosis. We observed a concordance between the most immunoreactive antigens in different host species and transmission settings. The antigen encoded by the LdBPK_323600.1 gene can diagnose Leishmania infections with high sensitivity and specificity in patient cohorts from different endemic regions including Bangladesh and Ethiopia. In longitudinal sampling of treated patients, we observed reductions in immunoreactivity to LdBPK_323600.1 suggesting it could be used to diagnose treatment success. In summary, we have identified new antigens that could contribute to improved serological diagnostic tests to help control the impact of this deadly tropical infectious disease. IMPORTANCE Visceral leishmaniasis is fatal if left untreated with patients often displaying mild and non-specific symptoms during the early stages of infection making accurate diagnosis important. Current methods for diagnosis require highly trained medical staff to perform highly invasive biopsies of the liver or bone marrow which pose risks to the patient. Less invasive molecular tests are available but can suffer from regional variations in their ability to accurately diagnose an infection. To identify new diagnostic markers of visceral leishmaniasis, we produced and tested a panel of 93 proteins identified from the genome of the parasite responsible for this disease. We found that the pattern of host antibody reactivity to these proteins was broadly consistent across naturally acquired infections in both human patients and dogs, as well as experimental rodent infections. We identified a new protein called LdBPK_323600.1 that could accurately diagnose visceral leishmaniasis infections in humans.
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Affiliation(s)
- Adam J. Roberts
- Hull York Medical School, University of York, Heslington, York, United Kingdom
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Han Boon Ong
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Simon Clare
- Pathogen Laboratory Support, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Cordelia Brandt
- Pathogen Laboratory Support, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Katherine Harcourt
- Pathogen Laboratory Support, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Yegnasew Takele
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Prakash Ghosh
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Angela Toepp
- College of Public Health, University of Iowa, Iowa City, USA
| | - Max Waugh
- College of Public Health, University of Iowa, Iowa City, USA
| | - Daniel Matano
- Centre for Clinical Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Anna Färnert
- Department of Medicine Solna and Center for Molecular Medicine, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Emily Adams
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Javier Moreno
- WHO Collaborating Centre for Leishmaniasis, National Centre for Microbiology, Instituto de Salud Carlos III, CIBER de Enfermedades Infecciosas—CIBERINFEC, Madrid, Spain
| | - Margaret Mbuchi
- Centre for Clinical Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | | | - Dinesh Mondal
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Pascale Kropf
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gavin J. Wright
- Hull York Medical School, University of York, Heslington, York, United Kingdom
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, United Kingdom
- Department of Biology and York, Biomedical Research Institute, University of York, York, United Kingdom
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5
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Trajano-Silva LAM, Mule SN, Palmisano G. Molecular tools to regulate gene expression in Trypanosoma cruzi. Adv Clin Chem 2024; 120:169-190. [PMID: 38762241 DOI: 10.1016/bs.acc.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Developing molecular strategies to manipulate gene expression in trypanosomatids is challenging, particularly with respect to the unique gene expression mechanisms adopted by these unicellular parasites, such as polycistronic mRNA transcription and multi-gene families. In the case of Trypanosoma cruzi (T. cruzi), the causative agent of Chagas Disease, the lack of RNA interference machinery further complicated functional genetic studies important for understanding parasitic biology and developing biomarkers and potential therapeutic targets. Therefore, alternative methods of performing knockout and/or endogenous labelling experiments were developed to identify and understand the function of proteins for survival and interaction with the host. In this review, we present the main tools for the genetic manipulation of T. cruzi, focusing on the Clustered Regularly Interspaced Short Palindromic Repeats Cas9-associated system technique widely used in this organism. Moreover, we highlight the importance of using these tools to elucidate the function of uncharacterized and glycosylated proteins. Further developments of these technologies will allow the identification of new biomarkers, therapeutic targets and potential vaccines against Chagas disease with greater efficiency and speed.
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Affiliation(s)
- Lays Adrianne M Trajano-Silva
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil
| | - Simon Ngao Mule
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil
| | - Giuseppe Palmisano
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil; School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
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Reis-Cunha JL, Pimenta-Carvalho SA, Almeida LV, Coqueiro-Dos-Santos A, Marques CA, Black JA, Damasceno J, McCulloch R, Bartholomeu DC, Jeffares DC. Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites. Genome Res 2024; 34:441-453. [PMID: 38604731 PMCID: PMC11067883 DOI: 10.1101/gr.278550.123] [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: 09/22/2023] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
Aneuploidy is widely observed in both unicellular and multicellular eukaryotes, usually associated with adaptation to stress conditions. Chromosomal duplication stability is a tradeoff between the fitness cost of having unbalanced gene copies and the potential fitness gained from increased dosage of specific advantageous genes. Trypanosomatids, a family of protozoans that include species that cause neglected tropical diseases, are a relevant group to study aneuploidies. Their life cycle has several stressors that could select for different patterns of chromosomal duplications and/or losses, and their nearly universal use of polycistronic transcription increases their reliance on gene expansion/contraction, as well as post-transcriptional control as mechanisms for gene expression regulation. By evaluating the data from 866 isolates covering seven trypanosomatid genera, we have revealed that aneuploidy tolerance is an ancestral characteristic of trypanosomatids but has a reduced occurrence in a specific monophyletic clade that has undergone large genomic reorganization and chromosomal fusions. We have also identified an ancient chromosomal duplication that was maintained across these parasite's speciation, named collectively as the trypanosomatid ancestral supernumerary chromosome (TASC). TASC has most genes in the same coding strand, is expressed as a disomic chromosome (even having four copies), and has increased potential for functional variation, but it purges highly deleterious mutations more efficiently than other chromosomes. The evidence of stringent control over gene expression in this chromosome suggests that these parasites have adapted to mitigate the fitness cost associated with this ancient chromosomal duplication.
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Affiliation(s)
- João L Reis-Cunha
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, United Kingdom;
| | - Samuel A Pimenta-Carvalho
- Instituto de Ciências Biológicas, Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Laila V Almeida
- Instituto de Ciências Biológicas, Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Anderson Coqueiro-Dos-Santos
- Instituto de Ciências Biológicas, Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Catarina A Marques
- The Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Jennifer A Black
- The Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14049-900, Brazil
| | - Jeziel Damasceno
- The Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Daniella C Bartholomeu
- Instituto de Ciências Biológicas, Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Daniel C Jeffares
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, United Kingdom
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7
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Román-Álamo L, Avalos-Padilla Y, Bouzón-Arnáiz I, Iglesias V, Fernández-Lajo J, Monteiro JM, Rivas L, Fisa R, Riera C, Andreu D, Pintado-Grima C, Ventura S, Arce EM, Muñoz-Torrero D, Fernàndez-Busquets X. Effect of the aggregated protein dye YAT2150 on Leishmania parasite viability. Antimicrob Agents Chemother 2024; 68:e0112723. [PMID: 38349159 PMCID: PMC10916400 DOI: 10.1128/aac.01127-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/15/2024] [Indexed: 03/07/2024] Open
Abstract
The problems associated with the drugs currently used to treat leishmaniasis, including resistance, toxicity, and the high cost of some formulations, call for the urgent identification of new therapeutic agents with novel modes of action. The aggregated protein dye YAT2150 has been found to be a potent antileishmanial compound, with a half-maximal inhibitory concentration (IC50) of approximately 0.5 µM against promastigote and amastigote stages of Leishmania infantum. The encapsulation in liposomes of YAT2150 significantly improved its in vitro IC50 to 0.37 and 0.19 µM in promastigotes and amastigotes, respectively, and increased the half-maximal cytotoxic concentration in human umbilical vein endothelial cells to >50 µM. YAT2150 became strongly fluorescent when binding intracellular protein deposits in Leishmania cells. This fluorescence pattern aligns with the proposed mode of action of this drug in the malaria parasite Plasmodium falciparum, the inhibition of protein aggregation. In Leishmania major, YAT2150 rapidly reduced ATP levels, suggesting an alternative antileishmanial mechanism. To the best of our knowledge, this first-in-class compound is the only one described so far having significant activity against both Plasmodium and Leishmania, thus being a potential drug for the treatment of co-infections of both parasites.
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Affiliation(s)
- Lucía Román-Álamo
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Doctoral School of Biotechnology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Yunuen Avalos-Padilla
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Inés Bouzón-Arnáiz
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Valentín Iglesias
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Jorge Fernández-Lajo
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Juan M. Monteiro
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Luis Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Roser Fisa
- Section of Parasitology Department of Biology, Health and Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Cristina Riera
- Section of Parasitology Department of Biology, Health and Environment, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - David Andreu
- Department of Medicine and Life Sciences, Barcelona Biomedical Research Park, Pompeu Fabra University, Barcelona, Spain
| | - Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Elsa M. Arce
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Xavier Fernàndez-Busquets
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Barcelona, Spain
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8
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Tarannum A, Rodríguez-Almonacid CC, Salazar-Bravo J, Karamysheva ZN. Molecular Mechanisms of Persistence in Protozoan Parasites. Microorganisms 2023; 11:2248. [PMID: 37764092 PMCID: PMC10534552 DOI: 10.3390/microorganisms11092248] [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: 07/28/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Protozoan parasites are known for their remarkable capacity to persist within the bodies of vertebrate hosts, which frequently results in prolonged infections and the recurrence of diseases. Understanding the molecular mechanisms that underlie the event of persistence is of paramount significance to develop innovative therapeutic approaches, given that these pathways still need to be thoroughly elucidated. The present article provides a comprehensive overview of the latest developments in the investigation of protozoan persistence in vertebrate hosts. The focus is primarily on the function of persisters, their formation within the host, and the specific molecular interactions between host and parasite while they persist. Additionally, we examine the metabolomic, transcriptional, and translational changes that protozoan parasites undergo during persistence within vertebrate hosts, focusing on major parasites such as Plasmodium spp., Trypanosoma spp., Leishmania spp., and Toxoplasma spp. Key findings of our study suggest that protozoan parasites deploy several molecular and physiological strategies to evade the host immune surveillance and sustain their persistence. Furthermore, some parasites undergo stage differentiation, enabling them to acclimate to varying host environments and immune challenges. More often, stressors such as drug exposure were demonstrated to impact the formation of protozoan persisters significantly. Understanding the molecular mechanisms regulating the persistence of protozoan parasites in vertebrate hosts can reinvigorate our current insights into host-parasite interactions and facilitate the development of more efficacious disease therapeutics.
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Affiliation(s)
| | | | | | - Zemfira N. Karamysheva
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA; (A.T.); (C.C.R.-A.); (J.S.-B.)
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9
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Goes WM, Brasil CRF, Reis-Cunha JL, Coqueiro-Dos-Santos A, Grazielle-Silva V, de Souza Reis J, Souto TC, Laranjeira-Silva MF, Bartholomeu DC, Fernandes AP, Teixeira SMR. Complete assembly, annotation of virulence genes and CRISPR editing of the genome of Leishmania amazonensis PH8 strain. Genomics 2023; 115:110661. [PMID: 37263313 DOI: 10.1016/j.ygeno.2023.110661] [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: 11/22/2022] [Revised: 05/04/2023] [Accepted: 05/27/2023] [Indexed: 06/03/2023]
Abstract
We report the sequencing and assembly of the PH8 strain of Leishmania amazonensis one of the etiological agents of leishmaniasis. After combining data from long Pacbio reads, short Illumina reads and synteny with the Leishmania mexicana genome, the sequence of 34 chromosomes with 8317 annotated genes was generated. Multigene families encoding three virulence factors, A2, amastins and the GP63 metalloproteases, were identified and compared to their annotation in other Leishmania species. As they have been recently recognized as virulence factors essential for disease establishment and progression of the infection, we also identified 14 genes encoding proteins involved in parasite iron and heme metabolism and compared to genes from other Trypanosomatids. To follow these studies with a genetic approach to address the role of virulence factors, we tested two CRISPR-Cas9 protocols to generate L. amazonensis knockout cell lines, using the Miltefosine transporter gene as a proof of concept.
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Affiliation(s)
- Wanessa Moreira Goes
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Carlos Rodolpho Ferreira Brasil
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - João Luis Reis-Cunha
- Departamento de Veterinária Preventiva, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil; Departamento de Parasitologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Anderson Coqueiro-Dos-Santos
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Viviane Grazielle-Silva
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Júlia de Souza Reis
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Tatiane Cristina Souto
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Maria Fernanda Laranjeira-Silva
- Departamento de Fisiologia, Universidade de São Paulo, Rua do Matão 101, Cidade Universitária, São Paulo, SP CEP 05508-900, Brazil
| | - Daniella Castanheira Bartholomeu
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil
| | - Ana Paula Fernandes
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil; Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Belo Horizonte, MG, CEP 31.210-360, Brazil
| | - Santuza Maria Ribeiro Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG CEP 31.270-901, Brazil; Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Belo Horizonte, MG, CEP 31.210-360, Brazil.
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10
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Takamiya NT, Rogerio LA, Torres C, Leonel JAF, Vioti G, de Sousa Oliveira TMF, Valeriano KC, Porcino GN, de Miranda Santos IKF, Costa CHN, Costa DL, Ferreira TS, Gurgel-Gonçalves R, da Silva JS, Teixeira FR, De Almeida RP, Ribeiro JMC, Maruyama SR. Parasite Detection in Visceral Leishmaniasis Samples by Dye-Based qPCR Using New Gene Targets of Leishmania infantum and Crithidia. Trop Med Infect Dis 2023; 8:405. [PMID: 37624343 PMCID: PMC10457869 DOI: 10.3390/tropicalmed8080405] [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: 07/03/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Visceral leishmaniasis (VL) is a neglected disease considered a serious public health problem, especially in endemic countries. Several studies have discovered monoxenous trypanosomatids (Leptomonas and Crithidia) in patients with VL. In different situations of leishmaniasis, investigations have examined cases of co-infection between Leishmania spp. and Crithidia spp. These coinfections have been observed in a wide range of vertebrate hosts, indicating that they are not rare. Diagnostic techniques require improvements and more robust tools to accurately detect the causative agent of VL. This study aimed to develop a real-time quantitative dye-based PCR (qPCR) assay capable of distinguishing Leishmania infantum from Crithidia-related species and to estimate the parasite load in samples of VL from humans and animals. The primer LinJ31_2420 targets an exclusive phosphatase of L. infantum; the primer Catalase_LVH60-12060_1F targets the catalase gene of Crithidia. Therefore, primers were designed to detect L. infantum and Crithidia sp. LVH60A (a novel trypanosomatid isolated from VL patients in Brazil), in samples related to VL. These primers were considered species-specific, based on sequence analysis using genome data retrieved from the TriTryp database and the genome assembling of Crithidia sp. LVH60A strain, in addition to experimental and clinical data presented herein. This novel qPCR assay was highly accurate in identifying and quantifying L. infantum and Crithidia sp. LVH60A in samples obtained experimentally (in vitro and in vivo) or collected from hosts (humans, dogs, cats, and vectors). Importantly, the screening of 62 cultured isolates from VL patients using these primers surprisingly revealed that 51 parasite cultures were PCR+ for Crithidia sp. In addition, qPCR assays identified the co-infection of L. infantum with Crithidia sp. LVH60A in two new VL cases in Brazil, confirming the suspicion of co-infection in a previously reported case of fatal VL. We believe that the species-specific genes targeted in this study can be helpful for the molecular diagnosis of VL, as well as for elucidating suspected co-infections with monoxenous-like trypanosomatids, which is a neglected fact of a neglected disease.
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Affiliation(s)
- Nayore Tamie Takamiya
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - Luana Aparecida Rogerio
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - Caroline Torres
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - João Augusto Franco Leonel
- Post-Graduate Program in Experimental Epidemiology Applied to Zoonoses at the Faculty of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, SP, Brazil
| | - Geovanna Vioti
- Post-Graduate Program in Experimental Epidemiology Applied to Zoonoses at the Faculty of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, SP, Brazil
| | - Tricia Maria Ferreira de Sousa Oliveira
- Post-Graduate Program in Experimental Epidemiology Applied to Zoonoses at the Faculty of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil
| | - Karoline Camila Valeriano
- Ribeirão Preto Medical School, University of São Paulo, FMRP-USP, Ribeirão Preto 14049-900, SP, Brazil
| | | | | | - Carlos H. N. Costa
- Natan Portela Institute of Tropical Diseases, Teresina 64002-510, PI, Brazil
| | | | - Tauana Sousa Ferreira
- Laboratory of Medical Parasitology and Vector Biology, Faculty of Medicine, University of Brasília, Brasília 70910-900, DF, Brazil
| | - Rodrigo Gurgel-Gonçalves
- Laboratory of Medical Parasitology and Vector Biology, Faculty of Medicine, University of Brasília, Brasília 70910-900, DF, Brazil
| | - João Santana da Silva
- Fiocruz-Bi-Institutional Translational Medicine Project, Oswaldo Cruz Foundation, Ribeirão Preto 14040-900, SP, Brazil
| | - Felipe Roberti Teixeira
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
| | - Roque Pacheco De Almeida
- Department of Medicine, Center for Biology and Health Sciences, Federal University of Sergipe (UFS), Aracaju 49060-108, SE, Brazil
| | - José M. C. Ribeiro
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, NIH/NIAID, Rockville, MD 20892, USA
| | - Sandra Regina Maruyama
- Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos (UFSCar), São Carlos 13565-905, SP, Brazil; (N.T.T.); (F.R.T.)
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11
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Kaushal RS, Naik N, Prajapati M, Rane S, Raulji H, Afu NF, Upadhyay TK, Saeed M. Leishmania species: A narrative review on surface proteins with structural aspects involved in host-pathogen interaction. Chem Biol Drug Des 2023; 102:332-356. [PMID: 36872849 DOI: 10.1111/cbdd.14227] [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: 01/13/2023] [Revised: 02/25/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023]
Abstract
In tropical and subtropical regions of the world, leishmaniasis is endemic and causes a range of clinical symptoms in people, from severe tegumentary forms (such as cutaneous, mucocutaneous, and diffuse leishmaniasis) to lethal visceral forms. The protozoan parasite of the genus Leishmania causes leishmaniasis, which is still a significant public health issue, according to the World Health Organization 2022. The public's worry about the neglected tropical disease is growing as new foci of the illness arise, which are exacerbated by alterations in behavior, changes in the environment, and an enlarged range of sand fly vectors. Leishmania research has advanced significantly during the past three decades in a few different avenues. Despite several studies on Leishmania, many issues, such as illness control, parasite resistance, parasite clearance, etc., remain unresolved. The key virulence variables that play a role in the pathogenicity-host-pathogen relationship of the parasite are comprehensively discussed in this paper. The important Leishmania virulence factors, such as Kinetoplastid Membrane Protein-11 (KMP-11), Leishmanolysin (GP63), Proteophosphoglycan (PPG), Lipophosphoglycan (LPG), Glycosylinositol Phospholipids (GIPL), and others, have an impact on the pathophysiology of the disease and enable the parasite to spread the infection. Leishmania infection may arise from virulence factors; they are treatable with medications or vaccinations more promptly and might greatly shorten the duration of treatment. Additionally, our research sought to present a modeled structure of a few putative virulence factors that might aid in the development of new chemotherapeutic approaches for the treatment of leishmaniasis. The predicted virulence protein's structure is utilized to design novel drugs, therapeutic targets, and immunizations for considerable advantage from a higher understanding of the host immune response.
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Affiliation(s)
- Radhey Shyam Kaushal
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara, 391760, Gujarat, India
| | - Nidhi Naik
- Department of Microbiology, Parul Institute of Applied Sciences, Parul University, Vadodara, 391760, Gujarat, India
| | - Maitri Prajapati
- Department of Microbiology, Parul Institute of Applied Sciences, Parul University, Vadodara, 391760, Gujarat, India
| | - Shruti Rane
- Department of Microbiology, Parul Institute of Applied Sciences, Parul University, Vadodara, 391760, Gujarat, India
| | - Himali Raulji
- Department of Microbiology, Parul Institute of Applied Sciences, Parul University, Vadodara, 391760, Gujarat, India
| | - Ngo Festus Afu
- Department of Biochemistry, Parul Institute of Applied Sciences, Parul University, Vadodara, 391760, Gujarat, India
| | - Tarun Kumar Upadhyay
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara, 391760, Gujarat, India
| | - Mohd Saeed
- Department of Biology, College of Sciences, University of Ha'il, P.O. Box 2440, Hail, 81411, Saudi Arabia
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12
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Ehya F, Kalantari S, Bandehpour M, Kazemi B. Preliminary Information of Iranian Lizard Leishmania Promastigote Transcriptome Sequencing by Next Generation Sequencing (NGS) Method. IRANIAN JOURNAL OF PARASITOLOGY 2023; 18:362-368. [PMID: 37886243 PMCID: PMC10597888 DOI: 10.18502/ijpa.v18i3.13759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 07/07/2023] [Indexed: 10/28/2023]
Abstract
Background A lizard Leishmania has been isolated from a lizard (Agama agilis) in Iran. Its genome sequence has not been determined, so far. Methods The study was done at Shahid Beheshti University of Medical Sciences, Tehran, Iran in 2017-2023. Leishmania promastigotes were cultured in RPMI1640 culture medium and collected at logarithmic phase by centrigugation. Parasite RNA was extracted by the Qiagene standard kit and its quantity and quality was determined and sequenced by NGS method with Illumina PE machine at BGI Company (China). Results The number of 8316 mRNA, 83 tRNA, 63 rRNA, 83 ncRNA, 5 snRNA, 1039 snoRNA, 36 region, and 3 repeat regions, 8343 CDS, 9597 Exon and 9292 Genes were identified in promastigote of Iranian lizard Leishmania. Conclusion Genomic elements of Iranian lizards Leishmania (with unique characteristics) were determined and identified by NGS system.
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Affiliation(s)
- Farveh Ehya
- Department of Biotechnology, Tarbiat Modares University, Tehran, Iran
| | - Sima Kalantari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
- Regenerative Medicine Group (REMED), Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Mojgan Bandehpour
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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13
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Jesus-Oliveira P, Silva-Couto L, Pinho N, Da Silva-Ferreira AT, Saboia-Vahia L, Cuervo P, Da-Cruz AM, Gomes-Silva A, Pinto EF. Identification of Immunodominant Proteins of the Leishmania (Viannia) naiffi SubProteome as Pan-Specific Vaccine Targets against Leishmaniasis. Vaccines (Basel) 2023; 11:1129. [PMID: 37514945 PMCID: PMC10386316 DOI: 10.3390/vaccines11071129] [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: 02/28/2023] [Revised: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 07/30/2023] Open
Abstract
Leishmaniasis is a wide-spectrum disease caused by parasites from Leishmania genus. A well-modulated immune response that is established after the long-lasting clinical cure of leishmaniasis can represent a standard requirement for a vaccine. Previous studies demonstrated that Leishmania (Viannia) naiffi causes benign disease and its antigens induce well-modulated immune responses in vitro. In this work we aimed to identify the immunodominant proteins present in the soluble extract of L. naiffi (sLnAg) as candidates for composing a pan-specific anti-leishmaniasis vaccine. After immunoblotting using cured patients of cutaneous leishmaniasis sera and proteomics approaches, we identified a group of antigenic proteins from the sLnAg. In silico analyses allowed us to select mildly similar proteins to the host; in addition, we evaluated the binding potential and degree of promiscuity of the protein epitopes to HLA molecules and to B-cell receptors. We selected 24 immunodominant proteins from a sub-proteome with 328 proteins. Homology analysis allowed the identification of 13 proteins with the most orthologues among seven Leishmania species. This work demonstrated the potential of these proteins as promising vaccine targets capable of inducing humoral and cellular pan-specific immune responses in humans, which may in the future contribute to the control of leishmaniasis.
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Affiliation(s)
- Prisciliana Jesus-Oliveira
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Luzinei Silva-Couto
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Nathalia Pinho
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Rede de Pesquisas de Neuroinflamação do Rio de Janeiro, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | | | - Leonardo Saboia-Vahia
- Laboratório de Vírus Respiratórios e Sarampo, Laboratório de Referência para COVID-19 (World Health Organization), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Patricia Cuervo
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Rede de Pesquisas de Neuroinflamação do Rio de Janeiro, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Alda Maria Da-Cruz
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Rede de Pesquisas em Saúde, Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro, Rio de Janeiro 20020-000, Brazil
- Disciplina de Parasitologia, Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade Estadual do Rio de Janeiro, Rio de Janeiro 20550-170, Brazil
- Instituto Nacional de Ciência e Tecnologia em Neuroimunomodulação (INCT-NIM), Rio de Janeiro 21040-900, Brazil
| | - Adriano Gomes-Silva
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Laboratório de Pesquisa Clínica em Micobacterioses, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Eduardo Fonseca Pinto
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Rede de Pesquisas em Saúde, Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro, Rio de Janeiro 20020-000, Brazil
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14
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Jacques Dit Lapierre TJW, Cruz MGFDML, Brito NPF, Resende DDM, Souza FDO, Pilau EJ, da Silva MFB, Neves BJ, Murta SMF, Rezende Júnior CDO. Hit-to-lead optimization of a pyrazinylpiperazine series against Leishmania infantum and Leishmania braziliensis. Eur J Med Chem 2023; 256:115445. [PMID: 37156183 DOI: 10.1016/j.ejmech.2023.115445] [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: 01/26/2023] [Revised: 04/17/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
An early hit-to-lead optimization of a novel pyrazinylpiperazine series against L. infantum and L. braziliensis has been performed after an extensive SAR focusing on the benzoyl fragment of hit (4). Deletion of the meta-Cl of (4) led to the obtention of the para-hydroxyl derivative (12), on which the design of most monosubstituted derivatives of the SAR was based. Further optimization of the series, involving disubstituted benzoyl fragments and the hydroxyl substituent of (12), allowed the obtention of a total of 15 compounds with increased antileishmanial potency (IC50 < 10 μM), nine of which displayed activity in the low micromolar range (IC50 < 5 μM). This optimization ultimately identified the ortho, meta-dihydroxyl derivative (46) as an early lead for this series (IC50 (L. infantum) = 2.8 μM, IC50 (L. braziliensis) = 0.2 μM). Additional assessment of some selected compounds against other trypanosomatid parasites revealed that this series is selective towards Leishmania parasites, and in silico ADMET predictions revealed satisfactory profiles for these compounds, allowing further lead optimization of the pyrazinylpiperazine class against Leishmania.
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Affiliation(s)
| | | | - Nícolas Peterson Ferreira Brito
- Laboratório de Síntese de Candidatos a Fármacos, Instituto de Química, Universidade Federal de Uberlândia (UFU), Uberlândia, MG, 38400-902, Brazil
| | - Daniela de Melo Resende
- Grupo de Genômica Funcional de Parasitos, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ Minas), Belo Horizonte, MG, 30190-002, Brazil
| | - Felipe de Oliveira Souza
- Laboratório de Biomoléculas e Espectrometria de Massas (LaBioMass), Universidade Estadual de Maringá (UEM), Maringá, PR, 807020-900, Brazil
| | - Eduardo Jorge Pilau
- Laboratório de Biomoléculas e Espectrometria de Massas (LaBioMass), Universidade Estadual de Maringá (UEM), Maringá, PR, 807020-900, Brazil
| | - Meryck Felipe Brito da Silva
- Laboratory of Cheminformatics (LabChem), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
| | - Bruno Junior Neves
- Laboratory of Cheminformatics (LabChem), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, 74605-170, Brazil
| | - Silvane Maria Fonseca Murta
- Grupo de Genômica Funcional de Parasitos, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ Minas), Belo Horizonte, MG, 30190-002, Brazil
| | - Celso de Oliveira Rezende Júnior
- Laboratório de Síntese de Candidatos a Fármacos, Instituto de Química, Universidade Federal de Uberlândia (UFU), Uberlândia, MG, 38400-902, Brazil.
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15
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Camacho E, González-de la Fuente S, Solana JC, Tabera L, Carrasco-Ramiro F, Aguado B, Requena JM. Leishmania infantum (JPCM5) Transcriptome, Gene Models and Resources for an Active Curation of Gene Annotations. Genes (Basel) 2023; 14:genes14040866. [PMID: 37107624 PMCID: PMC10137940 DOI: 10.3390/genes14040866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/25/2023] [Accepted: 04/01/2023] [Indexed: 04/08/2023] Open
Abstract
Leishmania infantum is one of the causative agents of visceral leishmaniases, the most severe form of leishmaniasis. An improved assembly for the L. infantum genome was published five years ago, yet delineation of its transcriptome remained to be accomplished. In this work, the transcriptome annotation was attained by a combination of both short and long RNA-seq reads. The good agreement between the results derived from both methodologies confirmed that transcript assembly based on Illumina RNA-seq and further delimitation according to the positions of spliced leader (SAS) and poly-A (PAS) addition sites is an adequate strategy to annotate the transcriptomes of Leishmania, a procedure previously used for transcriptome annotation in other Leishmania species and related trypanosomatids. These analyses also confirmed that the Leishmania transcripts boundaries are relatively slippery, showing extensive heterogeneity at the 5′- and 3′-ends. However, the use of RNA-seq reads derived from the PacBio technology (referred to as Iso-Seq) allowed the authors to uncover some complex transcription patterns occurring at particular loci that would be unnoticed by the use of short RNA-seq reads alone. Thus, Iso-Seq analysis provided evidence that transcript processing at particular loci would be more dynamic than expected. Another noticeable finding was the observation of a case of allelic heterozygosity based on the existence of chimeric Iso-Seq reads that might be generated by an event of intrachromosomal recombination. In addition, we are providing the L. infantum gene models, including both UTRs and CDS regions, that would be helpful for undertaking whole-genome expression studies. Moreover, we have built the foundations of a communal database for the active curation of both gene/transcript models and functional annotations for genes and proteins.
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Affiliation(s)
- Esther Camacho
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | - Jose Carlos Solana
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Laura Tabera
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Fernando Carrasco-Ramiro
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Begoña Aguado
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Jose M. Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Devsani N, Vemula D, Bhandari V. The glycoprotein gp63- a potential pan drug target for developing new antileishmanial agents. Biochimie 2023; 207:75-82. [PMID: 36473603 DOI: 10.1016/j.biochi.2022.11.015] [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: 08/14/2022] [Revised: 11/02/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Leishmaniasis is a tropical parasitic disease caused by Leishmania spp. They cause several presentations of illness ranging from cutaneous leishmaniasis to visceral leishmaniasis. The current arsenal of drugs to treat leishmaniasis is limited, and drug resistance further impedes the problem. Therefore, it is necessary to revisit the available information to identify an alternative or new target for treatment. The glycoprotein 63 (gp63), is a potential anti-leishmanial target that plays a significant role in host-pathogen interaction and virulence. Many studies are ongoing to develop gp63 inhibitors or use it as a vaccine target. In this review, we will discuss the potential of gp63 as a drug target. This review summarises the studies focusing on gp63 as a drug target and its inhibitors identified using in silico approaches.
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Affiliation(s)
- Namrata Devsani
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Divya Vemula
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Vasundhra Bhandari
- National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India.
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17
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Costa SS, Santos LMO, Freire LC, Tedeschi ALF, Ribeiro NR, Queiroz MHR, Neto EB, Pimenta DC, Galvani NC, Luiz GP, de Oliveira ME, de Ávila RAM, Carvalho AMRS, Brigido BVS, Reis AB, Fernandes APSM, Coelho EAF, Roatt BM, Menezes-Souza D, Duarte MC. Immunoproteomics approach for the discovery of antigens applied to the diagnosis of canine visceral leishmaniasis. Acta Trop 2023; 241:106865. [PMID: 36787861 DOI: 10.1016/j.actatropica.2023.106865] [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: 10/25/2022] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023]
Abstract
In the present study, an immunoproteomic approach using Leishmania infantum parasites isolated from naturally infected dogs from an endemic region of the disease, was carried out to identify new antigens to be used in the diagnosis of canine visceral leishmaniasis (CVL). Protein extracts, obtained from parasites isolated from asymptomatic (CanLA) and symptomatic (CanLS) dogs, were used to perform the two-dimensional gels. Western Blotting assays were carried out by employing a pool of sera from dogs with visceral leishmaniasis (CanLA or CanLS), healthy dogs from an endemic area, or dogs with similar diseases associated with cross-reactions (babesiosis and ehrlichiosis). With these results, it was possible to exclude the spots that showed a cross-reactivity of the sera from groups of healthy dogs, and those with babesiosis or ehrlichiosis. Taken together, 20 proteins were identified, 15 of which have already been described in the literature and 5 of which are hypothetical. An immunogenomic screen strategy was applied to identify conserved linear B-cell epitopes in the identified hypothetical proteins. Two peptides were synthesized and tested in ELISA experiments as a proof of concept for the validation of our immunoproteomics findings. The results demonstrated that the antigens presented sensitivity and specificity values ranging from 81.93% to 97.59% and 78.14 to 85.12%, respectively. As a comparative antigen, a preparation of a Leishmania extract showed sensitivity and specificity values of 75.90% and 74.88%, respectively. The present study was able to identify proteins capable of being used for the serodiagnosis of canine visceral leishmaniasis.
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Affiliation(s)
- Scarleth Silva Costa
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lucas Magno Oliveira Santos
- Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Larissa Chaves Freire
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Luiza Filizzola Tedeschi
- Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Naianda Rezende Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Emídio Beraldo Neto
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, São Paulo, Brazil
| | | | - Nathalia Coral Galvani
- Programa de Pós-Graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma, Santa Catarina, Brazil
| | - Gabriel Paulino Luiz
- Programa de Pós-Graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma, Santa Catarina, Brazil
| | - Maria Eduarda de Oliveira
- Programa de Pós-graduação em Microbiologia, Parasitologia e Patologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Ricardo Andrez Machado de Ávila
- Programa de Pós-Graduação em Ciências da Saúde, Universidade do Extremo Sul Catarinense, Criciúma, Santa Catarina, Brazil; Programa de Pós-graduação em Microbiologia, Parasitologia e Patologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Ana Maria Ravena Severino Carvalho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bryan Victor Serafim Brigido
- Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alexandre Barbosa Reis
- Laboratório de Morfopatologia, Núcleo de Pesquisas em Ciências Biológicas/NUPEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil; Laboratório de Pesquisas Clínicas, Programa de Pós-graduação em Ciências Farmacêuticas/CiPharma, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | | | - Eduardo Antonio Ferraz Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruno Mendes Roatt
- Laboratório de Morfopatologia, Núcleo de Pesquisas em Ciências Biológicas/NUPEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil; Laboratório de Pesquisas Clínicas, Programa de Pós-graduação em Ciências Farmacêuticas/CiPharma, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Daniel Menezes-Souza
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Mariana Costa Duarte
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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18
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Kamran M, Bhattacharjee R, Das S, Mukherjee S, Ali N. The paradigm of intracellular parasite survival and drug resistance in leishmanial parasite through genome plasticity and epigenetics: Perception and future perspective. Front Cell Infect Microbiol 2023; 13:1001973. [PMID: 36814446 PMCID: PMC9939536 DOI: 10.3389/fcimb.2023.1001973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Leishmania is an intracellular, zoonotic, kinetoplastid eukaryote with more than 1.2 million cases all over the world. The leishmanial chromosomes are divided into polymorphic chromosomal ends, conserved central domains, and antigen-encoding genes found in telomere-proximal regions. The genome flexibility of chromosomal ends of the leishmanial parasite is known to cause drug resistance and intracellular survival through the evasion of host defense mechanisms. Therefore, in this review, we discuss the plasticity of Leishmania genome organization which is the primary cause of drug resistance and parasite survival. Moreover, we have not only elucidated the causes of such genome plasticity which includes aneuploidy, epigenetic factors, copy number variation (CNV), and post-translation modification (PTM) but also highlighted their impact on drug resistance and parasite survival.
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Affiliation(s)
| | | | - Sonali Das
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Sohitri Mukherjee
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
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19
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Abstract
In this work we reviewed historical and recent data on Leishmania spp. infection combining data collected in Turkmenistan, Uzbekistan, Kazakhstan, Kyrgyzstan, Iran, China and Mongolia. We specifically focused on a complex of co-existing species (Leishmania major, Leishmania turanica and Leishmania gerbilli) sharing the same animal reservoirs and vectors. In addition, we analysed the presence of dsRNA viruses in these species and discussed future research directions to identify species-specific traits, which may determine susceptibility of different Leishmania spp. to viral infection.
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20
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Kumari P, Mamud A, Jha AN. Review on the Drug Intolerance and Vaccine Development for the Leishmaniasis. Curr Drug Targets 2023; 24:1023-1031. [PMID: 37823567 DOI: 10.2174/0113894501254585230927100440] [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: 03/23/2023] [Revised: 07/07/2023] [Accepted: 09/01/2023] [Indexed: 10/13/2023]
Abstract
Leishmaniasis is one of the Neglected Tropical Diseases (NTDs), a zoonotic disease of vector-borne nature that is caused by a protozoan parasite Leishmania. This parasite is transmitted by the vector sandfly into the human via a bite. Visceral leishmaniasis (VL), also called kala-azar, is the most fatal among the types of leishmaniasis, with high mortality mostly spread in the East Africa and South Asia regions. WHO report stated that approximately 3.3 million disabilities occur every year due to the disease along with approximately 50,000 annual deaths. The real matter of concern is that there is no particular effective medicine/vaccine available against leishmaniasis to date except a few approved drugs and chemotherapy for the infected patient. The current selection of small compounds was constrained, and their growing drug resistance had been a major worry. Additionally, the serious side effects on humans of the available therapy or drugs have made it essential to discover efficient and low-cost methods to speed up the development of new drugs against leishmaniasis. Ideally, the vaccine could be a low risk and effective alternative for both CL and VL and elicit long-lasting immunity against the disease. There are a number of vaccine candidates at various stages of clinical development and preclinical stage. However, none has successfully passed all clinical trials. But, the successful development and approval of commercially available vaccines for dogs against canine leishmaniasis (CanL) provides evidence that it can be possible for humans in distant future. In the present article, the approaches used for the development of vaccines for leishmaniasis are discussed and the progress being made is briefly reviewed.
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Affiliation(s)
- Priya Kumari
- Centre of Sustainable Polymers, Indian Institute of Technology, Guwahati, Assam, India
| | - Afrin Mamud
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Anupam Nath Jha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
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21
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Andrade YMFDS, Castro MVD, Tavares VDS, Souza RDSO, Faccioli LH, Lima JB, Sorgi CA, Borges VM, Araújo-Santos T. Polyunsaturated fatty acids alter the formation of lipid droplets and eicosanoid production in Leishmania promastigotes. Mem Inst Oswaldo Cruz 2023; 118:e220160. [PMID: 36888851 PMCID: PMC9991015 DOI: 10.1590/0074-02760220160] [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: 07/07/2022] [Accepted: 01/24/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND The knowledge about eicosanoid metabolism and lipid droplet (LD) formation in the Leishmania is very limited and new approaches are needed to identify which bioactive molecules are produced of them. OBJECTIVES Herein, we compared LDs and eicosanoids biogenesis in distinct Leishmania species which are etiologic agents of different clinical forms of leishmaniasis. METHODS For this, promastigotes of Leishmania amazonensis, L. braziliensis and L. infantum were stimulated with polyunsaturated fatty acids (PUFA) and LD and eicosanoid production was evaluated. We also compared mutations in structural models of human-like cyclooxygenase-2 (GP63) and prostaglandin F synthase (PGFS) proteins, as well as the levels of these enzymes in parasite cell extracts. FINDINGS PUFAs modulate the LD formation in L. braziliensis and L. infantum. Leishmania spp with equivalent tissue tropism had same protein mutations in GP63 and PGFS. No differences in GP63 production were observed among Leishmania spp, however PGFS production increased during the parasite differentiation. Stimulation with arachidonic acid resulted in elevated production of hydroxyeicosatetraenoic acids compared to prostaglandins. MAIN CONCLUSIONS Our data suggest LD formation and eicosanoid production are distinctly modulated by PUFAS dependent of Leishmania species. In addition, eicosanoid-enzyme mutations are more similar between Leishmania species with same host tropism.
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Affiliation(s)
| | - Monara Viera de Castro
- Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil
| | - Victor de Souza Tavares
- Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil
| | - Rayane da Silva Oliveira Souza
- Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil
| | - Lúcia Helena Faccioli
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Ribeirão Preto, SP, Brasil
| | - Jonilson Berlink Lima
- Fundação Oswaldo Cruz-Fiocruz, Instituto Gonçalo Moniz, Salvador, BA, Brasil.,Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil.,Universidade Federal da Bahia, Faculdade de Medicina, Salvador, BA, Brasil
| | | | - Valéria M Borges
- Fundação Oswaldo Cruz-Fiocruz, Instituto Gonçalo Moniz, Salvador, BA, Brasil.,Universidade Federal da Bahia, Faculdade de Medicina, Salvador, BA, Brasil
| | - Théo Araújo-Santos
- Fundação Oswaldo Cruz-Fiocruz, Instituto Gonçalo Moniz, Salvador, BA, Brasil.,Universidade Federal do Oeste da Bahia, Centro das Ciências Biológicas e da Saúde, Núcleo de Estudos de Agentes Infecciosos e Vetores, Barreiras, BA, Brasil
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An RNA Interference (RNAi) Toolkit and Its Utility for Functional Genetic Analysis of Leishmania ( Viannia). Genes (Basel) 2022; 14:genes14010093. [PMID: 36672832 PMCID: PMC9858808 DOI: 10.3390/genes14010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
RNA interference (RNAi) is a powerful tool whose efficacy against a broad range of targets enables functional genetic tests individually or systematically. However, the RNAi pathway has been lost in evolution by a variety of eukaryotes including most Leishmania sp. RNAi was retained in species of the Leishmania subgenus Viannia, and here we describe the development, optimization, and application of RNAi tools to the study of L. (Viannia) braziliensis (Lbr). We developed vectors facilitating generation of long-hairpin or "stem-loop" (StL) RNAi knockdown constructs, using GatewayTM site-specific recombinase technology. A survey of applications of RNAi in L. braziliensis included genes interspersed within multigene tandem arrays such as quinonoid dihydropteridine reductase (QDPR), a potential target or modulator of antifolate sensitivity. Other tests include genes involved in cell differentiation and amastigote proliferation (A600), and essential genes of the intraflagellar transport (IFT) pathway. We tested a range of stem lengths targeting the L. braziliensis hypoxanthine-guanine phosphoribosyl transferase (HGPRT) and reporter firefly luciferase (LUC) genes and found that the efficacy of RNAi increased with stem length, and fell off greatly below about 128 nt. We used the StL length dependency to establish a useful 'hypomorphic' approach not possible with other gene ablation strategies, with shorter IFT140 stems yielding viable cells with compromised flagellar morphology. We showed that co-selection for RNAi against adenine phosphoryl transferase (APRT1) using 4-aminopyrazolpyrimidine (APP) could increase the efficacy of RNAi against reporter constructs, a finding that may facilitate improvements in future work. Thus, for many genes, RNAi provides a useful tool for studying Leishmania gene function with some unique advantages.
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Comparative Genomic Analyses of New and Old World Viscerotropic Leishmanine Parasites: Further Insights into the Origins of Visceral Leishmaniasis Agents. Microorganisms 2022; 11:microorganisms11010025. [PMID: 36677318 PMCID: PMC9865424 DOI: 10.3390/microorganisms11010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Visceral leishmaniasis (VL), also known as kala-azar, is an anthropozoonotic disease affecting human populations on five continents. Aetiologic agents belong to the Leishmania (L.) donovani complex. Until the 1990s, three leishmanine parasites comprised this complex: L. (L.) donovani Laveran & Mesnil 1903, L. (L.) infantum Nicolle 1908, and L. (L.) chagasi Lainson & Shaw 1987 (=L. chagasi Cunha & Chagas 1937). The VL causal agent in the New World (NW) was previously identified as L. (L.) chagasi. After the development of molecular characterization, however, comparisons between L. (L.) chagasi and L. (L.) infantum showed high similarity, and L. (L.) chagasi was then regarded as synonymous with L. (L.) infantum. It was, therefore, suggested that L. (L.) chagasi was not native to the NW but had been introduced from the Old World by Iberian colonizers. However, in light of ecological evidence from the NW parasite’s enzootic cycle involving a wild phlebotomine vector (Lutzomyia longipalpis) and a wild mammal reservoir (the fox, Cerdocyon thous), we have recently analyzed by molecular clock comparisons of the DNA polymerase alpha subunit gene the whole-genome sequence of L. (L.) infantum chagasi of the most prevalent clinical form, atypical dermal leishmaniasis (ADL), from Honduras (Central America) with that of the same parasite from Brazil (South America), as well as those of L. (L.) donovani (India) and L. (L.) infantum (Europe), which revealed that the Honduran parasite is older ancestry (382,800 ya) than the parasite from Brazil (143,300 ya), L. (L.) donovani (33,776 ya), or L. (L.) infantum (13,000 ya). In the present work, we have now amplified the genomic comparisons among these leishmanine parasites, exploring mainly the variations in the genome for each chromosome, and the number of genomic SNPs for each chromosome. Although the results of this new analysis have confirmed a high genomic similarity (~99%) among these parasites [except L. (L.) donovani], the Honduran parasite revealed a single structural variation on chromosome 17, and the highest frequency of genomic SNPs (more than twice the number seen in the Brazilian one), which together to its extraordinary ancestry (382,800 ya) represent strong evidence that L. (L.) chagasi/L. (L.) infantum chagasi is, in fact, native to the NW, and therefore with valid taxonomic status. Furthermore, the Honduran parasite, the most ancestral viscerotropic leishmanine parasite, showed genomic and clinical taxonomic characteristics compatible with a new Leishmania species causing ADL in Central America.
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24
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Alaeenovin E, Parvizi P, Ghafari SM. Two Leishmania species separation targeting the ITS-rDNA and Cyt b genes by developing and evaluating HRM- qPCR. Rev Soc Bras Med Trop 2022; 55:S0037-86822022000100342. [PMID: 36542013 PMCID: PMC9757716 DOI: 10.1590/0037-8682-0186-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Incidence of Cutaneous Leishmaniasis as an infectious and neglected disease is increasing, for the diagnosis of which several traditional methods and conventional PCR techniques have been developed, employing different genes for species identification. METHODS Leishmania parasites were sampled, DNA was extracted, and new specific and sensitive primers were designed. Two ITS-rDNA and Cyt b genes were targeted by qPCR using the High- Resolution Melting method to identify Leishmania parasites. The standard curves were drawn, compared, and identified by high-resolution melting curve analysis. RESULTS Melting temperature and Cycle of Threshold of ITS-rDNA was higher than Cyt b but Cyt b was more sensitive than ITS-rDNA when Leishmania major and Leishmania tropica were analyzed and evaluated. By aligning melt curves, normalizing fluorescence curves, and difference plotting melt curves, each Leishmania species was distinguished easily. L. major and L. tropica were separated at 83.6 °C and 84.7 °C, respectively, with less than 0.9 °C of temperature difference. Developing sensitivity and specificity of real-time PCR based on EvaGreen could detect DNA concentration to less than one pmol. CONCLUSIONS Precise identification of Leishmania parasites is crucial for strategies of disease control. Real-time PCR using EvaGreen provides rapid, highly sensitive, and specific detection of parasite's DNA. The modified High-Resolution Melting could determine unique curves and was able to detect single nucleotide polymorphisms according to small differences in the nucleotide content of Leishmania parasites.
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Affiliation(s)
- Elnaz Alaeenovin
- Pasteur Institute of Iran, Molecular Systematics Laboratory, Parasitology Department, Tehran, Iran
| | - Parviz Parvizi
- Pasteur Institute of Iran, Molecular Systematics Laboratory, Parasitology Department, Tehran, Iran
| | - Seyedeh Maryam Ghafari
- Pasteur Institute of Iran, Molecular Systematics Laboratory, Parasitology Department, Tehran, Iran
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25
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Bigot S, Leprohon P, Vasquez A, Bhadoria R, Skouta R, Ouellette M. Thiophene derivatives activity against the protozoan parasite Leishmania infantum. Int J Parasitol Drugs Drug Resist 2022; 21:13-20. [PMID: 36525934 PMCID: PMC9772499 DOI: 10.1016/j.ijpddr.2022.11.004] [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: 08/31/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/26/2022]
Abstract
Treatments against leishmaniasis are limited and the development of new molecules is crucial. One class of developmental drug that has shown activity against the parasite Leishmania are thiophene derivatives. Here we synthetized thirty-eight novel thiophene compounds and characterized their activity and potential for resistance against L. infantum. Half of the molecules had an EC50 in the low micromolar range, the piperidine derivatives being more potent than the tetramethylpyran derivatives. Resistance was challenging to select for, and resistant cells could only be raised against one (GC1-19) of the four most active compounds. Using chemogenomic screens we show that a gene conversion event at the ABCG2 locus as well as the overexpression of a tryparedoxin peroxidase are responsible for a weak but significant resistance to the GC1-19 drug candidate. Together, our results suggest that thiophene is a scaffold of interest for further drug development against leishmaniasis.
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Affiliation(s)
- Sophia Bigot
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec, Canada,Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec City, Quebec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec, Canada,Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec City, Quebec, Canada
| | - Abimael Vasquez
- Department of Biology, University of Massachusetts, Amherst, MA, USA
| | - Rohit Bhadoria
- Department of Biology, University of Massachusetts, Amherst, MA, USA
| | - Rachid Skouta
- Department of Biology, University of Massachusetts, Amherst, MA, USA,Department of Chemistry, University of Massachusetts, Amherst, MA, USA,Corresponding author. University of Massachusetts Amherst, MA, 01003, USA.
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec, Canada,Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec City, Quebec, Canada,Corresponding author. Centre de Recherche du CHU Québec, 2705, Boulevard Laurier, Quebec City, Quebec, G1V 4G2, Canada.
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Pacakova L, Harant K, Volf P, Lestinova T. Three types of Leishmania mexicana amastigotes: Proteome comparison by quantitative proteomic analysis. Front Cell Infect Microbiol 2022; 12:1022448. [DOI: 10.3389/fcimb.2022.1022448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
Leishmania is the unicellular parasite transmitted by phlebotomine sand fly bite. It exists in two different forms; extracellular promastigotes, occurring in the gut of sand flies, and intracellular, round-shaped amastigotes residing mainly in vertebrate macrophages. As amastigotes originating from infected animals are often present in insufficient quality and quantity, two alternative types of amastigotes were introduced for laboratory experiments: axenic amastigotes and amastigotes from macrophages infected in vitro. Nevertheless, there is very little information about the degree of similarity/difference among these three types of amastigotes on proteomic level, whose comparison is crucial for assessing the suitability of using alternative types of amastigotes in experiments. In this study, L. mexicana amastigotes obtained from lesion of infected BALB/c mice were proteomically compared with alternatively cultivated amastigotes (axenic and macrophage-derived ones). Amastigotes of all three types were isolated, individually treated and analysed by LC-MS/MS proteomic analysis with quantification using TMT10-plex isobaric labeling. Significant differences were observed in the abundance of metabolic enzymes, virulence factors and proteins involved in translation and condensation of DNA. The most pronounced differences were observed between axenic amastigotes and lesion-derived amastigotes, macrophage-derived amastigotes were mostly intermediate between axenic and lesion-derived ones.
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Cerone M, Roberts M, Smith TK. The lipidome of Crithidia fasiculataand its plasticity. Front Cell Infect Microbiol 2022; 12:945750. [DOI: 10.3389/fcimb.2022.945750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Crithidia fasiculata belongs to the trypanosomatidae order of protozoan parasites, bearing close relation to other kinetoplastid parasites such as Trypanosoma brucei and Leishmania spp. As an early diverging lineage of eukaryotes, the study of kinetoplastid parasites has provided unique insights into alternative mechanisms to traditional eukaryotic metabolic pathways. Crithidia are a monogenetic parasite for mosquito species and have two distinct lifecycle stages both taking place in the mosquito gut. These consist of a motile choanomastigote form and an immotile amastigote form morphologically similar to amastigotes in Leishmania. Owing to their close relation to Leishmania, Crithidia are a growing research tool, with continuing interest in its use as a model organism for kinetoplastid research with the added benefit that they are non-pathogenic to humans and can be grown with no special equipment or requirements for biological containment. Although comparatively little research has taken place on Crithidia, similarities to other kinetoplast species has been shown in terms of energy metabolism and genetics. Crithidia also show similarities to kinetoplastids in their production of the monosaccharide D-arabinopyranose similar to Leishmania, which is incorporated into a lipoarabinogalactan a major cell surface GPI-anchored molecule. Additionally, Crithidia have been used as a eukaryotic expression system to express proteins from other kinetoplastids and potentially other eukaryotes including human proteins allowing various co- and post-translational protein modifications to the recombinant proteins. Despite the obvious usefulness and potential of this organism very little is known about its lipid metabolism. Here we describe a detailed lipidomic analyses and demonstrate the possible placidity of Crithidia’s lipid metabolis. This could have important implications for biotechnology approaches and how other kinetoplastids interact with, and scavenge nutrients from their hosts.
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Abrahim M, Machado E, Alvarez-Valín F, de Miranda AB, Catanho M. Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps' Genomes. Genome Biol Evol 2022; 14:6754225. [PMID: 36208292 PMCID: PMC9576210 DOI: 10.1093/gbe/evac142] [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: 08/10/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 01/24/2023] Open
Abstract
Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and mechanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames, with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages.
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Affiliation(s)
- Mayla Abrahim
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Edson Machado
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Brazil
| | - Fernando Alvarez-Valín
- Unidad de Genómica Evolutiva, Sección Biomatemática, Universidad de la República del Uruguay, Montevideo, Uruguay
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Llanes A, Cruz G, Morán M, Vega C, Pineda VJ, Ríos M, Penagos H, Suárez JA, Saldaña A, Lleonart R, Restrepo CM. Genomic diversity and genetic variation of Leishmania panamensis within its endemic range. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105342. [PMID: 35878820 DOI: 10.1016/j.meegid.2022.105342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Species belonging to the Leishmania (Viannia) subgenus are important causative agents of cutaneous and mucocutaneous leishmaniasis in Central and South America. These parasites possess several distinctive biological features that are influenced by their genetics, population structure, and genome instability. To date, several studies have revealed varying degrees of genetic diversity within Leishmania species. Particularly, in species of the L. (Viannia) subgenus, a generalized high intraspecific genetic diversity has been reported, although, conflicting conclusions have been drawn using different molecular techniques. Despite being the most common Leishmania species circulating in Panama and Colombia, few studies have analyzed clinical samples of Leishmania panamensis using whole-genome sequencing, and their restricted number of samples has limited the information they can provide to understand the population structure of L. panamensis. Here, we used next generation sequencing (NGS) to explore the genetic diversity of L. panamensis within its endemic range, analyzing data from 43 isolates of Colombian and Panamanian origin. Our results show the occurrence of three well-defined geographically correlated groups, and suggests the possible occurrence of additional phylogeographic groups. Furthermore, these results support the existence of a mixed mode of reproduction in L. panamensis, with varying frequencies of events of genetic recombination occurring primarily within subpopulations of closely related strains. This study offers important insights into the population genetics and reproduction mode of L. panamensis, paving the way to better understand their population structure and the emergence and maintenance of key eco-epidemiological traits.
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Affiliation(s)
- Alejandro Llanes
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama
| | - Génesis Cruz
- Escuela de Biología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panama City, Panama, Panama
| | - Mitchelle Morán
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama
| | - Carlos Vega
- Escuela de Biología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panama City, Panama, Panama
| | - Vanessa J Pineda
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama
| | - Margarita Ríos
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama
| | - Homero Penagos
- Hospital Regional Dr. Rafael Hernández, Caja de Seguro Social, David, Chiriquí, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama
| | - José A Suárez
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama
| | - Azael Saldaña
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama
| | - Ricardo Lleonart
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama.
| | - Carlos M Restrepo
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama.
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Vega-Benedetti AF, Loi E, Zavattari P. DNA methylation alterations caused by Leishmania infection may generate a microenvironment prone to tumour development. Front Cell Infect Microbiol 2022; 12:984134. [PMID: 36105147 PMCID: PMC9465093 DOI: 10.3389/fcimb.2022.984134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/10/2022] [Indexed: 01/10/2023] Open
Abstract
DNA methylation is an epigenetic signature consisting of a methyl group at the 5’ cytosine of CpG dinucleotides. Modifications in DNA methylation pattern have been detected in cancer and infectious diseases and may be associated with gene expression changes. In cancer development DNA methylation aberrations are early events whereas in infectious diseases these epigenetic changes may be due to host/pathogen interaction. In particular, in leishmaniasis, a parasitic disease caused by the protozoan Leishmania, DNA methylation alterations have been detected in macrophages upon infection with Leishmania donovani and in skin lesions from patients with cutaneous leishmaniasis. Interestingly, different types of cancers, such as cutaneous malignant lesions, lymphoma and hepatocellular carcinoma, have been diagnosed in patients with a history of leishmaniasis. In fact, it is known that there exists an association between cancer and infectious diseases. Leishmania infection may increase susceptibility to develop cancer, but the mechanisms involved are not entirely clear. Considering these aspects, in this review we discuss the hypothesis that DNA methylation alterations induced by Leishmania may trigger tumorigenesis in long term infection since these epigenetic modifications may enhance and accumulate during chronic leishmaniasis.
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Lesani M, Gosmanov C, Paun A, Lewis MD, McCall LI. Impact of Visceral Leishmaniasis on Local Organ Metabolism in Hamsters. Metabolites 2022; 12:metabo12090802. [PMID: 36144206 PMCID: PMC9506185 DOI: 10.3390/metabo12090802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Leishmania is an intracellular parasite with different species pathogenic to humans and causing the disease leishmaniasis. Leishmania donovani causes visceral leishmaniasis (VL) that manifests as hepatosplenomegaly, fever, pancytopenia and hypergammaglobulinemia. If left without treatment, VL can cause death, especially in immunocompromised people. Current treatments have often significant adverse effects, and resistance has been reported in some countries. Determining the metabolites perturbed during VL can lead us to find new treatments targeting disease pathogenesis. We therefore compared metabolic perturbation between L. donovani-infected and uninfected hamsters across organs (spleen, liver, and gut). Metabolites were extracted, analyzed by liquid chromatography-mass spectrometry, and processed with MZmine and molecular networking to annotate metabolites. We found few metabolites commonly impacted by infection across all three sites, including glycerophospholipids, ceramides, acylcarnitines, peptides, purines and amino acids. In accordance with VL symptoms and parasite tropism, we found a greater overlap of perturbed metabolites between spleen and liver compared to spleen and gut, or liver and gut. Targeting pathways related to these metabolite families would be the next focus that can lead us to find more effective treatments for VL.
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Affiliation(s)
- Mahbobeh Lesani
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Camil Gosmanov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Andrea Paun
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Michael D. Lewis
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Laura-Isobel McCall
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
- Correspondence:
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Anuntasomboon P, Siripattanapipong S, Unajak S, Choowongkomon K, Burchmore R, Leelayoova S, Mungthin M, E-kobon T. Making the Most of Its Short Reads: A Bioinformatics Workflow for Analysing the Short-Read-Only Data of Leishmania orientalis (Formerly Named Leishmania siamensis) Isolate PCM2 in Thailand. BIOLOGY 2022; 11:biology11091272. [PMID: 36138751 PMCID: PMC9495971 DOI: 10.3390/biology11091272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Leishmaniasis is a parasitic disease caused by flagellated protozoa of the genus Leishmania. Multiple genome sequencing platforms have been employed to complete Leishmania genomes at the expense of high cost. This study proposes an integrative bioinformatic workflow for assembling only the short-read data of Leishmania orientalis isolate PCM2 from Thailand and produce an acceptable-quality genome for further genomic analysis. This workflow gives extensive information required for identifying strain-specific markers and virulence-associated genes useful for drug and vaccine development before a more exhaustive and expensive investigation. Abstract Background: Leishmania orientalis (formerly named Leishmania siamensis) has been neglected for years in Thailand. The genomic study of L. orientalis has gained much attention recently after the release of the first high-quality reference genome of the isolate LSCM4. The integrative approach of multiple sequencing platforms for whole-genome sequencing has proven effective at the expense of considerably expensive costs. This study presents a preliminary bioinformatic workflow including the use of multi-step de novo assembly coupled with the reference-based assembly method to produce high-quality genomic drafts from the short-read Illumina sequence data of L. orientalis isolate PCM2. Results: The integrating multi-step de novo assembly by MEGAHIT and SPAdes with the reference-based method using the L. enriettii genome and salvaging the unmapped reads resulted in the 30.27 Mb genomic draft of L. orientalis isolate PCM2 with 3367 contigs and 8887 predicted genes. The results from the integrated approach showed the best integrity, coverage, and contig alignment when compared to the genome of L. orientalis isolate LSCM4 collected from the northern province of Thailand. Similar patterns of gene ratios and frequency were observed from the GO biological process annotation. Fifty GO terms were assigned to the assembled genomes, and 23 of these (accounting for 61.6% of the annotated genes) showed higher gene counts and ratios when results from our workflow were compared to those of the LSCM4 isolate. Conclusions: These results indicated that our proposed bioinformatic workflow produced an acceptable-quality genome of L. orientalis strain PCM2 for functional genomic analysis, maximising the usage of the short-read data. This workflow would give extensive information required for identifying strain-specific markers and virulence-associated genes useful for drug and vaccine development before a more exhaustive and expensive investigation.
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Affiliation(s)
- Pornchai Anuntasomboon
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | | | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Richard Burchmore
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Saovanee Leelayoova
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok 10400, Thailand
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok 10400, Thailand
| | - Teerasak E-kobon
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: ; Tel.: +66-812-85-4672
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Ait Maatallah I, Akarid K, Lemrani M. Tissue tropism: Is it an intrinsic characteristic of Leishmania species? Acta Trop 2022; 232:106512. [PMID: 35568069 DOI: 10.1016/j.actatropica.2022.106512] [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: 03/22/2022] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 11/26/2022]
Abstract
The genus Leishmania comprises a wide range of species, some of which are pathogenic to humans and each of which has a different tissue preference, resulting in one of the three clinical forms of human leishmaniasis: visceral, cutaneous, or mucocutaneous. Although, all pathogenic species are deposited intradermally in the mammalian host upon an infectious sand fly bite, only the viscerotropic strains can leave the skin and reach the internal organs. We assume that Leishmania tissue tropism is not only the result of Leishmania genetic determinism but is also governed by the interaction of the parasite with different vectorial and human host elements. To shed light on these elements and key steps determining the course of the infection, we describe throughout this review the disease's progression from the early stages of infection taking place in the skin to the late stages succeeding in the parasite's visceral dissemination. Hence, we address the question of Leishmania tropism, through providing relevant hypotheses and answers gathered from the literature.
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Identification of Novel Inhibitor of Enoyl-Acyl Carrier Protein Reductase (InhA) Enzyme in Mycobacterium tuberculosis from Plant-Derived Metabolites: An In Silico Study. Antibiotics (Basel) 2022; 11:antibiotics11081038. [PMID: 36009907 PMCID: PMC9405319 DOI: 10.3390/antibiotics11081038] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 12/03/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb.) enoyl-acyl carrier protein (ACP) reductase (InhA) is validated as a useful target for tuberculosis therapy and is considered an attractive enzyme to drug discovery. This study aimed to identify the novel inhibitor of the InhA enzyme, a potential target of M.tb. involved in the type II fatty acid biosynthesis pathway that controls mycobacterial cell envelope synthesis. We compiled 80 active compounds from Ruta graveolens and citrus plants belonging to the Rutaceae family for pharmacokinetics and molecular docking analyses. The chemical structures of the 80 phytochemicals and the 3D structure of the target protein were retrieved from the PubChem database and RCSB Protein Data Bank, respectively. The evaluation of druglikeness was performed based on Lipinski’s Rule of Five, while the computed phytochemical properties and molecular descriptors were used to predict the ADMET of the compounds. Amongst these, 11 pharmacokinetically-screened compounds were further examined by performing molecular docking analysis with an InhA target using AutoDock 4.2. The docking results showed that gravacridonediol, a major glycosylated natural alkaloid from Ruta graveolens, might possess a promising inhibitory potential against InhA, with a binding energy (B.E.) of −10.80 kcal/mole and inhibition constant (Ki) of 600.24 nM. These contrast those of the known inhibitor triclosan, which has a B.E. of −6.69 kcal/mole and Ki of 12.43 µM. The binding efficiency of gravacridonediol was higher than that of the well-known inhibitor triclosan against the InhA target. The present study shows that the identified natural compound gravacridonediol possesses drug-like properties and also holds promise in inhibiting InhA, a key target enzyme of M.tb.
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Abstract
In mammalian cells, DNA double-strand breaks (DSBs) are mainly repaired by nonhomologous end joining (NHEJ) pathway. Ku (a heterodimer formed by Ku70 and Ku80 proteins) and DNA ligase IV are the core NHEJ factors. Ku could also be involved in other cellular processes, including telomere length regulation, DNA replication, transcription, and translation control. Leishmania, an early branching eukaryote and the causative agent of leishmaniasis, has no functional NHEJ pathway due to its lack of DNA ligase IV and other NHEJ factors but retains Ku70 and Ku80 proteins. In this study, we generated Leishmania donovani Ku70 disruption mutants and Ku70 and Ku80 double gene (Ku70/80) disruption mutants. We found that Leishmania Ku is still involved in DSB repair, possibly through its binding to DNA ends to block and slowdown 5′ end resections and Ku-Ku or other protein interactions. Depending on location of a DSB between the direct repeat genomic sequences, Leishmania Ku could have an inhibiting effect, no effect or a promoting effect on the DSB repair mediated by single strand annealing (SSA), the most frequently used DSB repair pathway in Leishmania. Ku70/80 proteins are also required for the healthy proliferation of Leishmania cells. Interestingly, unlike in Trypanosoma brucei and L. mexicana, Ku70/80 proteins are dispensable for maintaining the normal lengths of telomeres in L. donovani. We also show it is possible to reconstitute the two components (Ku and Ligase D) NHEJ pathway derived from Mycobacterium marinum in Leishmania. This improved DSB repair fidelity and efficiency in Leishmania and sets up an example that the bacterial NHEJ pathway can be successfully reconstructed in an NHEJ-deficient eukaryotic parasite. IMPORTANCE Nonhomologous end joining (NHEJ) is the most efficient double-stranded DNA break (DSB) repair pathway in mammalian cells. In contrast, the protozoan parasite Leishmania has no functional NHEJ pathway but retains the core NHEJ factors of Ku70 and Ku80 proteins. In this study, we found that Leishmania Ku heterodimers are still participating in DSB repair possibly through blocking 5′ end resections and Ku-Ku protein interactions. Depending on the DSB location, Ku could have an inhibiting or promoting effect on DSB repair mediated by the single-strand annealing repair pathway. Ku is also required for the normal growth of the parasite but surprisingly dispensable for maintaining the telomere lengths. Further, we show it is possible to introduce Mycobacterium marinum NHEJ pathway into Leishmania. Understanding DSB repair mechanisms of Leishmania may improve the CRISPR gene targeting specificity and efficiency and help identify new drug targets for this important human parasite.
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de Andrade Ferraz I, Carvalho AMRS, de Brito RCF, Roatt BM, Martins VT, Lage DP, Dos Reis Cruz L, Medeiros FAC, Gonçalves DU, da Costa Rocha MO, Coelho EAF, de Oliveira Mendes TA, Duarte MC, Menezes-Souza D. Development of an immunogen containing CD4 +/CD8 + T-cell epitopes for the prophylaxis of tegumentary leishmaniasis. Appl Microbiol Biotechnol 2022; 106:4627-4641. [PMID: 35759035 PMCID: PMC9244519 DOI: 10.1007/s00253-022-12033-7] [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: 05/04/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
Abstract
Abstract Tegumentary leishmaniasis (TL) is a disease of high severity and incidence in Brazil, and Leishmania braziliensis is its main etiological agent. The inefficiency of control measures, such as high toxicity and costs of current treatments and the lack of effective immunoprophylactic strategies, makes the development of vaccines indispensable and imminent. In this light, the present work developed a gene encoding multiple T-cell (CD4+/CD8+) epitope, derived from conserved proteins found in Leishmania species and associated with TL, to generate a chimeric protein (rMEP/TL) and compose a vaccine formulation. For this, six T-cell epitopes were selected by immunoinformatics approaches from proteins present in the amastigote stage and associated with host-parasite interactions. The following formulations were then tested in an L. braziliensis murine infection model: rMEP/TL in saline or associated with MPLA-PHAD®. Our data revealed that, after immunization (three doses; 14-day intervals) and subsequent challenging, rMEP/TL and rMEP/TL + MPLA-vaccinated mice showed an increased production of key immunological biomarkers of protection, such as IgG2a, IgG2a/IgG1, NO, CD4+, and CD8+ T-cells with IFN-γ and TNF-α production, associated with a reduction in CD4+IL-10+ and CD8+IL-10+ T-cells. Vaccines also induced the development of central (CD44highCD62Lhigh) and effector (CD44highCD62Llow) memory of CD4+ and CD8+ T-cells. These findings, associated with the observation of lower rates of parasite burdens in the vaccinated groups, when compared to the control groups, suggest that immunization with rMEP/TL and, preferably, associated with an adjuvant, may be considered an effective tool to prevent TL. Key points • Rational design approaches for vaccine development.
• Central and effector memory of CD4+ and CD8+ T-cells. • Vaccine comprised of rMEP/TL plus MPLA as an effective tool to prevent TL. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12033-7.
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Affiliation(s)
- Isabela de Andrade Ferraz
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil
| | - Ana Maria Ravena Severino Carvalho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil
| | - Rory Cristiane Fortes de Brito
- Núcleo de Pesquisas Em Ciências Biológicas/NUPEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, 35400-000, Brazil
| | - Bruno Mendes Roatt
- Núcleo de Pesquisas Em Ciências Biológicas/NUPEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, 35400-000, Brazil
| | - Vívian Tamietti Martins
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil
| | - Daniela Pagliara Lage
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil
| | - Luiza Dos Reis Cruz
- Laboratório de Química Orgânica Sintética, Instituto de Química, Universidade de Campinas, Campinas, Brazil
| | - Fernanda Alvarenga Cardoso Medeiros
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil
| | - Denise Utsch Gonçalves
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil
| | - Manoel Otávio da Costa Rocha
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil
| | - Eduardo Antonio Ferraz Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil.,Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | | | - Mariana Costa Duarte
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil.,Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Daniel Menezes-Souza
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil. .,Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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Valdivia HO, Roatt BM, Baptista RDP, Ottino J, Coqueiro-dos-Santos A, Sanders MJ, Reis AB, Cotton JA, Bartholomeu DC. Replacement of Leishmania (Leishmania) infantum Populations in an Endemic Focus of Visceral Leishmaniasis in Brazil. Front Cell Infect Microbiol 2022; 12:900084. [PMID: 35811682 PMCID: PMC9263273 DOI: 10.3389/fcimb.2022.900084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
Visceral leishmaniasis is an important global health problem with an estimated of 50,000 to 90,000 new cases per year. VL is the most serious form of leishmaniasis as it can be fatal in 95% of the cases if it remains untreated. VL is a particularly acute problem in Brazil which contributed with 97% of all cases reported in 2020 in the Americas. In this country, VL affects mainly the poorest people in both urban and rural areas and continues to have a high mortality rate estimated around 8.15%. Here, we performed a temporal parasite population study using whole genome sequence data from a set of 34 canine isolates sampled in 2008, 2012 and 2015 from a re-emergent focus in Southeastern Brazil. Our study found the presence of two distinct sexual subpopulations that corresponded to two isolation periods. These subpopulations diverged hundreds of years ago with no apparent gene flow between them suggesting a process of rapid replacement during a two-year period. Sequence comparisons and analysis of nucleotide diversity also showed evidence of balancing selection acting on transport-related genes and antigenic families. To our knowledge this is the first population genomic study showing a turn-over of parasite populations in an endemic region for leishmaniasis. The complexity and rapid adaptability of these parasites pose new challenges to control activities and demand more integrated approaches to understand this disease in New World foci.
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Affiliation(s)
- Hugo O. Valdivia
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- U.S. Naval Medical Research Unit Six, Department of Parasitology, Lima, Peru
| | - Bruno M. Roatt
- Núcleo de Pesquisas em Ciências Biológicas/NUPEB, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Rodrigo de Paula Baptista
- CTEGD- Center for Tropical and Emerging Global Diseases and IOB - Institute of Bioinformatics, University of Georgia, Athens, United States
- Houston Methodist Research Institute, Houston, United States
| | - Jennifer Ottino
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Anderson Coqueiro-dos-Santos
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Alexandre B. Reis
- Núcleo de Pesquisas em Ciências Biológicas/NUPEB, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - James A. Cotton
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Daniella C. Bartholomeu
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- *Correspondence: Daniella C. Bartholomeu,
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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
- *Correspondence: Mariana De Niz,
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Zakharova A, Albanaz ATS, Opperdoes FR, Škodová-Sveráková I, Zagirova D, Saura A, Chmelová L, Gerasimov ES, Leštinová T, Bečvář T, Sádlová J, Volf P, Lukeš J, Horváth A, Butenko A, Yurchenko V. Leishmania guyanensis M4147 as a new LRV1-bearing model parasite: Phosphatidate phosphatase 2-like protein controls cell cycle progression and intracellular lipid content. PLoS Negl Trop Dis 2022; 16:e0010510. [PMID: 35749562 PMCID: PMC9232130 DOI: 10.1371/journal.pntd.0010510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
Leishmaniasis is a parasitic vector-borne disease caused by the protistan flagellates of the genus Leishmania. Leishmania (Viannia) guyanensis is one of the most common causative agents of the American tegumentary leishmaniasis. It has previously been shown that L. guyanensis strains that carry the endosymbiotic Leishmania RNA virus 1 (LRV1) cause more severe form of the disease in a mouse model than those that do not. The presence of the virus was implicated into the parasite’s replication and spreading. In this respect, studying the molecular mechanisms of cellular control of viral infection is of great medical importance. Here, we report ~30.5 Mb high-quality genome assembly of the LRV1-positive L. guyanensis M4147. This strain was turned into a model by establishing the CRISPR-Cas9 system and ablating the gene encoding phosphatidate phosphatase 2-like (PAP2L) protein. The orthologue of this gene is conspicuously absent from the genome of an unusual member of the family Trypanosomatidae, Vickermania ingenoplastis, a species with mostly bi-flagellated cells. Our analysis of the PAP2L-null L. guyanensis showed an increase in the number of cells strikingly resembling the bi-flagellated V. ingenoplastis, likely as a result of the disruption of the cell cycle, significant accumulation of phosphatidic acid, and increased virulence compared to the wild type cells. Worldwide, over one million people are getting infected by the parasitic flagellates of the genus Leishmania annually leading to ~30,000 deaths. Notably, there is still no approved vaccine against human leishmaniases. A range of methods of forward and reverse genetics has recently been developed for several model Leishmania species. Unfortunately, these methods are often not transferrable to non-model species, which may be of even greater medical importance. Leishmania guyanensis is one of such cases. It frequently carries a symbiotic RNA virus that contributes to the development of a more aggressive form of leishmaniasis in an experimental murine model. In order to establish and optimize the system for genetic manipulations in L. guyanensis, we sequenced and annotated its genome. Next, we applied the CRISPR-Cas9 technology to target a gene of interest. This approach was validated by ablating a gene encoding a protein involved in lipid metabolism. In this work, we document that deletion of this gene leads to the disturbance of cell cycle and affects the ratio of critical intracellular lipids. We believe that our study will facilitate research into more effective treatment of leishmaniases.
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Affiliation(s)
- Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Amanda T. S. Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R. Opperdoes
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Diana Zagirova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Lˇubomíra Chmelová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Evgeny S. Gerasimov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Tereza Leštinová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomáš Bečvář
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jovana Sádlová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Anton Horváth
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- * E-mail:
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Franssen SU, Sanders MJ, Berriman M, Petersen CA, Cotton JA. Geographic Origin and Vertical Transmission of Leishmania infantum Parasites in Hunting Hounds, United States. Emerg Infect Dis 2022; 28:1211-1223. [PMID: 35608628 PMCID: PMC9155895 DOI: 10.3201/eid2806.211746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Vertical transmission of leishmaniasis is common but is difficult to study against the background of pervasive vector transmission. We present genomic data from dogs in the United States infected with Leishmania infantum parasites; these infections have persisted in the apparent absence of vector transmission. We demonstrate that these parasites were introduced from the Old World separately and more recently than L. infantum from South America. The parasite population shows unusual genetics consistent with a lack of meiosis: a high level of heterozygous sites shared across all isolates and no decrease in linkage with genomic distance between variants. Our data confirm that this parasite population has been evolving with little or no sexual reproduction. This demonstration of vertical transmission has profound implications for the population genetics of Leishmania parasites. When investigating transmission in complex natural settings, considering vertical transmission alongside vector transmission is vital.
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Prava J, Pan A. In silico analysis of Leishmania proteomes and protein-protein interaction network: Prioritizing therapeutic targets and drugs for repurposing to treat leishmaniasis. Acta Trop 2022; 229:106337. [PMID: 35134348 DOI: 10.1016/j.actatropica.2022.106337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/07/2022] [Accepted: 01/29/2022] [Indexed: 01/31/2023]
Abstract
Leishmaniasis is a serious world health problem and its current therapies have several limitations demanding to develop novel therapeutics for this disease. The present study aims to prioritize novel broad-spectrum targets using proteomics and protein-protein interaction network (PPIN) data for 11 Leishmania species. Proteome comparison and host non-homology analysis resulted in 3605 pathogen-specific conserved core proteins. Gene ontology analysis indicated their involvement in major molecular functions like DNA binding, transportation, dioxygenase, and catalytic activity. PPIN analysis of these core proteins identified eight hub proteins (viz., vesicle-trafficking protein (LBRM2903_190011800), ribosomal proteins S17 (LBRM2903_34004790) and L2 (LBRM2903_080008100), eukaryotic translation initiation factor 3 (LBRM2903_350086700), replication factor A (LBRM2903_150008000), U3 small nucleolar RNA-associated protein (LBRM2903_340025600), exonuclease (LBRM2903_200021800), and mitochondrial RNA ligase (LBRM2903_200074100)). Among the hub proteins, six were classified as drug targets and two as vaccine candidates. Further, druggability analysis indicated three hub proteins, namely eukaryotic translation initiation factor 3, ribosomal proteins S17 and L2 as druggable. Their three-dimensional structures were modelled and docked with the identified ligands (2-methylthio-N6-isopentenyl-adenosine-5'-monophosphate, artenimol and omacetaxine mepesuccinate). These ligands could be experimentally validated (in vitro and in vivo) and repurposed for the development of novel antileishmanial agents.
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The History of Live Attenuated Centrin Gene-Deleted Leishmania Vaccine Candidates. Pathogens 2022; 11:pathogens11040431. [PMID: 35456106 PMCID: PMC9025045 DOI: 10.3390/pathogens11040431] [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: 03/07/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/08/2023] Open
Abstract
Leishmaniasis, caused by an infection of the Leishmania protozoa, is a neglected tropical disease and a major health problem in tropical and subtropical regions of the world, with approximately 350 million people worldwide at risk and 2 million new cases occurring annually. Current treatments for leishmaniasis are not highly efficacious and are associated with high costs, especially in low- and middle-income endemic countries, and high toxicity. Due to a surge in the incidence of leishmaniases worldwide, the development of new strategies such as a prophylactic vaccine has become a high priority. However, the ability of Leishmania to undermine immune recognition has limited our efforts to design safe and efficacious vaccines against leishmaniasis. Numerous antileishmanial vaccine preparations based on DNA, subunit, and heat-killed parasites with or without adjuvants have been tried in several animal models but very few have progressed beyond the experimental stage. However, it is known that people who recover from Leishmania infection can be protected lifelong against future infection, suggesting that a successful vaccine requires a controlled infection to develop immunologic memory and subsequent long-term immunity. Live attenuated Leishmania parasites that are non-pathogenic and provide a complete range of antigens similarly to their wild-type counterparts could evoke such memory and, thus, would be effective vaccine candidates. Our laboratory has developed several live attenuated Leishmania vaccines by targeted centrin gene disruptions either by homologous recombination or, more recently, by using genome editing technologies involving CRISPR-Cas9. In this review, we focused on the sequential history of centrin gene-deleted Leishmania vaccine development, along with the characterization of its safety and efficacy. Further, we discussed other major considerations regarding the transition of dermotropic live attenuated centrin gene-deleted parasites from the laboratory to human clinical trials.
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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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Anuntasomboon P, Siripattanapipong S, Unajak S, Choowongkomon K, Burchmore R, Leelayoova S, Mungthin M, E-kobon T. Comparative Draft Genomes of Leishmania orientalis Isolate PCM2 (Formerly Named Leishmania siamensis) and Leishmania martiniquensis Isolate PCM3 from the Southern Province of Thailand. BIOLOGY 2022; 11:biology11040515. [PMID: 35453714 PMCID: PMC9031872 DOI: 10.3390/biology11040515] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 11/22/2022]
Abstract
Simple Summary This study successfully sequenced the draft genomes of the southern isolates of Leishmania orientalis and Leishmania martiniquensis in Thailand. The comparison with the genomes of the northern isolates revealed species-level similarity with a level of genome and proteome variation, suggesting the different emerging strains. Comparing the proteins of these southern strains to those of the northern ones and 14 other Leishmania species showed six protein groups with numerous unique proteins: 53 for the southern strain PCM2 of L. orientalis and 97 for the strain PCM3 of L. martiniquensis. Some of these proteins were related to virulence, drug resistance, drug target, and stress response, which could be targeted for further experimental characterization. Therefore, the findings could initiate further genetic and population genomic investigation, and the close monitoring of L. orientalis and L. martiniquensis in Thailand and neighboring regions. Abstract (1) Background: Autochthonous leishmaniasis, a sandfly-borne disease caused by the protozoan parasites Leishmania orientalis (formerly named Leishmania siamensis) and Leishmania martiniquensis, has been reported for immunocompromised and immunocompetent patients in the southern province of Thailand. Apart from the recent genomes of the northern isolates, limited information is known on the emergence and genetics of these parasites. (2) Methods: This study sequenced and compared the genomes of L. orientalis isolate PCM2 and L. martiniquensis isolate PCM3 with those of the northern isolates and other 14 Leishmania species using short-read whole-genome sequencing methods and comparative bioinformatic analyses. (3) Results: The genomes of the southern isolates of L. orientalis and L. martiniquensis were 30.01 Mbp and 32.39 Mbp, and the comparison with the genomes of the northern isolates revealed species-level similarity with a level of genome and proteome variation, suggesting the different strains. Comparative proteome analysis showed six protein groups with 53 unique proteins for the strain PCM2 and 97 for the strain PCM3. Certain proteins were related to virulence, drug resistance, and stress response. (4) Conclusion: Therefore, the findings could indicate the need for more genetic and population genomic investigation, and the close monitoring of L. orientalis and L. martiniquensis in Thailand and neighboring regions.
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Affiliation(s)
- Pornchai Anuntasomboon
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University, Bangkok 10900, Thailand
| | | | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.U.); (K.C.)
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.U.); (K.C.)
| | - Richard Burchmore
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Saovanee Leelayoova
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok 10400, Thailand; (S.L.); (M.M.)
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok 10400, Thailand; (S.L.); (M.M.)
| | - Teerasak E-kobon
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University, Bangkok 10900, Thailand
- Correspondence: ; Tel.: +66-812-85-4672
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Roberts AJ, Ong HB, Clare S, Brandt C, Harcourt K, Franssen SU, Cotton JA, Müller-Sienerth N, Wright GJ. Systematic identification of genes encoding cell surface and secreted proteins that are essential for in vitro growth and infection in Leishmania donovani. PLoS Pathog 2022; 18:e1010364. [PMID: 35202447 PMCID: PMC8903277 DOI: 10.1371/journal.ppat.1010364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/08/2022] [Accepted: 02/11/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is an infectious disease caused by protozoan parasites belonging to the genus Leishmania for which there are no approved human vaccines. Infections localise to different tissues in a species-specific manner with the visceral form of the disease caused by Leishmania donovani and L. infantum being the most deadly in humans. Although Leishmania spp. parasites are predominantly intracellular, the visceral disease can be prevented in dogs by vaccinating with a complex mixture of secreted products from cultures of L. infantum promastigotes. With the logic that extracellular parasite proteins make good subunit vaccine candidates because they are directly accessible to vaccine-elicited host antibodies, here we attempt to discover proteins that are essential for in vitro growth and host infection with the goal of identifying subunit vaccine candidates. Using an in silico analysis of the Leishmania donovani genome, we identified 92 genes encoding proteins that are predicted to be secreted or externally anchored to the parasite membrane by a single transmembrane region or a GPI anchor. By selecting a transgenic L. donovani parasite that expresses both luciferase and the Cas9 nuclease, we systematically attempted to target all 92 genes by CRISPR genome editing and identified four that were required for in vitro growth. For fifty-five genes, we infected cohorts of mice with each mutant parasite and by longitudinally quantifying parasitaemia with bioluminescent imaging, showed that nine genes had evidence of an attenuated infection although all ultimately established an infection. Finally, we expressed two genes as full-length soluble recombinant proteins and tested them as subunit vaccine candidates in a murine preclinical infection model. Both proteins elicited significant levels of protection against the uncontrolled development of a splenic infection warranting further investigation as subunit vaccine candidates against this deadly infectious tropical disease. Leishmaniasis is a parasitic infectious disease that is responsible for many tens of thousands of human deaths per year, primarily in impoverished parts of the world. Although there are drugs to treat this parasite infection, resistance is emerging and there are no approved human vaccines. Extracellular parasite proteins can make good vaccine targets because they are directly accessible to host antibodies; however, not all parasite surface proteins can elicit protective immune responses. With the goal of identifying new vaccine targets, we selected over 90 genes that encode parasite cell surface and secreted proteins and used the latest CRISPR gene editing technology to individually target them. Using these mutant parasites, we identified four genes required for parasite growth in the laboratory. We expressed two of the proteins as subunit vaccines and a preclinical infection model was used to determine if they could elicit protective immune responses. We found that two of our candidates were able to confer significant levels of protection in a murine model of visceral leishmaniasis. Our study will contribute to the search for a highly effective vaccine against visceral leishmaniasis to improve the lives of people living in some of the poorest regions on the planet.
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Affiliation(s)
- Adam J. Roberts
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Han B. Ong
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Simon Clare
- Pathogen Support Team, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Cordelia Brandt
- Pathogen Support Team, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Katherine Harcourt
- Pathogen Support Team, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Susanne U. Franssen
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - James A. Cotton
- Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Nicole Müller-Sienerth
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Gavin J. Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
- * E-mail:
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Sharma R, Avendaño Rangel F, Reis-Cunha JL, Marques LP, Figueira CP, Borba PB, Viana SM, Beneke T, Bartholomeu DC, de Oliveira CI. Targeted Deletion of Centrin in Leishmania braziliensis Using CRISPR-Cas9-Based Editing. Front Cell Infect Microbiol 2022; 11:790418. [PMID: 35252020 PMCID: PMC8892584 DOI: 10.3389/fcimb.2021.790418] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/22/2021] [Indexed: 12/25/2022] Open
Abstract
Leishmania braziliensis is the main causative agent of Tegumentary Leishmaniasis in the Americas. However, difficulties related to genome manipulation, experimental infection, and parasite growth have so far limited studies with this species. CRISPR-Cas9-based technology has made genome editing more accessible, and here we have successfully employed the LeishGEdit approach to attenuate L. braziliensis. We generated a transgenic cell line expressing Cas9 and T7 RNA polymerase, which was employed for the targeted deletion of centrin, a calcium-binding cytoskeletal protein involved in the centrosome duplication in eukaryotes. Centrin-deficient Leishmania exhibit growth arrest at the amastigote stage. Whole-genome sequencing of centrin-deficient L. braziliensis (LbCen−/−) did not indicate the presence of off-target mutations. In vitro, the growth rates of LbCen−/− and wild-type promastigotes were similar, but axenic and intracellular LbCen−/− amastigotes showed a multinucleated phenotype with impaired survival following macrophage infection. Upon inoculation into BALB/c mice, LbCen−/− were detected at an early time point but failed to induce lesion formation, contrary to control animals, infected with wild-type L. braziliensis. A significantly lower parasite burden was also observed in mice inoculated with LbCen−/−, differently from control mice. Given that centrin-deficient Leishmania sp. have become candidates for vaccine development, we propose that LbCen−/− can be further explored for the purposes of immunoprophylaxis against American Tegumentary Leishmaniasis.
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Affiliation(s)
- Rohit Sharma
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
| | - Francys Avendaño Rangel
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - João Luís Reis-Cunha
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Sayonara M. Viana
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
| | - Tom Beneke
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Camila I. de Oliveira
- Instituto Gonçalo Moniz, Fiocruz, Salvador, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- INCT—Instituto de Investigação em Doenças Tropicais, Salvador, Brazil
- *Correspondence: Camila I. de Oliveira,
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Mutation Characteristics and Phylogenetic Analysis of Five Leishmania Clinical Isolates. Animals (Basel) 2022; 12:ani12030321. [PMID: 35158645 PMCID: PMC8833617 DOI: 10.3390/ani12030321] [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: 11/22/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Leishmaniasis, a neglected tropical disease, is caused by infection with the Leishmania species, threatening millions of people in approximately 100 endemic countries. The emergence of antimony-resistant Leishmania strains have brought difficulties to the treatment and elimination of leishmaniasis. This study performed genome-wide resequencing and phylogenetic analysis of five isolates from the Leishmania donovani complex, focusing on finding mutations related to antimony resistance and virulence of the newly isolated Leishmania strain L_HCZ in 2016. By combining whole-genome sequencing and whole-genome phylogenetic analysis, Leishmania isolates L_801, L_9044 and L_Liu were identified as Leishmania donovani, and L_HCZ as Leishmania infantum. By discovering genome-wide single-nucleotide polymorphisms and structural variations, we identified mutations of drug resistance-related genes in the antimony-resistant Leishmania isolate L_HCZ. The new Leishmania isolate L_HCZ has strong virulence and strong drug resistance, which should be taken seriously by the relevant health departments and scientific researchers. Abstract Leishmaniasis is a neglected tropical disease threatening millions of people worldwide. The emergence of antimony-resistant Leishmania strains have brought difficulties to the treatment and elimination of leishmaniasis. This study performed genome sequencing, phylogenetic analysis and mutation analysis of five Leishmania clinical isolates, especially the Leishmania strain L_HCZ isolated in 2016, which shows strong virulence and antimony resistance. By phylogenetic analysis, four isolates (L_DD8, L_801, L_Liu and L_9044) were identified as Leishmania donovani, the isolate L_HCZ was identified as Leishmania infantum and the isolate L_DD8 as a standard strain of L.donovani. Genome-wide mutation analysis was applied to identify mutations related to the drug resistance and virulence of the newly isolated L_HCZ. Compared with the other four Leishmania isolates, L_HCZ had the most mutations in genes associated with antimony resistance, including the ABC transporter, ascorbate-dependent peroxidase, gamma–glutamylcysteine synthetase, glucose-6-phosphate 1-dehydrogenase, ATP-binding cassette protein subfamily A and multi-drug resistance protein-like genes. Among the genes associated with virulence, L_HCZ had the most mutations in cysteine peptidase A, cysteine peptidase B, cysteine peptidase C, heat-shock protein 70, gp63, acid phosphatase, kinesin k39, kinesin, phosphoglycan beta 1, amastin-like surface protein and amastin-like proteins. The mutations in L_HCZ might possibly contribute to its antimony resistance and strong virulence in clinical patients. Whole-genome resequencing has exhibited broad application prospects and may be put into clinical use in the future for parasite identifying and epidemiological investigations.
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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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Abstract
The parasitic trypanosomatids cause lethal and debilitating diseases, the leishmaniases, Chagas disease, and the African trypanosomiases, with major impacts on human and animal health. Sustained research has borne fruit by assisting efforts to reduce the burden of disease and by improving our understanding of fundamental molecular and cell biology. But where has the research primarily been conducted, and which research areas have received the most attention? These questions are addressed below using publication and citation data from the past few decades.
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Affiliation(s)
- David Horn
- The Wellcome Trust Centre for Anti-Infectives Research, Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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Qin H, Zhang J, Dong K, Chen D, Yuan D, Chen J. Metabolic characterization and biomarkers screening for visceral leishmaniasis in golden hamsters. Acta Trop 2022; 225:106222. [PMID: 34757045 DOI: 10.1016/j.actatropica.2021.106222] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/26/2022]
Abstract
A better understanding of the changes in metabolic molecules during visceral leishmaniasis (VL) is essential to develop new strategies for diagnosis and treatment. Previous metabolomics studies on Leishmania have increased our knowledge of leishmaniasis and its causative pathogen. As these studies were mainly carried out in vitro, to go further, we conducted this global metabolomics analysis on the serum of golden hamsters. Serum samples were detected over a time course of 2, 4, 8 and 12 weeks post infection. Our results revealed that under extensively disturbed metabolomes between the infection group and controls, glycerophospholipid (GPL) metabolism was most affected over the infection time, followed by α-linoleic acid metabolism and arachidonic acid metabolism. Within GPLs, phosphatidylcholine (PC) and phosphatidylethanolamine (PE) were found to be significantly increased, while their enzyme-catalysed metabolites lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE) showed no significant changes. Moreover, eight differential metabolites were selected. The ability of these metabolites to be used as a diagnostic biomarker panel was supported by receiver operating characteristic (ROC) analysis. Our findings revealed that GPL metabolism might play an important role in the response of the host to Leishmania infection. The metabolism of PC and PE might be crucial in the in vivo progression of VL. The panel of eight potential biomarkers might contribute to the diagnosis of VL.
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Affiliation(s)
- Hanxiao Qin
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Jianhui Zhang
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Kai Dong
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Dongmei Yuan
- Department of Human Anatomy, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China.
| | - Jianping Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China.
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