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Silva H, Ferreira TR, Muneeswaran K, Samarasinghe SR, Alves-Ferreira EVC, Grigg ME, Chandrasekharan NV, Sacks DL, Karunaweera ND. Autochthonous Leishmaniasis Caused by Leishmania tropica, Identified by Using Whole-Genome Sequencing, Sri Lanka. Emerg Infect Dis 2024; 30:1872-1883. [PMID: 39174018 PMCID: PMC11347009 DOI: 10.3201/eid3009.231238] [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] [Indexed: 08/24/2024] Open
Abstract
Cutaneous leishmaniasis is atypical in Sri Lanka because Leishmania donovani, which typically causes visceral disease, is the causative agent. The origins of recently described hybrids between L. donovani and other Leishmania spp. usually responsible for cutaneous leishmaniasis remain unknown. Other endemic dermotropic Leishmania spp. have not been reported in Sri Lanka. Genome analysis of 27 clinical isolates from Sri Lanka and 32 Old World Leishmania spp. strains found 8 patient isolates clustered with L. tropica and 19 with L. donovani. The L. tropica isolates from Sri Lanka shared markers with strain LtK26 reported decades ago in India, indicating they were not products of recent interspecies hybridization. Because L. tropica was isolated from patients with leishmaniasis in Sri Lanka, our findings indicate L. donovani is not the only cause of cutaneous leishmaniasis in Sri Lanka and potentially explains a haplotype that led to interspecies dermotropic L. donovani hybrids.
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Roca-Geronès X, Sala C, Marteles D, Villanueva-Saz S, Riera C, Alcover MM, Fisa R. Genetic Variability in Leishmaniasis-Causing Leishmania infantum in Humans and Dogs from North-East Spain. Animals (Basel) 2024; 14:1796. [PMID: 38929415 PMCID: PMC11200389 DOI: 10.3390/ani14121796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Leishmania infantum is the primary cause of visceral and cutaneous leishmaniasis in the European Mediterranean region. Subspecies-level characterization of L. infantum aids epidemiological studies by offering insights into the evolution and geographical distribution of the parasite and reservoir identity. In this study, conducted in north-east Spain, 26 DNA samples of L. infantum were analyzed, comprising 21 from 10 humans and 5 from 5 dogs. Minicircle kinetoplast DNA (kDNA) polymerase chain reaction assays using primers MC1 and MC2, followed by sequencing, were employed to assess intraspecific genetic variability. Single-nucleotide polymorphism (SNP) analysis detected seven genotypes (G1, G2, G12*-G15*, and G17*), with five being reported for the first time (*). The most prevalent was the newly described G13 (54%), while the other currently identified genotypes were predominantly found in single samples. The in silico restriction fragment length polymorphism (RFLP) method revealed five genotypes (B, F, N, P, and W), one of them previously unreported (W). Genotype B was the most prevalent (85%), comprising three SNP genotypes (G1, G2, and G13), whereas the other RFLP genotypes were associated with single SNP genotypes. These kDNA genotyping methods revealed significant intraspecific genetic diversity in L. infantum, demonstrating their suitability for fingerprinting and strain monitoring.
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Affiliation(s)
- Xavier Roca-Geronès
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Parasitologia, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Clara Sala
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Parasitologia, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Diana Marteles
- Animal Pathology Department, Veterinary Faculty, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain (S.V.-S.)
- Clinical Immunology Laboratory, Veterinary Faculty, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza), 50013 Zaragoza, Spain
| | - Sergio Villanueva-Saz
- Animal Pathology Department, Veterinary Faculty, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain (S.V.-S.)
- Clinical Immunology Laboratory, Veterinary Faculty, University of Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza), 50013 Zaragoza, Spain
| | - Cristina Riera
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Parasitologia, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Mª Magdalena Alcover
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Parasitologia, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Roser Fisa
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Parasitologia, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Spain
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3
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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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4
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Dirkx L, Van Acker SI, Nicolaes Y, Cunha JLR, Ahmad R, Hendrickx R, Caljon B, Imamura H, Ebo DG, Jeffares DC, Sterckx YGJ, Maes L, Hendrickx S, Caljon G. Long-term hematopoietic stem cells trigger quiescence in Leishmania parasites. PLoS Pathog 2024; 20:e1012181. [PMID: 38656959 PMCID: PMC11073788 DOI: 10.1371/journal.ppat.1012181] [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: 09/05/2023] [Revised: 05/06/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
Addressing the challenges of quiescence and post-treatment relapse is of utmost importance in the microbiology field. This study shows that Leishmania infantum and L. donovani parasites rapidly enter into quiescence after an estimated 2-3 divisions in both human and mouse bone marrow stem cells. Interestingly, this behavior is not observed in macrophages, which are the primary host cells of the Leishmania parasite. Transcriptional comparison of the quiescent and non-quiescent metabolic states confirmed the overall decrease of gene expression as a hallmark of quiescence. Quiescent amastigotes display a reduced size and signs of a rapid evolutionary adaptation response with genetic alterations. Our study provides further evidence that this quiescent state significantly enhances resistance to treatment. Moreover, transitioning through quiescence is highly compatible with sand fly transmission and increases the potential of parasites to infect cells. Collectively, this work identified stem cells in the bone marrow as a niche where Leishmania quiescence occurs, with important implications for antiparasitic treatment and acquisition of virulence traits.
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Affiliation(s)
- Laura Dirkx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Sara I. Van Acker
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Yasmine Nicolaes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - João Luís Reis Cunha
- York Biomedical Research Institute and Department of Biology, University of York, York, United Kingdom
| | - Rokaya Ahmad
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Rik Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Ben Caljon
- Brussels Interuniversity Genomics High Throughput core (BRIGHTcore) platform, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Hideo Imamura
- Brussels Interuniversity Genomics High Throughput core (BRIGHTcore) platform, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Didier G. Ebo
- Department of Immunology–Allergology–Rheumatology, Faculty of Medicine and Health Science, Infla-Med Centre of Excellence, University of Antwerp, Antwerp University Hospital, Antwerp, Belgium
| | - Daniel C. Jeffares
- York Biomedical Research Institute and Department of Biology, University of York, York, United Kingdom
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Sarah Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
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5
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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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6
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Sádlová J, Yeo M, Mateus DS, Phelan J, Hai LA, Bhattacharyya T, Kurtev S, Sebesta O, Myskova J, Seblova V, Andersson B, Florez de Sessions P, Volf P, Miles MA. Comparative genomics of Leishmania donovani progeny from genetic crosses in two sand fly species and impact on the diversity of diagnostic and vaccine candidates. PLoS Negl Trop Dis 2024; 18:e0011920. [PMID: 38295092 PMCID: PMC10830044 DOI: 10.1371/journal.pntd.0011920] [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: 05/10/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
Sand fly transmitted Leishmania species are responsible for severe, wide ranging, visceral and cutaneous leishmaniases. Genetic exchange can occur among natural Leishmania populations and hybrids can now be produced experimentally, with limitations. Feeding Phlebotomus orientalis or Phlebotomus argentipes on two strains of Leishmania donovani yielded hybrid progeny, selected using double drug resistance and fluorescence markers. Fluorescence activated cell sorting of cultured clones derived from these hybrids indicated diploid progeny. Multilocus sequence typing of the clones showed hybridisation and nuclear heterozygosity, although with inheritance of single haplotypes in a kinetoplastid target. Comparative genomics showed diversity of clonal progeny between single chromosomes, and extraordinary heterozygosity across all 36 chromosomes. Diversity between progeny was seen for the HASPB antigen, which has been noted previously as having implications for design of a therapeutic vaccine. Genomic diversity seen among Leishmania strains and hybrid progeny is of great importance in understanding the epidemiology and control of leishmaniasis. As an outcome of this study we strongly recommend that wider biological archives of different Leishmania species from endemic regions should be established and made available for comparative genomics. However, in parallel, performance of genetic crosses and genomic comparisons should give fundamental insight into the specificity, diversity and limitations of candidate diagnostics, vaccines and drugs, for targeted control of leishmaniasis.
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Affiliation(s)
- Jovana Sádlová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - David S. Mateus
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Le Anh Hai
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Tapan Bhattacharyya
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Stefan Kurtev
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
| | - Ondrej Sebesta
- Laboratory of Confocal and Fluorescence Microscopy, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jitka Myskova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Veronika Seblova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Paola Florez de Sessions
- Genome Institute of Singapore, Biomedical Sciences Institutes, Agency for Science, Technology and Research, Singapore
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michael A. Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London United Kingdom
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7
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Catta-Preta CMC, Ferreira TR, Ghosh K, Paun A, Sacks D. HOP1 and HAP2 are conserved components of the meiosis-related machinery required for successful mating in Leishmania. Nat Commun 2023; 14:7159. [PMID: 37935664 PMCID: PMC10630298 DOI: 10.1038/s41467-023-42789-z] [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: 06/22/2023] [Accepted: 10/21/2023] [Indexed: 11/09/2023] Open
Abstract
Whole genome analysis of Leishmania hybrids generated experimentally in sand flies supports a meiotic mechanism of genetic exchange, with Mendelian segregation of the nuclear genome. Here, we perform functional analyses through the generation of double drug-resistant hybrids in vitro and in vivo (during sand fly infections) to assess the importance of conserved meiosis-related genes in recombination and plasmogamy. We report that HOP1 and a HAP2-paralog (HAP2-2) are essential components of the Leishmania meiosis machinery and cell-to-cell fusion mechanism, respectively, since deletion of either gene in one or both parents significantly reduces or completely abrogates mating competence. These findings significantly advance our understanding of sexual reproduction in Leishmania, with likely relevance to other trypanosomatids, by formally demonstrating the involvement of a meiotic protein homolog and a distinct fusogen that mediates non-canonical, bilateral fusion in the hybridizing cells.
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Affiliation(s)
- Carolina Moura Costa Catta-Preta
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tiago Rodrigues Ferreira
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kashinath Ghosh
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrea Paun
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Sacks
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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8
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Jara M, Arevalo J, Llanos-Cuentas A, den Broeck FV, Domagalska MA, Dujardin JC. Unveiling drug-tolerant and persister-like cells in Leishmania braziliensis lines derived from patients with cutaneous leishmaniasis. Front Cell Infect Microbiol 2023; 13:1253033. [PMID: 37790908 PMCID: PMC10543814 DOI: 10.3389/fcimb.2023.1253033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/21/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction Resistance against anti-Leishmania drugs (DR) has been studied for years, giving important insights into long-term adaptations of these parasites to drugs, through genetic modifications. However, microorganisms can also survive lethal drug exposure by entering into temporary quiescence, a phenomenon called drug tolerance (DT), which is rather unexplored in Leishmania. Methods We studied a panel of nine Leishmania braziliensis strains highly susceptible to potassium antimonyl tartrate (PAT), exposed promastigotes to lethal PAT pressure, and compared several cellular and molecular parameters distinguishing DT from DR. Results and discussion We demonstrated in vitro that a variable proportion of cells remained viable, showing all the criteria of DT and not of DR: i) signatures of quiescence, under drug pressure: reduced proliferation and significant decrease of rDNA transcription; ii) reversibility of the phenotype: return to low IC50 after removal of drug pressure; and iii) absence of significant genetic differences between exposed and unexposed lineages of each strain and absence of reported markers of DR. We found different levels of quiescence and DT among the different L. braziliensis strains. We provide here a new in-vitro model of drug-induced quiescence and DT in Leishmania. Research should be extended in vivo, but the current model could be further exploited to support R&D, for instance, to guide the screening of compounds to overcome the quiescence resilience of the parasite, thereby improving the therapy of leishmaniasis.
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Affiliation(s)
- Marlene Jara
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Jorge Arevalo
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Frederik Van den Broeck
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
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9
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Negreira GH, de Groote R, Van Giel D, Monsieurs P, Maes I, de Muylder G, Van den Broeck F, Dujardin J, Domagalska MA. The adaptive roles of aneuploidy and polyclonality in Leishmania in response to environmental stress. EMBO Rep 2023; 24:e57413. [PMID: 37470283 PMCID: PMC10481652 DOI: 10.15252/embr.202357413] [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: 04/28/2023] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 07/21/2023] Open
Abstract
Aneuploidy is generally considered harmful, but in some microorganisms, it can act as an adaptive mechanism against environmental stress. Here, we use Leishmania-a protozoan parasite with remarkable genome plasticity-to study the early steps of aneuploidy evolution under high drug pressure (using antimony or miltefosine as stressors). By combining single-cell genomics, lineage tracing with cellular barcodes, and longitudinal genome characterization, we reveal that aneuploidy changes under antimony pressure result from polyclonal selection of pre-existing karyotypes, complemented by further and rapid de novo alterations in chromosome copy number along evolution. In the case of miltefosine, early parasite adaptation is associated with independent point mutations in a miltefosine transporter gene, while aneuploidy changes only emerge later, upon exposure to increased drug levels. Therefore, polyclonality and genome plasticity are hallmarks of parasite adaptation, but the scenario of aneuploidy dynamics depends on the nature and strength of the environmental stress as well as on the existence of other pre-adaptive mechanisms.
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Affiliation(s)
- Gabriel H Negreira
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Robin de Groote
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Dorien Van Giel
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Pieter Monsieurs
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Ilse Maes
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | | | - Frederik Van den Broeck
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical ResearchKatholieke Universiteit LeuvenLeuvenBelgium
| | - Jean‐Claude Dujardin
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
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10
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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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11
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Ellis JT, Reichel MP. Twitter trends in #Parasitology determined by text mining and topic modelling. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2023; 4:100138. [PMID: 37670843 PMCID: PMC10475476 DOI: 10.1016/j.crpvbd.2023.100138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
This study investigated the emergence and use of Twitter, as of July 2023 being rebranded as X, as the main forum for social media communication in parasitology. A dataset of tweets was constructed using a keyword search of Twitter with the search terms 'malaria', 'Plasmodium', 'Leishmania', 'Trypanosoma', 'Toxoplasma' and 'Schistosoma' for the period from 2011 to 2020. Exploratory data analyses of tweet content were conducted, including language, usernames and hashtags. To identify parasitology topics of discussion, keywords and phrases were extracted using KeyBert and biterm topic modelling. The sentiment of tweets was analysed using VADER. The results show that the number of tweets including the keywords increased from 2011 (for malaria) and 2013 (for the others) to 2020, with the highest number of tweets being recorded in 2020. The maximum number of yearly tweets for Plasmodium, Leishmania, Toxoplasma, Trypanosoma and Schistosoma was recorded in 2020 (2804, 2161, 1570, 680 and 360 tweets, respectively). English was the most commonly used language for tweeting, although the percentage varied across the searches. In tweets mentioning Leishmania, only ∼37% were in English, with Spanish being more common. Across all the searches, Portuguese was another common language found. Popular tweets on Toxoplasma contained keywords relating to mental health including depression, anxiety and schizophrenia. The Trypanosoma tweets referenced drugs (benznidazole, nifurtimox) and vectors (bugs, triatomines, tsetse), while the Schistosoma tweets referenced areas of biology including pathology, eggs and snails. A wide variety of individuals and organisations were shown to be associated with Twitter activity. Many journals in the parasitology arena regularly tweet about publications from their journal, and professional societies promote activity and events that are important to them. These represent examples of trusted sources of information, often by experts in their fields. Social media activity of influencers, however, who have large numbers of followers, might have little or no training in science. The existence of such tweeters does raise cause for concern to parasitology, as one may start to question the quality of information being disseminated.
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Affiliation(s)
- John T. Ellis
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
| | - Michael P. Reichel
- Department of Population Medicine & Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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12
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Gerasimov ES, Novozhilova TS, Zimmer SL, Yurchenko V. Kinetoplast Genome of Leishmania spp. Is under Strong Purifying Selection. Trop Med Infect Dis 2023; 8:384. [PMID: 37624322 PMCID: PMC10458658 DOI: 10.3390/tropicalmed8080384] [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: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Instability is an intriguing characteristic of many protist genomes, and trypanosomatids are not an exception in this respect. Some regions of trypanosomatid genomes evolve fast. For instance, the trypanosomatid mitochondrial (kinetoplast) genome consists of fairly conserved maxicircle and minicircle molecules that can, nevertheless, possess high nucleotide substitution rates between closely related strains. Recent experiments have demonstrated that rapid laboratory evolution can result in the non-functionality of multiple genes of kinetoplast genomes due to the accumulation of mutations or loss of critical genomic components. An example of a loss of critical components is the reported loss of entire minicircle classes in Leishmania tarentolae during laboratory cultivation, which results in an inability to generate some correctly encoded genes. In the current work, we estimated the evolutionary rates of mitochondrial and nuclear genome regions of multiple natural Leishmania spp. We analyzed synonymous and non-synonymous substitutions and, rather unexpectedly, found that the coding regions of kinetoplast maxicircles are among the most variable regions of both genomes. In addition, we demonstrate that synonymous substitutions greatly predominate among maxicircle coding regions and that most maxicircle genes show signs of purifying selection. These results imply that maxicircles in natural Leishmania populations remain functional despite their high mutation rate.
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Affiliation(s)
- Evgeny S. Gerasimov
- Department of Molecular Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, 127051 Moscow, Russia
| | - Tatiana S. Novozhilova
- Department of Molecular Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Sara L. Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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13
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Domagalska MA, Barrett MP, Dujardin JC. Drug resistance in Leishmania: does it really matter? Trends Parasitol 2023; 39:251-259. [PMID: 36803859 DOI: 10.1016/j.pt.2023.01.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/19/2023]
Abstract
Treatment failure (TF) jeopardizes the management of parasitic diseases, including leishmaniasis. From the parasite's point of view, drug resistance (DR) is generally considered as central to TF. However, the link between TF and DR, as measured by in vitro drug susceptibility assays, is unclear, some studies revealing an association between treatment outcome and drug susceptibility, others not. Here we address three fundamental questions aiming to shed light on these ambiguities. First, are the right assays being used to measure DR? Second, are the parasites studied, which are generally those that adapt to in vitro culture, actually appropriate? Finally, are other parasite factors - such as the development of quiescent forms that are recalcitrant to drugs - responsible for TF without DR?
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Affiliation(s)
| | - Michael P Barrett
- School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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14
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Leishmania allelic selection during experimental sand fly infection correlates with mutational signatures of oxidative DNA damage. Proc Natl Acad Sci U S A 2023; 120:e2220828120. [PMID: 36848551 PMCID: PMC10013807 DOI: 10.1073/pnas.2220828120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Trypanosomatid pathogens are transmitted by blood-feeding insects, causing devastating human infections. These parasites show important phenotypic shifts that often impact parasite pathogenicity, tissue tropism, or drug susceptibility. The evolutionary mechanisms that allow for the selection of such adaptive phenotypes remain only poorly investigated. Here, we use Leishmania donovani as a trypanosomatid model pathogen to assess parasite evolutionary adaptation during experimental sand fly infection. Comparing the genome of the parasites before and after sand fly infection revealed a strong population bottleneck effect as judged by allele frequency analysis. Apart from random genetic drift caused by the bottleneck effect, our analyses revealed haplotype and allelic changes during sand fly infection that seem under natural selection given their convergence between independent biological replicates. Our analyses further uncovered signature mutations of oxidative DNA damage in the parasite genomes after sand fly infection, suggesting that Leishmania suffers from oxidative stress inside the insect digestive tract. Our results propose a model of Leishmania genomic adaptation during sand fly infection, with oxidative DNA damage and DNA repair processes likely driving haplotype and allelic selection. The experimental and computational framework presented here provides a useful blueprint to assess evolutionary adaptation of other eukaryotic pathogens inside their insect vectors, such as Plasmodium spp, Trypanosoma brucei, and Trypanosoma cruzi.
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15
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Pilling OA, Reis-Cunha JL, Grace CA, Berry ASF, Mitchell MW, Yu JA, Malekshahi CR, Krespan E, Go CK, Lombana C, Song YS, Amorim CF, Lago AS, Carvalho LP, Carvalho EM, Brisson D, Scott P, Jeffares DC, Beiting DP. Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies. PLoS Pathog 2023; 19:e1011230. [PMID: 36940219 PMCID: PMC10063166 DOI: 10.1371/journal.ppat.1011230] [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: 09/03/2022] [Revised: 03/30/2023] [Accepted: 02/22/2023] [Indexed: 03/21/2023] Open
Abstract
In Brazil, Leishmania braziliensis is the main causative agent of the neglected tropical disease, cutaneous leishmaniasis (CL). CL presents on a spectrum of disease severity with a high rate of treatment failure. Yet the parasite factors that contribute to disease presentation and treatment outcome are not well understood, in part because successfully isolating and culturing parasites from patient lesions remains a major technical challenge. Here we describe the development of selective whole genome amplification (SWGA) for Leishmania and show that this method enables culture-independent analysis of parasite genomes obtained directly from primary patient skin samples, allowing us to circumvent artifacts associated with adaptation to culture. We show that SWGA can be applied to multiple Leishmania species residing in different host species, suggesting that this method is broadly useful in both experimental infection models and clinical studies. SWGA carried out directly on skin biopsies collected from patients in Corte de Pedra, Bahia, Brazil, showed extensive genomic diversity. Finally, as a proof-of-concept, we demonstrated that SWGA data can be integrated with published whole genome data from cultured parasite isolates to identify variants unique to specific geographic regions in Brazil where treatment failure rates are known to be high. SWGA provides a relatively simple method to generate Leishmania genomes directly from patient samples, unlocking the potential to link parasite genetics with host clinical phenotypes.
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Affiliation(s)
- Olivia A. Pilling
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - João L. Reis-Cunha
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Cooper A. Grace
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Alexander S. F. Berry
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew W. Mitchell
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jane A. Yu
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
| | - Clara R. Malekshahi
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Elise Krespan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Christina K. Go
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Cláudia Lombana
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yun S. Song
- Computer Science Division, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Camila F. Amorim
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexsandro S. Lago
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Lucas P. Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Edgar M. Carvalho
- Serviço de Imunologia, Complexo Hospitalar Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, Bahia, Brazil
- Laboratório de Pesquisas Clínicas do Instituto de Pesquisas Gonçalo Moniz, Fiocruz Bahia, Brazil
| | - Dustin Brisson
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Phillip Scott
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Daniel C. Jeffares
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Daniel P. Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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16
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Novozhilova TS, Chistyakov DS, Akhmadishina LV, Lukashev AN, Gerasimov ES, Yurchenko V. Genomic analysis of Leishmania turanica strains from different regions of Central Asia. PLoS Negl Trop Dis 2023; 17:e0011145. [PMID: 36877735 PMCID: PMC10019736 DOI: 10.1371/journal.pntd.0011145] [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: 10/13/2022] [Revised: 03/16/2023] [Accepted: 02/06/2023] [Indexed: 03/07/2023] Open
Abstract
The evolution in Leishmania is governed by the opposite forces of clonality and sexual reproduction, with vicariance being an important factor. As such, Leishmania spp. populations may be monospecific or mixed. Leishmania turanica in Central Asia is a good model to compare these two types. In most areas, populations of L. turanica are mixed with L. gerbilli and L. major. Notably, co-infection with L. turanica in great gerbils helps L. major to withstand a break in the transmission cycle. Conversely, the populations of L. turanica in Mongolia are monospecific and geographically isolated. In this work, we compare genomes of several well-characterized strains of L. turanica originated from monospecific and mixed populations in Central Asia in order to shed light on genetic factors, which may drive evolution of these parasites in different settings. Our results illustrate that evolutionary differences between mixed and monospecific populations of L. turanica are not dramatic. On the level of large-scale genomic rearrangements, we confirmed that different genomic loci and different types of rearrangements may differentiate strains originated from mixed and monospecific populations, with genome translocations being the most prominent example. Our data suggests that L. turanica has a significantly higher level of chromosomal copy number variation between the strains compared to its sister species L. major with only one supernumerary chromosome. This suggests that L. turanica (in contrast to L. major) is in the active phase of evolutionary adaptation.
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Affiliation(s)
| | - Daniil S. Chistyakov
- Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | | | | | | | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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17
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Urán Landaburu L, Didier Garnham M, Agüero F. Targeting trypanosomes: how chemogenomics and artificial intelligence can guide drug discovery. Biochem Soc Trans 2023; 51:195-206. [PMID: 36606702 DOI: 10.1042/bst20220618] [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: 10/20/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
Trypanosomatids are protozoan parasites that cause human and animal neglected diseases. Despite global efforts, effective treatments are still much needed. Phenotypic screens have provided several chemical leads for drug discovery, but the mechanism of action for many of these chemicals is currently unknown. Recently, chemogenomic screens assessing the susceptibility or resistance of parasites carrying genome-wide modifications started to define the mechanism of action of drugs at large scale. In this review, we discuss how genomics is being used for drug discovery in trypanosomatids, how integration of chemical and genomics data from these and other organisms has guided prioritisations of candidate therapeutic targets and additional chemical starting points, and how these data can fuel the expansion of drug discovery pipelines into the era of artificial intelligence.
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Affiliation(s)
- Lionel Urán Landaburu
- Instituto de Investigaciones Biotecnológicas (IIB), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Argentina
- Escuela de Bio y Nanociencias (EByN), Universidad Nacional de San Martín, San Martín, Argentina
| | - Mercedes Didier Garnham
- Instituto de Investigaciones Biotecnológicas (IIB), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Argentina
- Escuela de Bio y Nanociencias (EByN), Universidad Nacional de San Martín, San Martín, Argentina
| | - Fernán Agüero
- Instituto de Investigaciones Biotecnológicas (IIB), Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Argentina
- Escuela de Bio y Nanociencias (EByN), Universidad Nacional de San Martín, San Martín, Argentina
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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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Black JA, Reis-Cunha JL, Cruz AK, Tosi LR. Life in plastic, it's fantastic! How Leishmania exploit genome instability to shape gene expression. Front Cell Infect Microbiol 2023; 13:1102462. [PMID: 36779182 PMCID: PMC9910336 DOI: 10.3389/fcimb.2023.1102462] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023] Open
Abstract
Leishmania are kinetoplastid pathogens that cause leishmaniasis, a debilitating and potentially life-threatening infection if untreated. Unusually, Leishmania regulate their gene expression largely post-transcriptionally due to the arrangement of their coding genes into polycistronic transcription units that may contain 100s of functionally unrelated genes. Yet, Leishmania are capable of rapid and responsive changes in gene expression to challenging environments, often instead correlating with dynamic changes in their genome composition, ranging from chromosome and gene copy number variations to the generation of extrachromosomal DNA and the accumulation of point mutations. Typically, such events indicate genome instability in other eukaryotes, coinciding with genetic abnormalities, but for Leishmania, exploiting these products of genome instability can provide selectable substrates to catalyse necessary gene expression changes by modifying gene copy number. Unorthodox DNA replication, DNA repair, replication stress factors and DNA repeats are recognised in Leishmania as contributors to this intrinsic instability, but how Leishmania regulate genome plasticity to enhance fitness whilst limiting toxic under- or over-expression of co-amplified and co-transcribed genes is unclear. Herein, we focus on fresh, and detailed insights that improve our understanding of genome plasticity in Leishmania. Furthermore, we discuss emerging models and factors that potentially circumvent regulatory issues arising from polycistronic transcription. Lastly, we highlight key gaps in our understanding of Leishmania genome plasticity and discuss future studies to define, in higher resolution, these complex regulatory interactions.
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Affiliation(s)
- Jennifer A. Black
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil,The Wellcome Centre for Integrative Parasitology, School of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, United Kingdom,*Correspondence: Luiz. R.O. Tosi, ; Jennifer A. Black,
| | | | - Angela. K. Cruz
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz. R.O. Tosi
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil,*Correspondence: Luiz. R.O. Tosi, ; Jennifer A. Black,
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20
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Patiño LH, Muñoz M, Ramírez AL, Vélez N, Escandón P, Parra-Giraldo CM, Ramírez JD. A Landscape of the Genomic Structure of Cryptococcus neoformans in Colombian Isolates. J Fungi (Basel) 2023; 9:jof9020135. [PMID: 36836249 PMCID: PMC9959405 DOI: 10.3390/jof9020135] [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: 12/14/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
Cryptococcus neoformans species complexes are recognized as environmental fungi responsible for lethal meningoencephalitis in immunocompromised individuals. Despite the vast knowledge about the epidemiology and genetic diversity of this fungus in different regions of the world, more studies are necessary to comprehend the genomic profiles across South America, including Colombia, considered to be the second country with the highest number of Cryptococcosis. Here, we sequenced and analyzed the genomic architecture of 29 Colombian C. neoformans isolates and evaluated the phylogenetic relationship of these strains with publicly available C. neoformans genomes. The phylogenomic analysis showed that 97% of the isolates belonged to the VNI molecular type and the presence of sub-lineages and sub-clades. We evidenced a karyotype without changes, a low number of genes with copy number variations, and a moderate number of single-nucleotide polymorphisms (SNPs). Additionally, a difference in the number of SNPs between the sub-lineages/sub-clades was observed; some were involved in crucial fungi biological processes. Our study demonstrated the intraspecific divergence of C. neoformans in Colombia. These findings provide evidence that Colombian C. neoformans isolates do not probably require significant structural changes as adaptation mechanisms to the host. To the best of our knowledge, this is the first study to report the whole genome sequence of Colombian C. neoformans isolates.
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Affiliation(s)
- Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
| | - Angie Lorena Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
| | - Nórida Vélez
- Unidad de Proteómica y Micosis Humanas, Grupo de Investigación en Enfermedades Infecciosas, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá 111321, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28001 Madrid, Spain
| | - Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Claudia-Marcela Parra-Giraldo
- Unidad de Proteómica y Micosis Humanas, Grupo de Investigación en Enfermedades Infecciosas, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá 111321, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28001 Madrid, Spain
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 111321, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: or ; Tel.: +1-(332)-2344161
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21
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Hadermann A, Heeren S, Maes I, Dujardin JC, Domagalska MA, Van den Broeck F. Genome diversity of Leishmania aethiopica. Front Cell Infect Microbiol 2023; 13:1147998. [PMID: 37153154 PMCID: PMC10157169 DOI: 10.3389/fcimb.2023.1147998] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Leishmania aethiopica is a zoonotic Old World parasite transmitted by Phlebotomine sand flies and causing cutaneous leishmaniasis in Ethiopia and Kenya. Despite a range of clinical manifestations and a high prevalence of treatment failure, L. aethiopica is one of the most neglected species of the Leishmania genus in terms of scientific attention. Here, we explored the genome diversity of L. aethiopica by analyzing the genomes of twenty isolates from Ethiopia. Phylogenomic analyses identified two strains as interspecific hybrids involving L. aethiopica as one parent and L. donovani and L. tropica respectively as the other parent. High levels of genome-wide heterozygosity suggest that these two hybrids are equivalent to F1 progeny that propagated mitotically since the initial hybridization event. Analyses of allelic read depths further revealed that the L. aethiopica - L. tropica hybrid was diploid and the L. aethiopica - L. donovani hybrid was triploid, as has been described for other interspecific Leishmania hybrids. When focusing on L. aethiopica, we show that this species is genetically highly diverse and consists of both asexually evolving strains and groups of recombining parasites. A remarkable observation is that some L. aethiopica strains showed an extensive loss of heterozygosity across large regions of the nuclear genome, which likely arose from gene conversion/mitotic recombination. Hence, our prospection of L. aethiopica genomics revealed new insights into the genomic consequences of both meiotic and mitotic recombination in Leishmania.
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Affiliation(s)
- Amber Hadermann
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Senne Heeren
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Malgorzata Anna Domagalska
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- *Correspondence: Frederik Van den Broeck, ; Malgorzata Anna Domagalska,
| | - Frederik Van den Broeck
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- *Correspondence: Frederik Van den Broeck, ; Malgorzata Anna Domagalska,
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Mano C, Kongkaew A, Tippawangkosol P, Somboon P, Roytrakul S, Pescher P, Späth GF, Uthaipibull C, Tantiworawit A, Siriyasatien P, Jariyapan N. Amphotericin B resistance correlates with increased fitness in vitro and in vivo in Leishmania ( Mundinia) martiniquensis. Front Microbiol 2023; 14:1156061. [PMID: 37089544 PMCID: PMC10116047 DOI: 10.3389/fmicb.2023.1156061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/15/2023] [Indexed: 04/25/2023] Open
Abstract
Amphotericin B (AmpB) deoxycholate is the available first-line drug used to treat visceral leishmaniasis caused by Leishmania (Mundinia) martiniquensis, however, some cases of AmpB treatment failure have been reported in Thailand. Resistance to drugs is known to affect parasite fitness with a potential impact on parasite transmission but still little is known about the effect of resistance to drugs on L. martiniquensis. Here we aimed to gain insight into the fitness changes occurring after treatment failure or in vitro-induced resistance to AmpB. L. martiniquensis parasites isolated from a patient before (LSCM1) and after relapse (LSCM1-6) were compared for in vitro and in vivo fitness changes together with an in vitro induced AmpB-resistant parasite generated from LSCM1 parasites (AmpBRP2i). Results revealed increased metacyclogenesis of the AmpBPR2i and LSCM1-6 strains (AmpB-resistant strains) compared to the LSCM1 strain and increased fitness with respect to growth and infectivity. The LSCM1-6 and AmpBRP2i strains were present in mice for longer periods compared to the LSCM1 strain, but no clinical signs of the disease were observed. These results suggest that the AmpB-resistant parasites could be more efficiently transmitted to humans and maintained in asymptomatic hosts longer than the susceptible strain. The asymptomatic hosts therefore may represent "reservoirs" for the resistant parasites enhancing transmission. The results in this study advocate an urgent need to search and monitor for AmpB-resistant L. martiniquensis in patients with relapsing leishmaniasis and in asymptomatic patients, especially, in HIV/Leishmania coinfected patients.
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Affiliation(s)
- Chonlada Mano
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Aphisek Kongkaew
- Animal House Unit, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pongsri Tippawangkosol
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pradya Somboon
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Pascale Pescher
- Institut Pasteur, INSERM U1201, Université Paris Cité, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | - Gerald F. Späth
- Institut Pasteur, INSERM U1201, Université Paris Cité, Unité de Parasitologie Moléculaire et Signalisation, Paris, France
| | | | - Adisak Tantiworawit
- Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Padet Siriyasatien
- Center of Excellence in Vector Biology and Vector-Borne Disease, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Narissara Jariyapan
- Center of Excellence in Vector Biology and Vector-Borne Disease, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- *Correspondence: Narissara Jariyapan,
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Abstract
Genetic exchange between different Leishmania strains in the sand fly vector has been experimentally demonstrated and is supported by population genetic studies. In nature, opportunities for Leishmania interstrain mating are restricted to flies biting multiply infected hosts or through multiple bites of different hosts. In contrast, self-mating could occur in any infected sand fly. By crossing two recombinant lines derived from the same Leishmania major strain, each expressing a different drug-resistance marker, self-hybridization in L. major was confirmed in a natural sand fly vector, Phlebotomus duboscqi, and in frequencies comparable to interstrain crosses. We provide the first high resolution, whole-genome sequencing analysis of large numbers of selfing progeny, their parents, and parental subclones. Genetic exchange consistent with classical meiosis is supported by the biallelic inheritance of the rare homozygous single nucleotide polymorphisms (SNPs) that arose by mutation during the generation of the parental clones. In contrast, heterozygous SNPs largely failed to be transmitted in Mendelian ratios for reasons not understood. SNPs that were heterozygous in both parents, however, recombined to produce homozygous alleles in some hybrids. For trisomic chromosomes present in both parents, transmittal to the progeny was only altered by self-hybridization, involving a gain or loss of somy in frequencies predicted by a meiotic process. Whole-genome polyploidization was also observed in the selfing progeny. Thus, self-hybridization in Leishmania, with its potential to occur in any infected sand fly, may be an important source of karyotype variation, loss of heterozygosity, and functional diversity. IMPORTANCE Leishmania are parasitic protozoa that cause a wide spectrum of diseases collectively known as the leishmaniases. Sexual reproduction in Leishmania has been proposed as an important source of genetic diversity and has been formally demonstrated to occur inside the sand fly vector midgut. Nevertheless, in the wild, opportunities for genetic exchange between different Leishmania species or strains are restricted by the capacity of different Leishmania strains to colonize the same sand fly. In this work, we report the first high resolution, whole-genome sequence analysis of intraclonal genetic exchange as a type of self-mating in Leishmania. Our data reveal that self-hybridization can occur with comparable frequency as interstrain mating under experimental lab conditions, leading to important genomic alterations that can potentially take place within every naturally infected sand fly.
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Paulini K, Lypaczewski P, Zhang WW, Perera DJ, Ndao M, Matlashewski G. Investigating the Leishmania donovani sacp Gene and Its Role in Macrophage Infection and Survival in Mice. Trop Med Infect Dis 2022; 7:384. [PMID: 36422936 PMCID: PMC9694005 DOI: 10.3390/tropicalmed7110384] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/31/2022] [Accepted: 11/11/2022] [Indexed: 11/22/2022] Open
Abstract
The protozoan parasite Leishmania donovani is a causative agent of the neglected tropical disease known as visceral leishmaniasis, which can be lethal when untreated. Studying Leishmania viru-lence factors is crucial in determining how the parasite causes disease and identifying new targets for treatment. One potential virulence factor is L. donovani's abundantly secreted protein: secreted acid phosphatase (SAcP). Whole-genome analysis revealed that the sacp gene was present in three copies in wild type L. donovani. Using CRISPR-Cas9 gene editing; we generated a sacp gene knockout termed LdΔSAcP, which demonstrated a loss of both the SAcP protein and an associated reduction in secreted acid phosphatase activity. Genome sequencing confirmed the precise dele-tion of the sacp gene in LdΔSAcP and identified several changes in the genome. LdΔSAcP demonstrated no significant changes in promastigote proliferation or its ability to infect and survive in macrophages compared to the wildtype strain. LdΔSAcP also demonstrated no change in murine liver infection; however, survival was impaired in the spleen. Taken together these results show that SAcP is not necessary for the survival of promastigotes in culture but may support long-term survival in the spleen. These observations also show that the use of CRISPR gene editing and WGS together are effective to investigate the function and phenotype of complex potential drug targets such as multicopy genes.
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Affiliation(s)
- Kayla Paulini
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Patrick Lypaczewski
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Wen-Wei Zhang
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Dilhan J. Perera
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Momar Ndao
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- National Reference Centre for Parasitology, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Greg Matlashewski
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
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Martí-Carreras J, Carrasco M, Gómez-Ponce M, Noguera-Julián M, Fisa R, Riera C, Alcover MM, Roura X, Ferrer L, Francino O. Identification of Leishmania infantum Epidemiology, Drug Resistance and Pathogenicity Biomarkers with Nanopore Sequencing. Microorganisms 2022; 10:2256. [PMID: 36422326 PMCID: PMC9697816 DOI: 10.3390/microorganisms10112256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 12/31/2023] Open
Abstract
The emergence of drug-resistant strains of the parasite Leishmania infantum infecting dogs and humans represents an increasing threat. L. infantum genomes are complex and unstable with extensive structural variations, ranging from aneuploidies to multiple copy number variations (CNVs). These CNVs have recently been validated as biomarkers of Leishmania concerning virulence, tissue tropism, and drug resistance. As a proof-of-concept to develop a novel diagnosis platform (LeishGenApp), four L. infantum samples from humans and dogs were nanopore sequenced. Samples were epidemiologically typed within the Mediterranean L. infantum group, identifying members of the JCP5 and non-JCP5 subgroups, using the conserved region (CR) of the maxicircle kinetoplast. Aneuploidies were frequent and heterogenous between samples, yet only chromosome 31 tetrasomy was common between all the samples. A high frequency of aneuploidies was observed for samples with long passage history (MHOM/TN/80/IPT-1), whereas fewer were detected for samples maintained in vivo (MCRI/ES/2006/CATB033). Twenty-two genes were studied to generate a genetic pharmacoresistance profile against miltefosine, allopurinol, trivalent antimonials, amphotericin, and paromomycin. MHOM/TN/80/IPT-1 and MCRI/ES/2006/CATB033 displayed a genetic profile with potential resistance against miltefosine and allopurinol. Meanwhile, MHOM/ES/2016/CATB101 and LCAN/ES/2020/CATB102 were identified as potentially resistant against paromomycin. All four samples displayed a genetic profile for resistance against trivalent antimonials. Overall, this proof-of-concept revealed the potential of nanopore sequencing and LeishGenApp for the determination of epidemiological, drug resistance, and pathogenicity biomarkers in L. infantum.
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Affiliation(s)
- Joan Martí-Carreras
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Marina Carrasco
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Marcel Gómez-Ponce
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Marc Noguera-Julián
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
| | - Roser Fisa
- Laboratori de Parasitologia, Departament de Biologia Sanitat i Mediambient, Facultat de Farmàcia I Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
| | - Cristina Riera
- Laboratori de Parasitologia, Departament de Biologia Sanitat i Mediambient, Facultat de Farmàcia I Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
| | - Maria Magdalena Alcover
- Laboratori de Parasitologia, Departament de Biologia Sanitat i Mediambient, Facultat de Farmàcia I Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain
| | - Xavier Roura
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
- Hospital Clínic Veterinari, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Lluís Ferrer
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
- Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Olga Francino
- Nano1Health S.L. (N1H), Edifici EUREKA, Parc de Recerca UAB, Bellaterra, 08193 Barcelona, Spain
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26
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Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania. PLoS Pathog 2022; 18:e1010848. [PMID: 36149920 PMCID: PMC9534393 DOI: 10.1371/journal.ppat.1010848] [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: 07/08/2022] [Revised: 10/05/2022] [Accepted: 08/30/2022] [Indexed: 11/19/2022] Open
Abstract
Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually high tolerance for aneuploidy, but the molecular and functional consequences for the pathogen remain poorly understood. Here, we addressed this question in vitro and present the first integrated analysis of the genome, transcriptome, proteome, and metabolome of highly aneuploid Leishmania donovani strains. Our analyses unambiguously establish that aneuploidy in Leishmania proportionally impacts the average transcript- and protein abundance levels of affected chromosomes, ultimately correlating with the degree of metabolic differences between closely related aneuploid strains. This proportionality was present in both proliferative and non-proliferative in vitro promastigotes. However, as in other Eukaryotes, we observed attenuation of dosage effects for protein complex subunits and in addition, non-cytoplasmic proteins. Differentially expressed transcripts and proteins between aneuploid Leishmania strains also originated from non-aneuploid chromosomes. At protein level, these were enriched for proteins involved in protein metabolism, such as chaperones and chaperonins, peptidases, and heat-shock proteins. In conclusion, our results further support the view that aneuploidy in Leishmania can be adaptive. Additionally, we believe that the high karyotype diversity in vitro and absence of classical transcriptional regulation make Leishmania an attractive model to study processes of protein homeostasis in the context of aneuploidy and beyond.
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27
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Alpizar-Sosa EA, Kumordzi Y, Wei W, Whitfield PD, Barrett MP, Denny PW. Genome deletions to overcome the directed loss of gene function in Leishmania. Front Cell Infect Microbiol 2022; 12:988688. [PMID: 36211960 PMCID: PMC9539739 DOI: 10.3389/fcimb.2022.988688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
With the global reach of the Neglected Tropical Disease leishmaniasis increasing, coupled with a tiny armory of therapeutics which all have problems with resistance, cost, toxicity and/or administration, the validation of new drug targets in the causative insect vector borne protozoa Leishmania spp is more important than ever. Before the introduction of CRISPR Cas9 technology in 2015 genetic validation of new targets was carried out largely by targeted gene knockout through homologous recombination, with the majority of genes targeted (~70%) deemed non-essential. In this study we exploit the ready availability of whole genome sequencing technology to reanalyze one of these historic cell lines, a L. major knockout in the catalytic subunit of serine palmitoyltransferase (LCB2), which causes a complete loss of sphingolipid biosynthesis but remains viable and infective. This revealed a number of Single Nucleotide Polymorphisms, but also the complete loss of several coding regions including a gene encoding a putative ABC3A orthologue, a putative sterol transporter. Hypothesizing that the loss of such a transporter may have facilitated the directed knockout of the catalytic subunit of LCB2 and the complete loss of de novo sphingolipid biosynthesis, we re-examined LCB2 in a L. mexicana line engineered for straightforward CRISPR Cas9 directed manipulation. Strikingly, LCB2 could not be knocked out indicating essentiality. However, simultaneous deletion of LCB2 and the putative ABC3A was possible. This indicated that the loss of the putative ABC3A facilitated the loss of sphingolipid biosynthesis in Leishmania, and suggested that we should re-examine the many other Leishmania knockout lines where genes were deemed non-essential.
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Affiliation(s)
| | - Yasmine Kumordzi
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Wenbin Wei
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Phillip D. Whitfield
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Michael P. Barrett
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom,Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Paul W. Denny
- Department of Biosciences, Durham University, Durham, United Kingdom,*Correspondence: Paul W. Denny,
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Ghosh S, Kumar V, Verma A, Sharma T, Pradhan D, Selvapandiyan A, Salotra P, Singh R. Genome-wide analysis reveals allelic variation and chromosome copy number variation in paromomycin-resistant Leishmania donovani. Parasitol Res 2022; 121:3121-3132. [PMID: 36056959 DOI: 10.1007/s00436-022-07645-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022]
Abstract
In the absence of adequate diagnosis and treatment, leishmaniasis remains a major public health concern on a global scale. Drug resistance remains a key obstacle in controlling and eliminating visceral leishmaniasis. The therapeutic gap due to lack of target-specific medicine and vaccine can be minimized by obtaining parasite's genomic information. This study compared whole-genome sequence of paromomycin-resistant parasite (K133PMM) developed through in vitro adaptation and selection with sensitive Leishmania clinical isolate (K133WT). We found a large number of upstream and intergenic gene variations in K133PMM. There were 259 single nucleotide polymorphisms (SNPs), 187 insertion-deletion (InDels), and 546 copy number variations (CNVs) identified. Most of the genomic variations were found in the gene's upstream and non-coding regions. Ploidy estimation revealed chromosome 5 in tetrasomy and 6, 9, and 12 in trisomy, uniquely in K133PMM. These contain the genes for protein degradation, parasite motility, autophagy, cell cycle maintenance, and drug efflux membrane transporters. Furthermore, we also observed reduction in ploidy of chromosomes 15, 20, and 23, in the resistant parasite containing mostly the genes for hypothetical proteins and membrane transporters. We chronicled correlated genomic conversion and aneuploidy in parasites and hypothesize that this led to rapid evolutionary changes in response to drug induced pressure, which causes them to become resistant.
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Affiliation(s)
- Sushmita Ghosh
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.,Department of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Vinay Kumar
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Aditya Verma
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Tanya Sharma
- ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, New Delhi, 110029, India
| | - Dibyabhaba Pradhan
- ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, New Delhi, 110029, India
| | | | - Poonam Salotra
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Ruchi Singh
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.
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29
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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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Transcriptome Analysis of Intracellular Amastigotes of Clinical Leishmania infantum Lines from Therapeutic Failure Patients after Infection of Human Macrophages. Microorganisms 2022; 10:microorganisms10071304. [PMID: 35889023 PMCID: PMC9324091 DOI: 10.3390/microorganisms10071304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is considered to be one of the most neglected tropical diseases affecting humans and animals around the world. Due to the absence of an effective vaccine, current treatment is based on chemotherapy. However, the continuous appearance of drug resistance and therapeutic failure (TF) lead to an early obsolescence of treatments. Identification of the factors that contribute to TF and drug resistance in leishmaniasis will constitute a useful tool for establishing future strategies to control this disease. In this manuscript, we evaluated the transcriptomic changes in the intracellular amastigotes of the Leishmania infantum parasites isolated from patients with leishmaniasis and TF at 96 h post-infection of THP-1 cells. The adaptation of the parasites to their new environment leads to expression alterations in the genes involved mainly in the transport through cell membranes, energy and redox metabolism, and detoxification. Specifically, the gene that codes for the prostaglandin f2α synthase seems to be relevant in the pathogenicity and TF since it appears substantially upregulated in all the L. infantum lines. Overall, our results show that at the late infection timepoint, the transcriptome of the parasites undergoes significant changes that probably improve the survival of the Leishmania lines in the host cells, contributing to the TF phenotype as well as drug therapy evasion.
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An In-depth Proteomic Map of Leishmania donovani Isolate from Post Kala-azar Dermal Leishmaniasis (PKDL) Patient. Acta Parasitol 2022; 67:687-696. [PMID: 35020128 DOI: 10.1007/s11686-021-00511-3] [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: 08/10/2021] [Accepted: 12/09/2021] [Indexed: 11/01/2022]
Abstract
BACKGROUND The trypanosomatid protozoan parasite Leishmania donovani is the etiological agent of visceral leishmaniasis (VL) or kala-azar. The patients that have undergone treatment may still harbor the parasite and in a small fraction of the patients the disease re-erupts in the form of post kala-azar dermal leishmaniasis (PKDL). PKDL is a pathological condition found to be intermediate between VL and complete cure of VL. The PKDL disease progression is determined by the host immune response to L. donovani. The majority of the proteomic studies on L. donovani till date have been undertaken on parasites either isolated from kala-azar patients or on established laboratory strains of L. donovani. However, no proteomic information is available on the cutaneous localized isolates of L. donovani from PKDL patients. METHODS The promastigote stage of L. donovani isolate from PKDL patient was cultured and harvested. The cell lysates were trypsin digested, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The LC-MS/MS raw data were analyzed on Proteome Discoverer. Further bioinformatics analysis was carried out. RESULTS In the present, we have used high-resolution mass spectrometry to map the global proteome of a L. donovani isolate from PKDL patient. This in-depth study resulted in the identification of 5537 unique proteins from PKDL isolate of L. donovani which covered 64% of its proteome. OUTCOME This study also identified proteins previously shown to be upregulated in PKDL L. donovani. This is the most in-depth proteome of Leishmania donovani parasite till date.
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Cruz-Saavedra L, Schwabl P, Vallejo GA, Carranza JC, Muñoz M, Patino LH, Paniz-Mondolfi A, Llewellyn MS, Ramírez JD. Genome plasticity driven by aneuploidy and loss of heterozygosity in Trypanosoma cruzi. Microb Genom 2022; 8. [PMID: 35748878 PMCID: PMC9455712 DOI: 10.1099/mgen.0.000843] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma cruzi the causative agent of Chagas disease shows a marked genetic diversity and divided into at least six Discrete Typing Units (DTUs). High intra genetic variability has been observed in the TcI DTU, the most widely distributed DTU, where patterns of genomic diversity can provide information on ecological and evolutionary processes driving parasite population structure and genome organization. Chromosomal aneuploidies and rearrangements across multigene families represent an evidence of T. cruzi genome plasticity. We explored genomic diversity among 18 Colombian T. cruzi I clones and 15 T. cruzi I South American strains. Our results confirm high genomic variability, heterozygosity and presence of a clade compatible with the TcIdom genotype, described for strains from humans in Colombia and Venezuela. TcI showed high structural plasticity across the geographical region studied. Differential events of whole and segmental aneuploidy (SA) along chromosomes even between clones from the same strain were found and corroborated by the depth and allelic frequency. We detected loss of heterozygosity (LOH) events in different chromosomes, however, the size and location of segments under LOH varied between clones. Genes adjacent to breakpoints were evaluated, and retrotransposon hot spot genes flanked the beginning of segmental aneuploidies. Our results suggest that T. cruzi genomes, like those of Leishmania, may have a highly unstable structure and there is now an urgent need to design experiments to explore any potential adaptive role for the plasticity observed.
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Affiliation(s)
- Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Philipp Schwabl
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Gustavo A Vallejo
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Julio C Carranza
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz Helena Patino
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Alberto Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Martin S Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.,Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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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: 4] [Impact Index Per Article: 2.0] [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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Matos GM, Lewis MD, Talavera-López C, Yeo M, Grisard EC, Messenger LA, Miles MA, Andersson B. Microevolution of Trypanosoma cruzi reveals hybridization and clonal mechanisms driving rapid genome diversification. eLife 2022; 11:75237. [PMID: 35535495 PMCID: PMC9098224 DOI: 10.7554/elife.75237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/22/2022] [Indexed: 12/11/2022] Open
Abstract
Protozoa and fungi are known to have extraordinarily diverse mechanisms of genetic exchange. However, the presence and epidemiological relevance of genetic exchange in Trypanosoma cruzi, the agent of Chagas disease, has been controversial and debated for many years. Field studies have identified both predominantly clonal and sexually recombining natural populations. Two of six natural T. cruzi lineages (TcV and TcVI) show hybrid mosaicism, using analysis of single-gene locus markers. The formation of hybrid strains in vitro has been achieved and this provides a framework to study the mechanisms and adaptive significance of genetic exchange. Using whole genome sequencing of a set of experimental hybrids strains, we have confirmed that hybrid formation initially results in tetraploid parasites. The hybrid progeny showed novel mutations that were not attributable to either (diploid) parent showing an increase in amino acid changes. In long-term culture, up to 800 generations, there was a variable but gradual erosion of progeny genomes towards triploidy, yet retention of elevated copy number was observed at several core housekeeping loci. Our findings indicate hybrid formation by fusion of diploid T. cruzi, followed by sporadic genome erosion, but with substantial potential for adaptive evolution, as has been described as a genetic feature of other organisms, such as some fungi.
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Affiliation(s)
- Gabriel Machado Matos
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianopolis, Brazil.,Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Michael D Lewis
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carlos Talavera-López
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.,Institute of Computational Biology, Computational Health Centre, Helmholtz Munich, Munich, Germany
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Edmundo C Grisard
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianopolis, Brazil
| | - Louisa A Messenger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael A Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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Späth GF, Bussotti G. GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells. Nucleic Acids Res 2022; 50:e36. [PMID: 34928370 PMCID: PMC8989552 DOI: 10.1093/nar/gkab1237] [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: 07/08/2021] [Revised: 11/01/2021] [Accepted: 12/03/2021] [Indexed: 11/25/2022] Open
Abstract
Genome instability has been recognized as a key driver for microbial and cancer adaptation and thus plays a central role in many diseases. Genome instability encompasses different types of genomic alterations, yet most available genome analysis software are limited to just one type of mutation. To overcome this limitation and better understand the role of genetic changes in enhancing pathogenicity we established GIP, a novel, powerful bioinformatic pipeline for comparative genome analysis. Here, we show its application to whole genome sequencing datasets of Leishmania, Plasmodium, Candida and cancer. Applying GIP on available data sets validated our pipeline and demonstrated the power of our tool to drive biological discovery. Applied to Plasmodium vivax genomes, our pipeline uncovered the convergent amplification of erythrocyte binding proteins and identified a nullisomic strain. Re-analyzing genomes of drug adapted Candida albicans strains revealed correlated copy number variations of functionally related genes, strongly supporting a mechanism of epistatic adaptation through interacting gene-dosage changes. Our results illustrate how GIP can be used for the identification of aneuploidy, gene copy number variations, changes in nucleic acid sequences, and chromosomal rearrangements. Altogether, GIP can shed light on the genetic bases of cell adaptation and drive disease biomarker discovery.
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Affiliation(s)
- Gerald F Späth
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
| | - Giovanni Bussotti
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
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36
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Cortez DR, Lima FM, Reis-Cunha JL, Bartholomeu DC, Villacis RAR, Rogatto SR, Costa-Martins AG, Marchiano FS, do Carmo RA, da Silveira JF, Marini MM. Trypanosoma cruzi Genomic Variability: Array Comparative Genomic Hybridization Analysis of Clone and Parental Strain. Front Cell Infect Microbiol 2022; 12:760830. [PMID: 35402315 PMCID: PMC8992781 DOI: 10.3389/fcimb.2022.760830] [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: 08/18/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, exhibits extensive inter- and intrastrain genetic diversity. As we have previously described, there are some genetic differences between the parental G strain and its clone D11, which was isolated by the limiting dilution method and infection of cultured mammalian cells. Electrophoretic karyotyping and Southern blot hybridization of chromosomal bands with specific markers revealed chromosome length polymorphisms of small size with additional chromosomal bands in clone D11 and the maintenance of large syntenic groups. Both G strain and clone D11 belong to the T. cruzi lineage TcI. Here, we designed intraspecific array-based comparative genomic hybridization (aCGH) to identify chromosomal regions harboring copy-number variations between clone D11 and the G strain. DNA losses were more extensive than DNA gains in clone D11. Most alterations were flanked by repeated sequences from multigene families that could be involved in the duplication and deletion events. Several rearrangements were detected by chromoblot hybridization and confirmed by aCGH. We have integrated the information of genomic sequence data obtained by aCGH to the electrophoretic karyotype, allowing the reconstruction of possible recombination events that could have generated the karyotype of clone D11. These rearrangements may be explained by unequal crossing over between sister or homologous chromatids mediated by flanking repeated sequences and unequal homologous recombination via break-induced replication. The genomic changes detected by aCGH suggest the presence of a dynamic genome that responds to environmental stress by varying the number of gene copies and generating segmental aneuploidy.
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Affiliation(s)
- Danielle Rodrigues Cortez
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fabio Mitsuo Lima
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Centro Universitário São Camilo, Biomedicina, São Paulo, Brazil
| | - João Luís Reis-Cunha
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Silvia Regina Rogatto
- Department of Clinical Genetics, Institute of Regional Health Research, University of Southern Denmark, Vejle, Denmark
| | - André Guilherme Costa-Martins
- Department of Clinical and Toxicological Analyses, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Fernanda Sycko Marchiano
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rafaela Andrade do Carmo
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Jose Franco da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- *Correspondence: Marjorie Mendes Marini, ; Jose Franco da Silveira,
| | - Marjorie Mendes Marini
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Centro Universitário São Camilo, Biomedicina, São Paulo, Brazil
- *Correspondence: Marjorie Mendes Marini, ; Jose Franco da Silveira,
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37
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Piel L, Rajan KS, Bussotti G, Varet H, Legendre R, Proux C, Douché T, Giai-Gianetto Q, Chaze T, Cokelaer T, Vojtkova B, Gordon-Bar N, Doniger T, Cohen-Chalamish S, Rengaraj P, Besse C, Boland A, Sadlova J, Deleuze JF, Matondo M, Unger R, Volf P, Michaeli S, Pescher P, Späth GF. Experimental evolution links post-transcriptional regulation to Leishmania fitness gain. PLoS Pathog 2022; 18:e1010375. [PMID: 35294501 PMCID: PMC8959184 DOI: 10.1371/journal.ppat.1010375] [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: 12/30/2021] [Revised: 03/28/2022] [Accepted: 02/15/2022] [Indexed: 12/30/2022] Open
Abstract
The protozoan parasite Leishmania donovani causes fatal human visceral leishmaniasis in absence of treatment. Genome instability has been recognized as a driver in Leishmania fitness gain in response to environmental change or chemotherapy. How genome instability generates beneficial phenotypes despite potential deleterious gene dosage effects is unknown. Here we address this important open question applying experimental evolution and integrative systems approaches on parasites adapting to in vitro culture. Phenotypic analyses of parasites from early and late stages of culture adaptation revealed an important fitness tradeoff, with selection for accelerated growth in promastigote culture (fitness gain) impairing infectivity (fitness costs). Comparative genomics, transcriptomics and proteomics analyses revealed a complex regulatory network associated with parasite fitness gain, with genome instability causing highly reproducible, gene dosage-independent and -dependent changes. Reduction of flagellar transcripts and increase in coding and non-coding RNAs implicated in ribosomal biogenesis and protein translation were not correlated to dosage changes of the corresponding genes, revealing a gene dosage-independent, post-transcriptional mechanism of regulation. In contrast, abundance of gene products implicated in post-transcriptional regulation itself correlated to corresponding gene dosage changes. Thus, RNA abundance during parasite adaptation is controled by direct and indirect gene dosage changes. We correlated differential expression of small nucleolar RNAs (snoRNAs) with changes in rRNA modification, providing first evidence that Leishmania fitness gain in culture may be controlled by post-transcriptional and epitranscriptomic regulation. Our findings propose a novel model for Leishmania fitness gain in culture, where differential regulation of mRNA stability and the generation of modified ribosomes may potentially filter deleterious from beneficial gene dosage effects and provide proteomic robustness to genetically heterogenous, adapting parasite populations. This model challenges the current, genome-centric approach to Leishmania epidemiology and identifies the Leishmania transcriptome and non-coding small RNome as potential novel sources for the discovery of biomarkers that may be associated with parasite phenotypic adaptation in clinical settings. Genome instability plays a central yet poorly understood role in human disease. Gene amplifications and deletions drive cancer development, microbial infection and therapeutic failure. The molecular mechanisms that harness the deleterious effects of genome instability to generate beneficial phenotypes in pathogenic systems are unknown. Here we study this important open question in the protozoan parasite Leishmania that causes devastating human diseases termed leishmaniases. Leishmania parasites lack transcriptional control and instead exploit genome instability to adapt to their host environment. Analyzing in vitro adaptation of hamster-derived parasites via gene copy number (genomic level) and gene expression changes (transcriptomic and proteomic levels), we show that these parasites likely exploit small nucleolar RNAs (snoRNAs) to mitigate toxic effects of genome instability by post-transcriptional regulation and the establishment of modified ribosomes. Our findings propose non-coding RNAs as potential novel biomarkers with diagnostic and prognostic value that may be linked to changes in parasite tissue tropism or drug susceptibility. This novel insight into Leishmania adaptation will be likely applicable to other fast evolving eukaryotic systems with unstable genomes, such as fungi or cancer cells.
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Affiliation(s)
- Laura Piel
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
| | - K. Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Giovanni Bussotti
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
| | - Hugo Varet
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Caroline Proux
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Thibaut Douché
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Quentin Giai-Gianetto
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Thibault Chaze
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Barbora Vojtkova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Nadav Gordon-Bar
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Praveenkumar Rengaraj
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Céline Besse
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Jovana Sadlova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Mariette Matondo
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Pascale Pescher
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- * E-mail: (PP); (GS)
| | - Gerald F. Späth
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- * E-mail: (PP); (GS)
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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: 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: 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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Genomic and Phenotypic Characterization of Experimentally Selected Resistant Leishmania donovani Reveals a Role for Dynamin-1-Like Protein in the Mechanism of Resistance to a Novel Antileishmanial Compound. mBio 2022; 13:e0326421. [PMID: 35012338 PMCID: PMC8749414 DOI: 10.1128/mbio.03264-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The implementation of prospective drug resistance (DR) studies in the research-and-development (R&D) pipeline is a common practice for many infectious diseases but not for neglected tropical diseases (NTDs). Here, we explored and demonstrated the importance of this approach using as paradigms Leishmania donovani, the etiological agent of visceral leishmaniasis (VL), and TCMDC-143345, a promising compound of the GlaxoSmithKline (GSK) "Leishbox" to treat VL. We experimentally selected resistance to TCMDC-143345 in vitro and characterized resistant parasites at the genomic and phenotypic levels. We found that it took more time to develop resistance to TCMDC-143345 than to other drugs in clinical use and that there was no cross-resistance to these drugs, suggesting a new and unique mechanism. By whole-genome sequencing, we found two mutations in the gene encoding the L. donovani dynamin-1-like protein (LdoDLP1) that were fixed at the highest drug pressure. Through phylogenetic analysis, we identified LdoDLP1 as a family member of the dynamin-related proteins, a group of proteins that impacts the shapes of biological membranes by mediating fusion and fission events, with a putative role in mitochondrial fission. We found that L. donovani lines genetically engineered to harbor the two identified LdoDLP1 mutations were resistant to TCMDC-143345 and displayed altered mitochondrial properties. By homology modeling, we showed how the two LdoDLP1 mutations may influence protein structure and function. Taken together, our data reveal a clear involvement of LdoDLP1 in the adaptation/reduced susceptibility of L. donovani to TCMDC-143345. IMPORTANCE Humans and their pathogens are continuously locked in a molecular arms race during which the eventual emergence of pathogen drug resistance (DR) seems inevitable. For neglected tropical diseases (NTDs), DR is generally studied retrospectively once it has already been established in clinical settings. We previously recommended to keep one step ahead in the host-pathogen arms race and implement prospective DR studies in the R&D pipeline, a common practice for many infectious diseases but not for NTDs. Here, using Leishmania donovani, the etiological agent of visceral leishmaniasis (VL), and TCMDC-143345, a promising compound of the GSK Leishbox to treat VL, as paradigms, we experimentally selected resistance to the compound and proceeded to genomic and phenotypic characterization of DR parasites. The results gathered in the present study suggest a new DR mechanism involving the L. donovani dynamin-1-like protein (LdoDLP1) and demonstrate the practical relevance of prospective DR studies.
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40
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Lypaczewski P, Thakur L, Jain A, Kumari S, Paulini K, Matlashewski G, Jain M. An intraspecies Leishmania donovani hybrid from the Indian subcontinent is associated with an atypical phenotype of cutaneous disease. iScience 2022; 25:103802. [PMID: 35198868 PMCID: PMC8841885 DOI: 10.1016/j.isci.2022.103802] [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: 11/12/2021] [Revised: 01/11/2022] [Accepted: 01/20/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is a neglected tropical disease endemic in over 90 countries. The disease has two main pathologies; cutaneous leishmaniasis (CL) that generally self-heals, and visceral leishmaniasis (VL) that is fatal if untreated. The majority of VL cases, concentrated on the Indian subcontinent (ISC) and East Africa, are caused by Leishmania donovani. However, recent foci of CL on the ISC have been attributed as an atypical phenotype of L. donovani including a recent outbreak in Himachal Pradesh, India. Whole genome sequencing and phylogenetic analysis was undertaken to investigate the origins and genetic factors leading to this pathology atypical of L. donovani. Here we demonstrate the isolate from Himachal Pradesh is derived from a genetic hybridization between two independent L. donovani parents from the 'Yeti' ISC1 divergent clade of parasites, identified in the Nepalese highlands. This reveals that intraspecies L. donovani hybrids can give rise to a novel strain associated with CL.
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Affiliation(s)
- Patrick Lypaczewski
- Department of Microbiology and Immunology, McGill University, 3775 University St, Montreal H3A 2B4, Canada
| | - Lovlesh Thakur
- Department of Zoology, Central University of Punjab, Bathinda, Punjab, India
| | - Aklank Jain
- Department of Zoology, Central University of Punjab, Bathinda, Punjab, India
| | - Sandhya Kumari
- Indira Gandhi Medical College, Shimla, Himachal Pradesh, India
| | - Kayla Paulini
- Department of Microbiology and Immunology, McGill University, 3775 University St, Montreal H3A 2B4, Canada
| | - Greg Matlashewski
- Department of Microbiology and Immunology, McGill University, 3775 University St, Montreal H3A 2B4, Canada
| | - Manju Jain
- Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, India
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41
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Monte-Neto RL, Fernandez-Prada C, Moretti NS. Sex under pressure: stress facilitates Leishmania in vitro hybridization. Trends Parasitol 2022; 38:274-276. [PMID: 35181250 DOI: 10.1016/j.pt.2022.02.001] [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: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 10/19/2022]
Abstract
The selection of Leishmania hybrids in axenic culture was considered rare until recently, when Louradour and Ferreira et al., demonstrated that induced DNA damage facilitates genetic exchange, resulting in full genome tetraploid progenies in vitro. Meiosis-related gene homologues HAP2, GEX1, and RAD51 were found to be involved, opening new avenues for functional genomic studies.
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Affiliation(s)
- Rubens L Monte-Neto
- Biotecnologia Aplicada ao Estudo de Patógenos (BAP) - Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brasil.
| | - Christopher Fernandez-Prada
- Faculté de Médecine Vétérinaire, Département de Pathologie et Microbiologie, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Nilmar S Moretti
- Laboratório de Biologia Molecular de Patógenos (LBMP) - Departamento de Microbiologia, Imunologia e Parasitologia - Universidade Federal de São Paulo, São Paulo, SP, Brasil
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Pinho N, Bombaça AC, Wiśniewski JR, Dias-Lopes G, Saboia-Vahia L, Cupolillo E, de Jesus JB, de Almeida RP, Padrón G, Menna-Barreto R, Cuervo P. Nitric Oxide Resistance in Leishmania ( Viannia) braziliensis Involves Regulation of Glucose Consumption, Glutathione Metabolism and Abundance of Pentose Phosphate Pathway Enzymes. Antioxidants (Basel) 2022; 11:277. [PMID: 35204161 PMCID: PMC8868067 DOI: 10.3390/antiox11020277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 11/16/2022] Open
Abstract
In American Tegumentary Leishmaniasis production of cytokines, reactive oxygen species and nitric oxide (NO) by host macrophages normally lead to parasite death. However, some Leishmania braziliensis strains exhibit natural NO resistance. NO-resistant strains cause more lesions and are frequently more resistant to antimonial treatment than NO-susceptible ones, suggesting that NO-resistant parasites are endowed with specific mechanisms of survival and persistence. To tests this, we analyzed the effect of pro- and antioxidant molecules on the infectivity in vitro of L. braziliensis strains exhibiting polar phenotypes of resistance or susceptibility to NO. In addition, we conducted a comprehensive quantitative mass spectrometry-based proteomics analysis of those parasites. NO-resistant parasites were more infective to peritoneal macrophages, even in the presence of high levels of reactive species. Principal component analysis of protein concentration values clearly differentiated NO-resistant from NO-susceptible parasites, suggesting that there are natural intrinsic differences at molecular level among those strains. Upon NO exposure, NO-resistant parasites rapidly modulated their proteome, increasing their total protein content and glutathione (GSH) metabolism. Furthermore, NO-resistant parasites showed increased glucose analogue uptake, and increased abundance of phosphotransferase and G6PDH after nitrosative challenge, which can contribute to NADPH pool maintenance and fuel the reducing conditions for the recovery of GSH upon NO exposure. Thus, increased glucose consumption and GSH-mediated redox capability may explain the natural resistance of L. braziliensis against NO.
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Affiliation(s)
- Nathalia Pinho
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (N.P.); (L.S.-V.); (E.C.); (G.P.)
| | - Ana Cristina Bombaça
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil;
| | - Jacek R. Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, 82152 Planegg, Germany;
| | - Geovane Dias-Lopes
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil;
| | - Leonardo Saboia-Vahia
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (N.P.); (L.S.-V.); (E.C.); (G.P.)
| | - Elisa Cupolillo
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (N.P.); (L.S.-V.); (E.C.); (G.P.)
| | - José Batista de Jesus
- Departamento de Medicina, Universidade Federal de São João Del Rei, São João del Rei 35501-296, MG, Brazil;
| | - Roque P. de Almeida
- Department of Medicine, Hospital Universitário, EBSERH, Universidade Federal de Sergipe, Aracaju 49100-000, SE, Brazil;
| | - Gabriel Padrón
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (N.P.); (L.S.-V.); (E.C.); (G.P.)
| | - Rubem Menna-Barreto
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil;
| | - Patricia Cuervo
- Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (N.P.); (L.S.-V.); (E.C.); (G.P.)
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43
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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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Negreira GH, Monsieurs P, Imamura H, Maes I, Kuk N, Yagoubat A, Van den Broeck F, Sterkers Y, Dujardin JC, Domagalska M. High throughput single-cell genome sequencing gives insights into the generation and evolution of mosaic aneuploidy in Leishmania donovani. Nucleic Acids Res 2022; 50:293-305. [PMID: 34893872 PMCID: PMC8886908 DOI: 10.1093/nar/gkab1203] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/17/2021] [Accepted: 11/23/2021] [Indexed: 11/14/2022] Open
Abstract
Leishmania, a unicellular eukaryotic parasite, is a unique model for aneuploidy and cellular heterogeneity, along with their potential role in adaptation to environmental stresses. Somy variation within clonal populations was previously explored in a small subset of chromosomes using fluorescence hybridization methods. This phenomenon, termed mosaic aneuploidy (MA), might have important evolutionary and functional implications but remains under-explored due to technological limitations. Here, we applied and validated a high throughput single-cell genome sequencing method to study for the first time the extent and dynamics of whole karyotype heterogeneity in two clonal populations of Leishmania promastigotes representing different stages of MA evolution in vitro. We found that drastic changes in karyotypes quickly emerge in a population stemming from an almost euploid founder cell. This possibly involves polyploidization/hybridization at an early stage of population expansion, followed by assorted ploidy reduction. During further stages of expansion, MA increases by moderate and gradual karyotypic alterations, affecting a defined subset of chromosomes. Our data provide the first complete characterization of MA in Leishmania and pave the way for further functional studies.
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Affiliation(s)
- Gabriel H Negreira
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
| | - Pieter Monsieurs
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
| | - Hideo Imamura
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
| | - Ilse Maes
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
| | - Nada Kuk
- MiVEGEC, University of Montpellier, CNRS, IRD,
Montpellier, France
| | - Akila Yagoubat
- MiVEGEC, University of Montpellier, CNRS, IRD,
Montpellier, France
| | - Frederik Van den Broeck
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation,
Rega Institute for Medical Research, Katholieke Universiteit
Leuven, 3000 Leuven, Belgium
| | - Yvon Sterkers
- MiVEGEC, University of Montpellier, CNRS, IRD,
Montpellier, France
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Institute of Tropical
Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of
Antwerp, Belgium
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45
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Glans H, Lind Karlberg M, Advani R, Bradley M, Alm E, Andersson B, Downing T. High genome plasticity and frequent genetic exchange in Leishmania tropica isolates from Afghanistan, Iran and Syria. PLoS Negl Trop Dis 2021; 15:e0010110. [PMID: 34968388 PMCID: PMC8754299 DOI: 10.1371/journal.pntd.0010110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/12/2022] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Background The kinetoplastid protozoan Leishmania tropica mainly causes cutaneous leishmaniasis in humans in the Middle East, and relapse or treatment failure after treatment are common in this area. L. tropica’s digenic life cycle includes distinct stages in the vector sandfly and the mammalian host. Sexual reproduction and genetic exchange appear to occur more frequently than in other Leishmania species. Understanding these processes is complicated by chromosome instability during cell division that yields aneuploidy, recombination and heterozygosity. This combination of rare recombination and aneuploid permits may reveal signs of hypothetical parasexual mating, where diploid cells fuse to form a transient tetraploid that undergoes chromosomal recombination and gradual chromosomal loss. Methodology/principal findings The genome-wide SNP diversity from 22 L. tropica isolates showed chromosome-specific runs of patchy heterozygosity and extensive chromosome copy number variation. All these isolates were collected during 2007–2017 in Sweden from patients infected in the Middle East and included isolates from a patient possessing two genetically distinct leishmaniasis infections three years apart with no evidence of re-infection. We found differing ancestries on the same chromosome (chr36) across multiple samples: matching the reference genome with few derived alleles, followed by blocks of heterozygous SNPs, and then by clusters of homozygous SNPs with specific recombination breakpoints at an inferred origin of replication. Other chromosomes had similar marked changes in heterozygosity at strand-switch regions separating polycistronic transcriptional units. Conclusion/significance These large-scale intra- and inter-chromosomal changes in diversity driven by recombination and aneuploidy suggest multiple mechanisms of cell reproduction and diversification in L. tropica, including mitotic, meiotic and parasexual processes. It underpins the need for more genomic surveillance of Leishmania, to detect emerging hybrids that could spread more widely and to better understand the association between genetic variation and treatment outcome. Furthering our understanding of Leishmania genome evolution and ancestry will aid better diagnostics and treatment for cutaneous leishmaniasis caused by L.tropica in the Middle East. Cutaneous leishmaniasis is mainly caused by Leishmania tropica in the Middle East, where it is known for treatment failure and a need for prolonged and/or multiple treatments. Several factors affect the clinical presentation and treatment outcome, such as host genetic variability and specific immune response, as well as environmental factors and the vector species. Little is known about the parasite genome and its influence on treatment response. By analysing the genome of 22 isolates of L. tropica, we have revealed extensive genomic variation and a complex population structure with evidence of genetic exchange within and among the isolates, indicating a possible presence of sexual or parasexual mechanisms. Understanding the Leishmania genome better may improve future treatment and better understanding of treatment failure and relapse.
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Affiliation(s)
- Hedvig Glans
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Dermatology & Venerology, Dept of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Maria Lind Karlberg
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Reza Advani
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Maria Bradley
- Division of Dermatology & Venerology, Dept of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venerology, Karolinska University Hospital, Stockholm, Sweden
| | - Erik Alm
- The European Center for Disease Prevention and Control, Stockholm, Sweden
| | - Björn Andersson
- Department of Cell & Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland
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46
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Genome instability drives epistatic adaptation in the human pathogen Leishmania. Proc Natl Acad Sci U S A 2021; 118:2113744118. [PMID: 34903666 PMCID: PMC8713814 DOI: 10.1073/pnas.2113744118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 01/25/2023] Open
Abstract
Chromosome and gene copy number variations often correlate with the evolution of microbial and cancer drug resistance, thus causing important human mortality. How genome instability is harnessed to generate beneficial phenotypes and how deleterious gene dosage effects are compensated remain open questions. The protist pathogen Leishmania exploits genome instability to regulate expression via gene dosage changes. Using these parasites as a unique model system, we uncover complex epistatic interactions between gene copy number variations and compensatory transcriptomic responses as key processes that harness genome instability for adaptive evolution in Leishmania. Our results propose a model of eukaryotic fitness gain that may be broadly applicable to pathogenic fungi or tumor cells known to exploit genome instability for adaptation. How genome instability is harnessed for fitness gain despite its potential deleterious effects is largely elusive. An ideal system to address this important open question is provided by the protozoan pathogen Leishmania, which exploits frequent variations in chromosome and gene copy number to regulate expression levels. Using ecological genomics and experimental evolution approaches, we provide evidence that Leishmania adaptation relies on epistatic interactions between functionally associated gene copy number variations in pathways driving fitness gain in a given environment. We further uncover posttranscriptional regulation as a key mechanism that compensates for deleterious gene dosage effects and provides phenotypic robustness to genetically heterogenous parasite populations. Finally, we correlate dynamic variations in small nucleolar RNA (snoRNA) gene dosage with changes in ribosomal RNA 2′-O-methylation and pseudouridylation, suggesting translational control as an additional layer of parasite adaptation. Leishmania genome instability is thus harnessed for fitness gain by genome-dependent variations in gene expression and genome-independent compensatory mechanisms. This allows for polyclonal adaptation and maintenance of genetic heterogeneity despite strong selective pressure. The epistatic adaptation described here needs to be considered in Leishmania epidemiology and biomarker discovery and may be relevant to other fast-evolving eukaryotic cells that exploit genome instability for adaptation, such as fungal pathogens or cancer.
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47
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Grace CA, Forrester S, Silva VC, Carvalho KSS, Kilford H, Chew YP, James S, Costa DL, Mottram JC, Costa CCHN, Jeffares DC. Candidates for Balancing Selection in Leishmania donovani Complex Parasites. Genome Biol Evol 2021; 13:6448231. [PMID: 34865011 PMCID: PMC8717319 DOI: 10.1093/gbe/evab265] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 12/19/2022] Open
Abstract
The Leishmania donovani species complex is the causative agent of visceral leishmaniasis, which cause 20–40,000 fatalities a year. Here, we conduct a screen for balancing selection in this species complex. We used 384 publicly available L. donovani and L. infantum genomes, and sequence 93 isolates of L. infantum from Brazil to describe the global diversity of this species complex. We identify five genetically distinct populations that are sufficiently represented by genomic data to search for signatures of selection. We find that signals of balancing selection are generally not shared between populations, consistent with transient adaptive events, rather than long-term balancing selection. We then apply multiple diversity metrics to identify candidate genes with robust signatures of balancing selection, identifying a curated set of 24 genes with robust signatures. These include zeta toxin, nodulin-like, and flagellum attachment proteins. This study highlights the extent of genetic divergence between L. donovani complex parasites and provides genes for further study.
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Affiliation(s)
- Cooper Alastair Grace
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Sarah Forrester
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Vladimir Costa Silva
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Kátia Silene Sousa Carvalho
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Hannah Kilford
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Yen Peng Chew
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom.,Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sally James
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Dorcas L Costa
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Jeremy C Mottram
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Carlos C H N Costa
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Daniel C Jeffares
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
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Cosentino RO, Brink BG, Siegel TN. Allele-specific assembly of a eukaryotic genome corrects apparent frameshifts and reveals a lack of nonsense-mediated mRNA decay. NAR Genom Bioinform 2021; 3:lqab082. [PMID: 34541528 PMCID: PMC8445201 DOI: 10.1093/nargab/lqab082] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/25/2021] [Accepted: 09/06/2021] [Indexed: 11/14/2022] Open
Abstract
To date, most reference genomes represent a mosaic consensus sequence in which the homologous chromosomes are collapsed into one sequence. This approach produces sequence artefacts and impedes analyses of allele-specific mechanisms. Here, we report an allele-specific genome assembly of the diploid parasite Trypanosoma brucei and reveal allelic variants affecting gene expression. Using long-read sequencing and chromosome conformation capture data, we could assign 99.5% of all heterozygote variants to a specific homologous chromosome and build a 66 Mb long allele-specific genome assembly. The phasing of haplotypes allowed us to resolve hundreds of artefacts present in the previous mosaic consensus assembly. In addition, it revealed allelic recombination events, visible as regions of low allelic heterozygosity, enabling the lineage tracing of T. brucei isolates. Interestingly, analyses of transcriptome and translatome data of genes with allele-specific premature termination codons point to the absence of a nonsense-mediated decay mechanism in trypanosomes. Taken together, this study delivers a reference quality allele-specific genome assembly of T. brucei and demonstrates the importance of such assemblies for the study of gene expression control. We expect the new genome assembly will increase the awareness of allele-specific phenomena and provide a platform to investigate them.
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Affiliation(s)
- Raúl O Cosentino
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität in Munich, Lena-Christ-Str. 48, Planegg-Martinsried 82152, Germany
| | - Benedikt G Brink
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität in Munich, Lena-Christ-Str. 48, Planegg-Martinsried 82152, Germany
| | - T Nicolai Siegel
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität in Munich, Lena-Christ-Str. 48, Planegg-Martinsried 82152, Germany
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49
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Patino LH, Castillo-Castañeda A, Muñoz M, Muskus C, Rivero-Rodríguez M, Pérez-Doria A, Bejarano EE, Ramírez JD. Revisiting the heterogeneous global genomic population structure of Leishmania infantum. Microb Genom 2021; 7. [PMID: 34491157 PMCID: PMC8715437 DOI: 10.1099/mgen.0.000640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Leishmania infantum is the main causative agent responsible for visceral leishmaniasis (VL), a disease with global distribution. The genomic structure and genetic variation of this species have been widely studied in different parts of the world. However, in some countries, this information is still yet unknown, as is the genomic behaviour of the main antigens used in VL diagnosis (rK39 and rK28), which have demonstrated variable sensitivity and specificity in a manner dependent on the geographic region analysed. The objective of this study was to explore the genomic architecture and diversity of four Colombian L. infantum isolates obtained in this study and to compare these results with the genetic analysis of 183 L. infantum isolates from across the world (obtained from public databases), as well as to analyse the whole rK39 and rK28 antigen sequences in our dataset. The results showed that, at the global level, L. infantum has high genetic homogeneity and extensive aneuploidy. Furthermore, we demonstrated that there are distinct populations of L. infantum circulating in various countries throughout the globe and that populations of distant countries have close genomic relationships. Additionally, this study demonstrated the high genetic variability of the rK28 antigen worldwide. In conclusion, our study allowed us to (i) expand our knowledge of the genomic structure of global L. infantum; (ii) describe the intra-specific genomic variability of this species; and (iii) understand the genomic characteristics of the main antigens used in the diagnosis of VL. Additionally, this is the first study to report whole-genome sequences of Colombian L. infantum isolates.
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Affiliation(s)
- Luz H Patino
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Adriana Castillo-Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Carlos Muskus
- Programa de Estudios y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Matilde Rivero-Rodríguez
- Grupo de Investigaciones Biomédicas, Universidad de Sucre, Sincelejo, Colombia.,Candidata a doctor en Medicina Tropical, Universidad de Cartagena-SUE Caribe, Colombia
| | - Alveiro Pérez-Doria
- Grupo de Investigaciones Biomédicas, Universidad de Sucre, Sincelejo, Colombia
| | - Eduar E Bejarano
- Grupo de Investigaciones Biomédicas, Universidad de Sucre, Sincelejo, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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Salloum T, Tokajian S, Hirt RP. Advances in Understanding Leishmania Pathobiology: What Does RNA-Seq Tell Us? Front Cell Dev Biol 2021; 9:702240. [PMID: 34540827 PMCID: PMC8440825 DOI: 10.3389/fcell.2021.702240] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/30/2021] [Indexed: 11/23/2022] Open
Abstract
Leishmaniasis is a vector-borne disease caused by a protozoa parasite from over 20 Leishmania species. The clinical manifestations and the outcome of the disease vary greatly. Global RNA sequencing (RNA-Seq) analyses emerged as a powerful technique to profile the changes in the transcriptome that occur in the Leishmania parasites and their infected host cells as the parasites progresses through their life cycle. Following the bite of a sandfly vector, Leishmania are transmitted to a mammalian host where neutrophils and macrophages are key cells mediating the interactions with the parasites and result in either the elimination the infection or contributing to its proliferation. This review focuses on RNA-Seq based transcriptomics analyses and summarizes the main findings derived from this technology. In doing so, we will highlight caveats in our understanding of the parasite's pathobiology and suggest novel directions for research, including integrating more recent data highlighting the role of the bacterial members of the sandfly gut microbiota and the mammalian host skin microbiota in their potential role in influencing the quantitative and qualitative aspects of leishmaniasis pathology.
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Affiliation(s)
- Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Robert P. Hirt
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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