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Mule SN, Saad JS, Sauter IP, Fernandes LR, de Oliveira GS, Quina D, Tano FT, Brandt-Almeida D, Padrón G, Stolf BS, Larsen MR, Cortez M, Palmisano G. The protein map of the protozoan parasite Leishmania (Leishmania) amazonensis, Leishmania (Viannia) braziliensis and Leishmania (Leishmania) infantum during growth phase transition and temperature stress. J Proteomics 2024; 295:105088. [PMID: 38237666 DOI: 10.1016/j.jprot.2024.105088] [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: 12/16/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
Leishmania parasites cause a spectrum of diseases termed leishmaniasis, which manifests in two main clinical forms, cutaneous and visceral leishmaniasis. Leishmania promastigotes transit from proliferative exponential to quiescent stationary phases inside the insect vector, a relevant step that recapitulates early molecular events of metacyclogenesis. During the insect blood meal of the mammalian hosts, the released parasites interact initially with the skin, an event marked by temperature changes. Deep knowledge on the molecular events activated during Leishmania-host interactions in each step is crucial to develop better therapies and to understand the pathogenesis. In this study, the proteomes of Leishmania (Leishmania) amazonensis (La), Leishmania (Viannia) braziliensis (Lb), and Leishmania (Leishmania) infantum (syn L. L. chagasi) (Lc) were analyzed using quantitative proteomics to uncover the proteome modulation in three different conditions related to growth phases and temperature shifts: 1) exponential phase (Exp); 2) stationary phase (Sta25) and; 3) stationary phase subjected to heat stress (Sta34). Functional validations were performed using orthogonal techniques, focusing on α-tubulin, gp63 and heat shock proteins (HSPs). Species-specific and condition-specific modulation highlights the plasticity of the Leishmania proteome, showing that pathways related to metabolism and cytoskeleton are significantly modulated from exponential to stationary growth phases, while protein folding, unfolded protein binding, signaling and microtubule-based movement were differentially altered during temperature shifts. This study provides an in-depth proteome analysis of three Leishmania spp., and contributes compelling evidence of the molecular alterations of these parasites in conditions mimicking the interaction of the parasites with the insect vector and vertebrate hosts. SIGNIFICANCE: Leishmaniasis disease manifests in two main clinical forms according to the infecting Leishmania species and host immune responses, cutaneous and visceral leishmaniasis. In Brazil, cutaneous leishmaniasis (CL) is associated with L. braziliensis and L. amazonensis, while visceral leishmaniasis, also called kala-azar, is caused by L. infantum. Leishmania parasites remodel their proteomes during growth phase transition and changes in their mileu imposed by the host, including temperature. In this study, we performed a quantitative mass spectrometry-based proteomics to compare the proteome of three New world Leishmania species, L. amazonensis (La), L. braziliensis (Lb) and L. infantum (syn L. chagasi) (Lc) in three conditions: a) exponential phase at 25 °C (Exp); b) stationary phase at 25 °C (Sta25) and; c) stationary phase subjected to temperature stress at 34 °C (Sta34). This study provides an in-depth proteome analysis of three Leishmania spp. with varying pathophysiological outcomes, and contributes compelling evidence of the molecular alterations of these parasites in conditions mimicking the interaction of the parasites with the insect vector and vertebrate hosts.
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Affiliation(s)
- Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Joyce Silva Saad
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Ismael Pretto Sauter
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Livia Rosa Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | | | - Daniel Quina
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Fabia Tomie Tano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Deborah Brandt-Almeida
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Gabriel Padrón
- Center for Genetic Engineering & Biotechnology, La Habana, Cuba
| | - Beatriz Simonsen Stolf
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mauro Cortez
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil.
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil; Analytical Glycoimmunology Group, Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia.
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Rambabu M, Konageni N, Vasudevan K, Dasegowda KR, Gokul A, Jayanthi S, Rohini K. Identification of key biomarkers and associated pathways of pancreatic cancer using integrated transcriptomic and gene network analysis. Saudi J Biol Sci 2023; 30:103819. [PMID: 37860809 PMCID: PMC10582056 DOI: 10.1016/j.sjbs.2023.103819] [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: 06/17/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Pancreatic cancer shows malignancy around the world standing in 4th position for causing death globally. This cancer is majorly divided into exocrine and neuroendocrine where exocrine pancreatic ductal adenocarcinoma is observed to be nearly 85% of cases. The lack of diagnosis of pancreatic cancer is considered to be one of the major drawbacks to the prognosis and treatment of pancreatic cancer patients. The survival rate after diagnosis is very low, due to the higher incidence of drug resistance to cancer which leads to an increase in the mortality rate. The transcriptome analysis for pancreatic cancer involves dataset collection from the ENA database, incorporating them into quality control analysis to the quantification process to get the summarized read counts present in collected samples and used for further differential gene expression analysis using the DESeq2 package. Additionally, explore the enriched pathways using GSEA software and represented them by utilizing the enrichment map finally, the gene network has been constructed by Cytoscape software. Furthermore, explored the hub genes that are present in the particular pathways and how they are interconnected from one pathway to another has been analyzed. Finally, we identified the CDKN1A, IL6, and MYC genes and their associated pathways can be better biomarker for the clinical processes to increase the survival rate of of pancreatic cancer.
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Affiliation(s)
- Majji Rambabu
- Department of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Nagaraj Konageni
- Department of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Karthick Vasudevan
- Department of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - K R Dasegowda
- Department of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Anand Gokul
- Department of Computer Science, University of Southern California, Los Angeles, CA, USA
| | - Sivaraman Jayanthi
- Department of Biotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Karunakaran Rohini
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
- Unit of Biochemistry, Faculty of Medicine, AIMST University, Semeling, Bedong, Malaysia
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Li Y, Ma B, Hua K, Gong H, He R, Luo R, Bi D, Zhou R, Langford PR, Jin H. PPNet: Identifying Functional Association Networks by Phylogenetic Profiling of Prokaryotic Genomes. Microbiol Spectr 2023; 11:e0387122. [PMID: 36602356 PMCID: PMC9927313 DOI: 10.1128/spectrum.03871-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/01/2022] [Indexed: 01/06/2023] Open
Abstract
Identification of microbial functional association networks allows interpretation of biological phenomena and a greater understanding of the molecular basis of pathogenicity and also underpins the formulation of control measures. Here, we describe PPNet, a tool that uses genome information and analysis of phylogenetic profiles with binary similarity and distance measures to derive large-scale bacterial gene association networks of a single species. As an exemplar, we have derived a functional association network in the pig pathogen Streptococcus suis using 81 binary similarity and dissimilarity measures which demonstrates excellent performance based on the area under the receiver operating characteristic (AUROC), the area under the precision-recall (AUPR), and a derived overall scoring method. Selected network associations were validated experimentally by using bacterial two-hybrid experiments. We conclude that PPNet, a publicly available (https://github.com/liyangjie/PPNet), can be used to construct microbial association networks from easily acquired genome-scale data. IMPORTANCE This study developed PPNet, the first tool that can be used to infer large-scale bacterial functional association networks of a single species. PPNet includes a method for assigning the uniqueness of a bacterial strain using the average nucleotide identity and the average nucleotide coverage. PPNet collected 81 binary similarity and distance measures for phylogenetic profiling and then evaluated and divided them into four groups. PPNet can effectively capture gene networks that are functionally related to phenotype from publicly prokaryotic genomes, as well as provide valuable results for downstream analysis and experiment testing.
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Affiliation(s)
- Yangjie Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Bin Ma
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Kexin Hua
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huimin Gong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rongrong He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Dingren Bi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Paul R. Langford
- Section of Paediatric Infectious Disease, Imperial College London, St Mary’s Campus, London, United Kingdom
| | - Hui Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Animal Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Provincial Key Laboratory of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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Nemati Haravani T, Parvizi P, Hejazi SH, Sedaghat MM, Eskandarian A, Nateghi Rostami M. Evaluation of expression variations in virulence-related genes of Leishmania major after several culture passages compared with Phlebotomus papatasi isolated promastigotes. PLoS One 2023; 18:e0284240. [PMID: 37053214 PMCID: PMC10101501 DOI: 10.1371/journal.pone.0284240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Cutaneous leishmaniasis (CL) is a prevalent infectious disease with considerable morbidity annually. Here, we aimed to investigate the likely variations in gene expression of glycoprotein63 (gp63), heat shock protein 70 (HSP70), histone, arginase, cysteine protease B (CPB), Leishmania homologue of receptors for activated C kinase (LACK), small hydrophilic endoplasmic reticulum-associated protein (SHERP) in metacyclic promastigotes of L. major isolated from Phlebotomus papatasi sand flies and promastigotes excessively cultured in culture medium. The parasites were collected from suspected CL cases in Pasteur Institute of Iran, cultured and inoculated into the female BALB/c mice (2×106 promastigotes). Sand flies were trapped in Qom province, fed with the blood of euthanized infected mice and subsequently dissected in order to isolate the midgut including stomodeal valve. The metacyclic promastigotes were isolated from Ph. papatasi (Pro-Ppap) using peanut agglutinin test (PNA), then continuously cultured in RPMI-1640 medium enriched with fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 mg/ml) to reach stationary phase (Pro-Stat). The gene expression was evaluated in both parasitic stages (Pro-Ppap and Pro-Stat) using qRT-PCR. Out results showed a significant increased gene expression at Pro-Ppap stage for gp63 (P = 0.002), SHERP (P = 0.001) and histone (P = 0.026) genes, in comparison with Pro-Stat stage. Noticeably, significant changes were, also, demonstrated in 10th to 15th passages [gp63 (P = 0.041), arginase (P = 0.016), LACK (P = 0.025)] and in 5th to 20th passage (SHERP) (P = 0.029). In conclusion, the findings of the present study seem to be essential in designing Leishmania studies, in particular regarding host-parasite interaction, immunization and infectivity studies.
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Affiliation(s)
- Taher Nemati Haravani
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Hossein Hejazi
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Mehdi Sedaghat
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbasali Eskandarian
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Cortazzo da Silva L, Aoki JI, Floeter-Winter LM. Finding Correlations Between mRNA and Protein Levels in Leishmania Development: Is There a Discrepancy? Front Cell Infect Microbiol 2022; 12:852902. [PMID: 35903202 PMCID: PMC9318571 DOI: 10.3389/fcimb.2022.852902] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
Multiple genes and proteins have been identified as differentially expressed in the stages of the Leishmania life cycle. The differentiation processes are implicated in specific transcriptional and proteomic adjustments driven by gene expression regulation mechanisms. Leishmania parasites lack gene-specific transcriptional control, and gene expression regulation mostly depends on posttranscriptional mechanisms. Due to the lack of transcriptional regulation, criticism regarding the relevance of transcript quantification as a possible and efficient prediction of protein levels is recurrent in studies that use transcriptomic information. The advent of high-throughput technologies has improved the analysis of genomes, transcriptomes and proteomes for different organisms under several conditions. Nevertheless, defining the correlation between transcriptional and proteomic profiles requires arduous and expensive work and remains a challenge in Leishmania. In this review, we analyze transcriptomic and proteomic data for several Leishmania species in two different stages of the parasite life cycle: metacyclogenesis and amastigogenesis (amastigote differentiation). We found a correlation between mRNA and protein levels of 60.9% and 69.8% for metacyclogenesis and amastigogenesis, respectively; showing that majority mRNA and protein levels increase or decrease concomitantly. Among the analyzed genes that did not present correlation indicate that transcriptomic data should be carefully interpreted as protein expression. We also discuss possible explanations and mechanisms involved for this lack of correlation.
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Venugopal G, Bird JT, Washam CL, Roys H, Bowlin A, Byrum SD, Weinkopff T. In vivo transcriptional analysis of mice infected with Leishmania major unveils cellular heterogeneity and altered transcriptomic profiling at single-cell resolution. PLoS Negl Trop Dis 2022; 16:e0010518. [PMID: 35789215 PMCID: PMC9286232 DOI: 10.1371/journal.pntd.0010518] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 07/15/2022] [Accepted: 05/18/2022] [Indexed: 01/02/2023] Open
Abstract
Leishmania parasites cause cutaneous leishmaniasis (CL), a disease characterized by disfiguring, ulcerative skin lesions. Both parasite and host gene expression following infection with various Leishmania species has been investigated in vitro, but global transcriptional analysis following L. major infection in vivo is lacking. Thus, we conducted a comprehensive transcriptomic profiling study combining bulk RNA sequencing (RNA-Seq) and single-cell RNA sequencing (scRNA-Seq) to identify global changes in gene expression in vivo following L. major infection. Bulk RNA-Seq analysis revealed that host immune response pathways like the antigen processing and presentation pathway were significantly enriched amongst differentially expressed genes (DEGs) upon infection, while ribosomal pathways were significantly downregulated in infected mice compared to naive controls. scRNA-Seq analyses revealed cellular heterogeneity including distinct resident and recruited cell types in the skin following murine L. major infection. Within the individual immune cell types, several DEGs indicative of many interferon induced GTPases and antigen presentation molecules were significantly enhanced in the infected ears including macrophages, resident macrophages, and inflammatory monocytes. Ingenuity Pathway Analysis of scRNA-Seq data indicated the antigen presentation pathway was increased with infection, while EIF2 signaling is the top downregulated pathway followed by eIF4/p70S6k and mTOR signaling in multiple cell types including macrophages, blood and lymphatic endothelial cells. Altogether, this transcriptomic profile highlights known recruitment of myeloid cells to lesions and recognizes a potential role for EIF2 signaling in murine L. major infection in vivo.
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Affiliation(s)
- Gopinath Venugopal
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Jordan T. Bird
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Arkansas Children’s Research Institute, Little Rock, Arkansas, United States of America
| | - Charity L. Washam
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Arkansas Children’s Research Institute, Little Rock, Arkansas, United States of America
| | - Hayden Roys
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Anne Bowlin
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Stephanie D. Byrum
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Arkansas Children’s Research Institute, Little Rock, Arkansas, United States of America
- * E-mail: (SDB); (TW)
| | - Tiffany Weinkopff
- Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- * E-mail: (SDB); (TW)
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Alonso A, Larraga J, Loayza FJ, Martínez E, Valladares B, Larraga V, Alcolea PJ. Stable Episomal Transfectant Leishmania infantum Promastigotes Over-Expressing the DEVH1 RNA Helicase Gene Down-Regulate Parasite Survival Genes. Pathogens 2022; 11:pathogens11070761. [PMID: 35890006 PMCID: PMC9323391 DOI: 10.3390/pathogens11070761] [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: 05/19/2022] [Revised: 06/10/2022] [Accepted: 06/20/2022] [Indexed: 12/10/2022] Open
Abstract
The compartmentalization of untranslated mRNA molecules in granules occurring in many eukaryotic organisms including trypanosomatids involves the formation of complexes between mRNA molecules and RNA-binding proteins (RBPs). The putative ATP-dependent DEAD/H RNA helicase (DEVH1) from Leishmania infantum (Kinetoplastida: Trypanosomatidae) is one such proteins. The objective of this research is finding differentially expressed genes in a stable episomal transfectant L. infantum promastigote line over-expressing DEVH1 in the stationary phase of growth in axenic culture to get insight into the biological roles of this RNA helicase in the parasite. Interestingly, genes related to parasite survival and virulence factors, such as the hydrophilic surface protein/small hydrophilic endoplasmic reticulum protein (HASP/SHERP) gene cluster, an amastin, and genes related to reactive oxygen species detoxification are down-regulated in DEVH1 transfectant promastigotes.
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Affiliation(s)
- Ana Alonso
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Jaime Larraga
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Francisco Javier Loayza
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Enrique Martínez
- Department of Obstetrics and Gynecology, Pediatrics, Preventive Medicine and Public Health, Toxicology, Legal and Forensic Medicine and Parasitology, Faculty of Pharmacy, University Institute of Public Health of the Canary Islands (IUETSPC), University of La Laguna (ULL), Avda, Astrofísico Francisco, Sánchez s/n, Campus de Anchieta, 38207 La Laguna, Spain; (E.M.); (B.V.)
| | - Basilio Valladares
- Department of Obstetrics and Gynecology, Pediatrics, Preventive Medicine and Public Health, Toxicology, Legal and Forensic Medicine and Parasitology, Faculty of Pharmacy, University Institute of Public Health of the Canary Islands (IUETSPC), University of La Laguna (ULL), Avda, Astrofísico Francisco, Sánchez s/n, Campus de Anchieta, 38207 La Laguna, Spain; (E.M.); (B.V.)
| | - Vicente Larraga
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Pedro José Alcolea
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
- Correspondence: ; Tel.: +34-9-1837-3112; Fax: +34-9-1536-0432
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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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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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Camacho E, González-de la Fuente S, Solana JC, Rastrojo A, Carrasco-Ramiro F, Requena JM, Aguado B. Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain. Genes (Basel) 2021; 12:genes12091359. [PMID: 34573340 PMCID: PMC8468144 DOI: 10.3390/genes12091359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.
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Alcoforado Diniz J, Chaves MM, Vaselek S, Miserani Magalhães RD, Ricci-Azevedo R, de Carvalho RVH, Lorenzon LB, Ferreira TR, Zamboni D, Walrad PB, Volf P, Sacks DL, Cruz AK. Protein methyltransferase 7 deficiency in Leishmania major increases neutrophil associated pathology in murine model. PLoS Negl Trop Dis 2021; 15:e0009230. [PMID: 33651805 PMCID: PMC7954300 DOI: 10.1371/journal.pntd.0009230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 03/12/2021] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
Leishmania major is the main causative agent of cutaneous leishmaniasis in the Old World. In Leishmania parasites, the lack of transcriptional control is mostly compensated by post-transcriptional mechanisms. Methylation of arginine is a conserved post-translational modification executed by Protein Arginine Methyltransferase (PRMTs). The genome from L. major encodes five PRMT homologs, including the cytosolic protein associated with several RNA-binding proteins, LmjPRMT7. It has been previously reported that LmjPRMT7 could impact parasite infectivity. In addition, a more recent work has clearly shown the importance of LmjPRMT7 in RNA-binding capacity and protein stability of methylation targets, demonstrating the role of this enzyme as an important epigenetic regulator of mRNA metabolism. In this study, we unveil the impact of PRMT7-mediated methylation on parasite development and virulence. Our data reveals that higher levels of LmjPRMT7 can impair parasite pathogenicity, and that deletion of this enzyme rescues the pathogenic phenotype of an attenuated strain of L. major. Interestingly, lesion formation caused by LmjPRMT7 knockout parasites is associated with an exacerbated inflammatory reaction in the tissue correlated with an excessive neutrophil recruitment. Moreover, the absence of LmjPRMT7 also impairs parasite development within the sand fly vector Phlebotomus duboscqi. Finally, a transcriptome analysis shed light onto possible genes affected by depletion of this enzyme. Taken together, this study highlights how post-transcriptional regulation can affect different aspects of the parasite biology. Understanding the genetics of Leishmania, a protozoan parasite causing leishmaniasis, is relevant for understanding fundamental questions on the pathogen’s biology and its interaction with hosts. We explore mechanisms used by Leishmania to promptly adapt to different hosts investigating the control of gene expression occurring at the post-transcriptional level in the parasite. Methylation of arginine performed by Protein Arginine Methyltransferase (PRMTs), among other post-translational modifications, may alter the function and interactions of target proteins, some of them are RNA binding proteins, known regulators of gene expression. In this study, we unveil the impact of PRMT7 on parasite development and pathogenicity. In addition to a negative correlation between the levels of LmjPRMT7 and parasite pathogenicity, we observed an impairment of the parasite development in the sand fly vector. Remarkably, despite a severe lesion development in mice, we observed no differences in parasite burden between infections with the pathogenic LmjPRMT7 knockout parasite or the attenuated parental line. Instead, the severe pathology observed is associated with an exacerbated inflammatory response correlated with excessive neutrophil recruitment.
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Affiliation(s)
- Juliana Alcoforado Diniz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Mariana M. Chaves
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Slavica Vaselek
- Department of Parasitology, Charles University, Prague, Czech Republic
| | - Rubens D. Miserani Magalhães
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rafael Ricci-Azevedo
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Renan V. H. de Carvalho
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Lucas B. Lorenzon
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Tiago R. Ferreira
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Dario Zamboni
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Petr Volf
- Department of Parasitology, Charles University, Prague, Czech Republic
| | - David L. Sacks
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Angela K. Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- * E-mail:
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Heat Shock Proteins as the Druggable Targets in Leishmaniasis: Promises and Perils. Infect Immun 2021; 89:IAI.00559-20. [PMID: 33139381 DOI: 10.1128/iai.00559-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Leishmania, the causative agent of leishmaniasis, is an intracellular pathogen that thrives in the insect gut and mammalian macrophages to complete its life cycle. Apart from temperature difference (26 to 37°C), it encounters several harsh conditions, including oxidative stress, inflammatory reactions, and low pH. Heat shock proteins (HSPs) play essential roles in cell survival by strategically reprogramming cellular processes and signaling pathways. HSPs assist cells in multiple functions, including differentiation, adaptation, virulence, and persistence in the host cell. Due to cyclical epidemiological patterns, limited chemotherapeutic options, drug resistance, and the absence of a vaccine, control of leishmaniasis remains a far-fetched dream. The essential roles of HSPs in parasitic differentiation and virulence and increased expression in drug-resistant strains highlight their importance in combating the disease. In this review, we highlighted the diverse physiological importance of HSPs present in Leishmania, emphasizing their significance in disease pathogenesis. Subsequently, we assessed the potential of HSPs as a chemotherapeutic target and underlined the challenges associated with it. Furthermore, we have summarized a few ongoing drug discovery initiatives that need to be explored further to develop clinically successful chemotherapeutic agents in the future.
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A Trypanosoma cruzi zinc finger protein that is implicated in the control of epimastigote-specific gene expression and metacyclogenesis. Parasitology 2020; 148:1171-1185. [PMID: 33190649 PMCID: PMC8312218 DOI: 10.1017/s0031182020002176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Trypanosoma cruzi has three biochemically and morphologically distinct developmental stages that are programmed to rapidly respond to environmental changes the parasite faces during its life cycle. Unlike other eukaryotes, Trypanosomatid genomes contain protein coding genes that are transcribed into polycistronic pre-mRNAs and have their expression controlled by post-transcriptional mechanisms. Transcriptome analyses comparing three stages of the T. cruzi life cycle revealed changes in gene expression that reflect the parasite adaptation to distinct environments. Several genes encoding RNA binding proteins (RBPs), known to act as key post-transcriptional regulatory factors, were also differentially expressed. We characterized one T. cruzi RBP, named TcZH3H12, which contains a zinc finger domain and is up-regulated in epimastigotes compared to trypomastigotes and amastigotes. TcZC3H12 knockout (KO) epimastigotes showed decreased growth rates and increased capacity to differentiate into metacyclic trypomastigotes. Transcriptome analyses comparing wild type and TcZC3H12 KOs revealed a TcZC3H12-dependent expression of epimastigote-specific genes such as genes encoding amino acid transporters and proteins associated with differentiation (PADs). RNA immunoprecipitation assays showed that transcripts from the PAD family interact with TcZC3H12. Taken together, these findings suggest that TcZC3H12 positively regulates the expression of genes involved in epimastigote proliferation and also acts as a negative regulator of metacyclogenesis.
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Tonione MA, Bi K, Tsutsui ND. Transcriptomic signatures of cold adaptation and heat stress in the winter ant (Prenolepis imparis). PLoS One 2020; 15:e0239558. [PMID: 33002025 PMCID: PMC7529264 DOI: 10.1371/journal.pone.0239558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
Climate change is a serious threat to biodiversity; it is therefore important to understand how animals will react to this stress. Ectotherms, such as ants, are especially sensitive to the climate as the environmental temperature influences myriad aspects of their biology, from optimal foraging time to developmental rate. In this study, we conducted an RNA-seq analysis to identify stress-induced genes in the winter ant (Prenolepis imparis). We quantified gene expression during heat and cold stress relative to a control temperature. From each of our conditions, we sequenced the transcriptome of three individuals. Our de novo assembly included 13,324 contigs that were annotated against the nr and SwissProt databases. We performed gene ontology and enrichment analyses to gain insight into the physiological processes involved in the stress response. We identified a total of 643 differentially expressed genes across both treatments. Of these, only seven genes were differentially expressed in the cold-stressed ants, which could indicate that the temperature we chose for trials did not induce a strong stress response, perhaps due to the cold adaptations of this species. Conversely, we found a strong response to heat: 426 upregulated genes and 210 downregulated genes. Of these, ten were expressed at a greater than ten-fold change relative to the control. The transcripts we could identify included those encoding for protein folding genes, heat shock proteins, histones, and Ca2+ ion transport. One of these transcripts, hsc70-4L was found to be under positive selection. We also characterized the functional categories of differentially expressed genes. These candidate genes may be functionally conserved and relevant for related species that will deal with rapid climate change.
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Affiliation(s)
- Maria Adelena Tonione
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, United States of America
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America.,Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California, United States of America
| | - Neil Durie Tsutsui
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, United States of America
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Masoudzadeh N, Östensson M, Persson J, Mashayekhi Goyonlo V, Agbajogu C, Taslimi Y, Erfanian Salim R, Zahedifard F, Mizbani A, Malekafzali Ardekani H, Gunn BM, Rafati S, Harandi AM. Molecular signatures of anthroponotic cutaneous leishmaniasis in the lesions of patients infected with Leishmania tropica. Sci Rep 2020; 10:16198. [PMID: 33004861 PMCID: PMC7529897 DOI: 10.1038/s41598-020-72671-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 08/10/2020] [Indexed: 12/23/2022] Open
Abstract
Anthroponotic cutaneous leishmaniasis (CL) caused by Leishmania tropica (L. tropica) represents a public health challenge in several resource poor settings. We herein employed a systems analysis approach to study molecular signatures of CL caused by L. tropica in the skin lesions of ulcerative CL (UCL) and non-ulcerative CL (NUCL) patients. Results from RNA-seq analysis determined shared and unique functional transcriptional pathways in the lesions of the UCL and NUCL patients. Several transcriptional pathways involved in inflammatory response were positively enriched in the CL lesions. A multiplexed inflammatory protein analysis showed differential profiles of inflammatory cytokines and chemokines in the UCL and NUCL lesions. Transcriptional pathways for Fcγ receptor dependent phagocytosis were among shared enriched pathways. Using L. tropica specific antibody (Ab)-mediated phagocytosis assays, we could substantiate Ab-dependent cellular phagocytosis (ADCP) and Ab-dependent neutrophil phagocytosis (ADNP) activities in the lesions of the UCL and NUCL patients, which correlated with L. tropica specific IgG Abs. Interestingly, a negative correlation was observed between parasite load and L. tropica specific IgG/ADCP/ADNP in the skin lesions of CL patients. These results enhance our understanding of human skin response to CL caused by L. tropica.
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Affiliation(s)
- Nasrin Masoudzadeh
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Malin Östensson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Josefine Persson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Christopher Agbajogu
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Yasaman Taslimi
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | | | - Farnaz Zahedifard
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | | | | | - Bronwyn M Gunn
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, 02139, USA
- Paul G. Allen School of Global Animal Health, Washington State University, Pullman, WA, 99164, USA
| | - Sima Rafati
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran.
| | - Ali M Harandi
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, Canada.
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Masoudzadeh N, Mizbani A, Rafati S. Transcriptomic profiling in Cutaneous Leishmaniasis patients. Expert Rev Proteomics 2020; 17:533-541. [PMID: 32886890 DOI: 10.1080/14789450.2020.1812390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Cutaneous leishmaniasis (CL), caused by different Leishmania parasite species, is associated with parasite-induced immune-mediated skin inflammation and ulceration. Whereas many CL studies focus on gene expression signatures in mouse models, the transcriptional response driving human patients in the field is less characterized. Human studies in CL disease provide the opportunity to directly investigate the host-pathogen interaction in the cutaneous lesion site. AREAS COVERED Advances in high-throughput sequencing technologies, particularly their application for evaluation of the global gene expression changes, have made transcriptomics as a powerful tool to understand the pathogen-host molecular interactions. EXPERT COMMENTARY In this review, we focus on the transcriptomics studies that have been performed so far on human blood or tissue-driven samples to investigate Leishmania parasites interplay with the CL patients. Further, we summarize microarray and RNA-seq studies associated with lesion biopsies of CL patients to discuss how current whole genome analysis along with systems biology approaches have developed novel CL biomarkers for further applications, not only for research, but also for accelerating vaccine development.
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Affiliation(s)
- Nasrin Masoudzadeh
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran , Tehran, Iran
| | - Amir Mizbani
- Department of Health Sciences and Technology, ETH Zurich , Switzerland
| | - Sima Rafati
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran , Tehran, Iran
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Aoki JI, Muxel SM, Laranjeira-Silva MF, Zampieri RA, Müller KE, Nerland AH, Floeter-Winter LM. Dual transcriptome analysis reveals differential gene expression modulation influenced by Leishmania arginase and host genetic background. Microb Genom 2020; 6:mgen000427. [PMID: 32886592 PMCID: PMC7643972 DOI: 10.1099/mgen.0.000427] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/13/2020] [Indexed: 01/04/2023] Open
Abstract
The outcome of Leishmania infection is strongly influenced by the host's genetic background. BALB/c mice are susceptible to Leishmania infection, while C57BL/6 mice show discrete resistance. Central to the fate of the infection is the availability of l-arginine and the related metabolic processes in the host and parasite. Depending on l-arginine availability, nitric oxide synthase 2 (NOS2) of the host cell produces nitric oxide (NO) controlling the parasite growth. On the other hand, Leishmania can also use host l-arginine for the production of polyamines through its own arginase activity, thus favouring parasite replication. Considering RNA-seq data, we analysed the dual modulation of host and parasite gene expression of BALB/c or C57BL/6 mouse bone marrow-derived macrophages (BMDMs) after 4 h of infection with Leishmania amazonensis wild-type (La-WT) or L. amazonensis arginase knockout (La-arg-). We identified 12 641 host transcripts and 8282 parasite transcripts by alignment analysis with the respective Mus musculus and L. mexicana genomes. The comparison of BALB/c_La-arg-versus BALB/c_La-WT revealed 233 modulated transcripts, with most related to the immune response and some related to the amino acid transporters and l-arginine metabolism. In contrast, the comparison of C57BL/6_La-arg-vs. C57BL/6_La-WT revealed only 30 modulated transcripts, including some related to the immune response but none related to amino acid transport or l-arginine metabolism. The transcriptome profiles of the intracellular amastigote revealed 94 modulated transcripts in the comparison of La-arg-_BALB/c vs. La-WT_BALB/c and 45 modulated transcripts in the comparison of La-arg-_C57BL/6 vs. La-WT_C57BL/6. Taken together, our data present new insights into the impact of parasite arginase activity on the orchestration of the host gene expression modulation, including in the immune response and amino acid transport and metabolism, mainly in susceptible BALB/c-infected macrophages. Moreover, we show how parasite arginase activity affects parasite gene expression modulation, including amino acid uptake and amastin expression.
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Affiliation(s)
- Juliana Ide Aoki
- Department of Physiology, Institute of Bioscience, University of São Paulo, São Paulo, Brazil
| | - Sandra Marcia Muxel
- Department of Physiology, Institute of Bioscience, University of São Paulo, São Paulo, Brazil
| | | | | | - Karl Erik Müller
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Internal Medicine, Drammen Hospital, Drammen, Norway
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Hailemariam S, Zhao S, Wang J. Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen. Front Microbiol 2020; 11:1826. [PMID: 33013723 PMCID: PMC7507024 DOI: 10.3389/fmicb.2020.01826] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/10/2020] [Indexed: 02/02/2023] Open
Abstract
The unclassified Succinivibrionaceae lineages are abundant in high yielding multiparous cows, and their presence is positively correlated with milk yield and fat percentage and reduces methane emissions. However, it is still unclear which species are associated with the most efficient feed nutrient utilization and productivity. Here, we used integrated whole genome sequencing and matrix-assisted laser desorption/ionization mass spectrometry, coupled with phenotypic and chemotaxonomic analysis, to characterize S. dextrinosolvens Z6, a species in Succinivibrionaceae isolated from the rumen. To assess the role of S. dextrinosolvens Z6 in nitrogen metabolism, cells grown in different nitrogen sources were analyzed by RNA sequencing. The whole genome sequence result revealed a genome size of 3.47 Mbp with 38.9% of G + C content. A total of 2993 encoding sequences account for 98%. The genes for regulating carbohydrate (10.6%) and amino acid (9%) transport and metabolism were the most abundant. ANI (Average nucleotide identity) showed that SD-Z6 was most closely related to SD-22B (99.96%). The whole genome alignment of SD-Z6 with SD-22B showed a more than 0.34 Mb nucleotide difference. Growth of SD-Z6 occurred at a temperature 36–42°C with an optimum at 39.7°C, pH 6–8; the optimum pH was 6.9 and with 0–1% (w/v) NaCl. The maximum growth (OD600 0.825 ± 0.12) and microbial crude protein (MCP) (178.2 μg/ml) were observed in cells grown in amino acid. The maximum concentration of ammonia (3.96 ± 1.2) was observed in urea containing media and 1.06 mM (26.7% of the produced) remained after 24 h incubation. Activities of urease and glutamine synthase (P < 0.01) and glutamate dehydrogenase (P < 0.05) were significantly different in nitrogen and growth phase. Glutamate synthetase (P < 0.01) was significantly different only at different growth phases. In total, 1246 differentially expressed genes (DEGs) were identified in all nitrogen. Among DEGs, 33 were related to nitrogen metabolism. Their expression correlated with nitrogen sources and the intensity of enzyme activity. This result enhances our understanding of the roles of Succinivibrionaceae in the efficient nitrogen utilization and on environmental protection.
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Affiliation(s)
- Samson Hailemariam
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Ulusan Ö, Mert U, Sadıqova A, Öztürk S, Caner A. Identification of gene expression profiles in Leishmania major infection by integrated bioinformatics analyses. Acta Trop 2020; 208:105517. [PMID: 32360239 DOI: 10.1016/j.actatropica.2020.105517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022]
Abstract
Gene expression profiling in mouse models of leishmaniasis has given useful information to understand the molecular pathways active in lesions and to discover new diagnostic/therapeutic targets. Although the host response plays a critical role in protection from leishmaniasis and promoting disease severity, there are still unexplained aspects in the mechanism of non-healing cutaneous lesions, which need biomarkers for both targeted- therapy and diagnosis. To address this, transcriptional profiling of the skin lesions obtained from BALB/c mice infected with Leishmania major and healthy skin from naïve mice were evaluated by bioinformatics analysis, and then the results were validated by Revers Transcriptase-PCR. Five genes among the up-regulated differentially expressed genes named FCGR4, CCL4, CXCL9, Arg1 and IL-1β were found to have relatively high diagnostic value for CL due to L. major. Pathway analysis revealed that Triggering Receptor Expressed On Myeloid Cells 1 (TREM1) signaling pathways are active in cutaneous lesions, providing new insights for the understanding and treatment of leishmaniasis.
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Affiliation(s)
- Özlem Ulusan
- Department of Parasitology, Ege University Medical School, Izmir, Turkey
| | - Ufuk Mert
- Department of Basic Oncology, Ege University, Institute of Health Sciences, Izmir, Turkey
| | - Aygül Sadıqova
- Infectious Disease Division, Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Sercan Öztürk
- Departments of Computer Science, Dokuz Eylül University, Izmir, Turkey
| | - Ayse Caner
- Department of Parasitology, Ege University Medical School, Izmir, Turkey; Department of Basic Oncology, Ege University, Institute of Health Sciences, Izmir, Turkey; Department of Bioinformatics, Ege University, Institute of Health Sciences, Izmir, Turkey; Departments of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Ballesteros N, Vásquez NM, Patiño LH, Cruz-Saavedra L, Ramírez JD. Minor temperature shifts do not affect chromosomal ploidy but cause transcriptomic changes in Leishmania braziliensis promastigotes in vitro. Mem Inst Oswaldo Cruz 2020; 115:e190413. [PMID: 32348407 PMCID: PMC7184772 DOI: 10.1590/0074-02760190413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/03/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The leishmaniases are complex neglected diseases caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the main etiological agent of cutaneous leishmaniasis in the New World. In recent studies, genomic changes such as chromosome and gene copy number variations (CNVs), as well as transcriptomic changes have been highlighted as mechanisms used by Leishmania species to adapt to stress situations. OBJECTIVES The aim of this study was to determine the effect of short-term minor temperature shifts in the genomic and transcriptomic responses of L. braziliensis promastigotes in vitro. METHODS Growth curves, genome and transcriptome sequencing of L. braziliensis promastigotes were conducted from cultures exposed to three different temperatures (24ºC, 28ºC and 30ºC) compared with the control temperature (26ºC). FINDINGS Our results showed a decrease in L. braziliensis proliferation at 30ºC, with around 3% of the genes showing CNVs at each temperature, and transcriptomic changes in genes encoding amastin surface-like proteins, heat shock proteins and transport proteins, which may indicate a direct response to temperature stress. MAIN CONCLUSIONS This study provides evidence that L. braziliensis promastigotes exhibit a decrease in cell density, and noticeable changes in the transcriptomic profiles. However, there were not perceptible changes at chromosome CNVs and only ~3% of the genes changed their copies in each treatment.
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Affiliation(s)
- Nathalia Ballesteros
- Universidad del Rosario, Facultad de Ciencias Naturales, Departamento de Biología, Grupo de Investigaciones Microbiológicas, Bogotá, Colombia
| | - Nubia M Vásquez
- Universidad del Rosario, Facultad de Ciencias Naturales, Departamento de Biología, Grupo de Investigaciones Microbiológicas, Bogotá, Colombia
| | - Luz H Patiño
- Universidad del Rosario, Facultad de Ciencias Naturales, Departamento de Biología, Grupo de Investigaciones Microbiológicas, Bogotá, Colombia
| | - Lissa Cruz-Saavedra
- Universidad del Rosario, Facultad de Ciencias Naturales, Departamento de Biología, Grupo de Investigaciones Microbiológicas, Bogotá, Colombia
| | - Juan David Ramírez
- Universidad del Rosario, Facultad de Ciencias Naturales, Departamento de Biología, Grupo de Investigaciones Microbiológicas, Bogotá, Colombia
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