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Feix AS, Tabaie EZ, Singh AN, Wittenberg NJ, Wilson EH, Joachim A. An in-depth exploration of the multifaceted roles of EVs in the context of pathogenic single-cell microorganisms. Microbiol Mol Biol Rev 2024:e0003724. [PMID: 38869292 DOI: 10.1128/mmbr.00037-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
SUMMARYExtracellular vesicles (EVs) have been recognized throughout scientific communities as potential vehicles of intercellular communication in both eukaryotes and prokaryotes, thereby influencing various physiological and pathological functions of both parent and recipient cells. This review provides an in-depth exploration of the multifaceted roles of EVs in the context of bacteria and protozoan parasite EVs, shedding light on their contributions to physiological processes and disease pathogenesis. These studies highlight EVs as a conserved mechanism of cellular communication, which may lead us to important breakthroughs in our understanding of infection, mechanisms of pathogenesis, and as indicators of disease. Furthermore, EVs are involved in host-microbe interactions, offering insights into the strategies employed by bacteria and protozoan parasites to modulate host responses, evade the immune system, and establish infections.
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Affiliation(s)
- Anna Sophia Feix
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Emily Z Tabaie
- Division of Biomedical Sciences, University of California, Riverside, California, USA
| | - Aarshi N Singh
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania, USA
| | | | - Emma H Wilson
- Division of Biomedical Sciences, University of California, Riverside, California, USA
| | - Anja Joachim
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
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2
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Moradimotlagh A, Brar HK, Chen S, Moon KM, Foster LJ, Reiner N, Nandan D. Characterization of Argonaute-containing protein complexes in Leishmania-infected human macrophages. PLoS One 2024; 19:e0303686. [PMID: 38781128 PMCID: PMC11115314 DOI: 10.1371/journal.pone.0303686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
The intracellular protozoan parasite Leishmania causes leishmaniasis in humans, leading to serious illness and death in tropical and subtropical areas worldwide. Unfortunately, due to the unavailability of approved vaccines for humans and the limited efficacy of available drugs, leishmaniasis is on the rise. A comprehensive understanding of host-pathogen interactions at the molecular level could pave the way to counter leishmaniasis. There is growing evidence that several intracellular pathogens target RNA interference (RNAi) pathways in host cells to facilitate their persistence. The core elements of the RNAi system are complexes of Argonaute (Ago) proteins with small non-coding RNAs, also known as RNA-induced silencing complexes (RISCs). Recently, we have shown that Leishmania modulates Ago1 protein of host macrophages for its survival. In this study, we biochemically characterize the Ago proteins' interactome in Leishmania-infected macrophages compared to non-infected cells. For this, a quantitative proteomic approach using stable isotope labelling by amino acids in cell culture (SILAC) was employed, followed by purification of host Ago-complexes using a short TNRC6 protein-derived peptide fused to glutathione S-transferase beads as an affinity matrix. Proteomic-based detailed biochemical analysis revealed Leishmania modulated host macrophage RISC composition during infection. This analysis identified 51 Ago-interacting proteins with a broad range of biological activities. Strikingly, Leishmania proteins were detected as part of host Ago-containing complexes in infected cells. Our results present the first report of comprehensive quantitative proteomics of Ago-containing complexes isolated from Leishmania-infected macrophages and suggest targeting the effector complex of host RNAi machinery. Additionally, these results expand knowledge of RISC in the context of host-pathogen interactions in parasitology in general.
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Affiliation(s)
- Atieh Moradimotlagh
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Harsimran Kaur Brar
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Stella Chen
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, B.C, Canada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, B.C, Canada
| | - Neil Reiner
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
| | - Devki Nandan
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, B.C, Canada
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3
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Menezes SA, Tasca T. Extracellular vesicles in parasitic diseases - from pathogenesis to future diagnostic tools. Microbes Infect 2024; 26:105310. [PMID: 38316376 DOI: 10.1016/j.micinf.2024.105310] [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: 11/08/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
Parasitic diseases are still a major public health problem especially among individuals of low socioeconomic status in underdeveloped countries. In recent years it has been demonstrated that parasites can release extracellular vesicles that participate in the host-parasite communication, immune evasion, and in governing processes associated with host infection. Extracellular vesicles are membrane-bound structures released into the extracellular space that can carry several types of biomolecules, including proteins, lipids, nucleic acids, and metabolites, which directly impact the target cells. Extracellular vesicles have attracted wide attention due to their relevance in host-parasite communication and for their potential value in applications such as in the diagnostic biomarker discovery. This review of the literature aimed to join the current knowledge on the role of extracellular vesicles in host-parasite interaction and summarize its molecular content, providing information for the acquisition of new tools that can be used in the diagnosis of parasitic diseases. These findings shed light to the potential of extracellular vesicle cargo derived from protozoan parasites as novel diagnostic tools.
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Affiliation(s)
- Saulo Almeida Menezes
- Faculdade de Farmácia e Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, RS, Brazil.
| | - Tiana Tasca
- Faculdade de Farmácia e Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, RS, Brazil.
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4
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Chen Q, Li D, Jiang L, Wu Y, Yuan H, Shi G, Liu F, Wu P, Jiang K. Biological functions and clinical significance of tRNA-derived small fragment (tsRNA) in tumors: Current state and future perspectives. Cancer Lett 2024; 587:216701. [PMID: 38369004 DOI: 10.1016/j.canlet.2024.216701] [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: 10/10/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
A new class of noncoding RNAs, tsRNAs are not only abundant in humans but also have high tissue specificity. Recently, an increasing number of studies have explored the correlations between tsRNAs and tumors, showing that tsRNAs can affect biological behaviors of tumor cells, such as proliferation, apoptosis and metastasis, by modulating protein translation, RNA transcription or posttranscriptional regulation. In addition, tsRNAs are widely distributed and stably expressed, which endows them with broad application prospects in diagnosing and predicting the prognosis of tumors, and they are expected to become new biomarkers. However, notably, the current research on tsRNAs still faces problems that need to be solved. In this review, we describe the characteristics of tsRNAs as well as their unique features and functions in tumors. Moreover, we also discuss the potential opportunities and challenges in clinical applications and research of tsRNAs.
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Affiliation(s)
- Qun Chen
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Danrui Li
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Luyang Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Yuan
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guodong Shi
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fengyuan Liu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengfei Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Kuirong Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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5
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Panstruga R, Spanu P. Transfer RNA and ribosomal RNA fragments - emerging players in plant-microbe interactions. THE NEW PHYTOLOGIST 2024; 241:567-577. [PMID: 37985402 DOI: 10.1111/nph.19409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023]
Abstract
According to current textbooks, the principal task of transfer and ribosomal RNAs (tRNAs and rRNAs, respectively) is synthesizing proteins. During the last decade, additional cellular roles for precisely processed tRNA and rRNAs fragments have become evident in all kingdoms of life. These RNA fragments were originally overlooked in transcriptome datasets or regarded as unspecific degradation products. Upon closer inspection, they were found to engage in a variety of cellular processes, in particular the modulation of translation and the regulation of gene expression by sequence complementarity- and Argonaute protein-dependent gene silencing. More recently, the presence of tRNA and rRNA fragments has also been recognized in the context of plant-microbe interactions, both on the plant and the microbial side. While most of these fragments are likely to affect endogenous processes, there is increasing evidence for their transfer across kingdoms in the course of such interactions; these processes may involve mutual exchange in association with extracellular vesicles. Here, we summarize the state-of-the-art understanding of tRNA and rRNA fragment's roles in the context of plant-microbe interactions, their potential biogenesis, presumed delivery routes, and presumptive modes of action.
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Affiliation(s)
- Ralph Panstruga
- RWTH Aachen University, Worringerweg 1, Aachen, 52056, Germany
| | - Pietro Spanu
- Department of Life Sciences, Imperial College London, Imperial College Road, London, SW7 2AZ, UK
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6
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Ma F, Zhang S, Akanyibah FA, Zhang W, Chen K, Ocansey DKW, Lyu C, Mao F. Exosome-mediated macrophage regulation for inflammatory bowel disease repair: a potential target of gut inflammation. Am J Transl Res 2023; 15:6970-6987. [PMID: 38186999 PMCID: PMC10767518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/14/2023] [Indexed: 01/09/2024]
Abstract
Inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC), is a complex condition without a definite cause. During IBD, immune cells such as macrophages release proinflammatory cytokines and chemokines, contributing to intestinal barrier integrity dysfunction. IBD is largely influenced by macrophages, which are classified into subtypes M1 and M2. M1 macrophages have been found to contribute to the development of IBD, whereas M2 macrophages alleviate IBD. Hence, agents that cause increased polarization of the M2 phenotype could help repair IBD. Exosomes, as ubiquitous conveyors of intercellular messages, are involved in immune responses and immune-mediated disease processes. Exosomes and their microRNA (miRNA) from healthy cells have been found to polarize macrophages to M2 to repair IBD due to their anti-inflammatory properties; however, those from inflammatory-driven cells and disease cells promote M1 macrophages to perpetuate IBD. Here, we review the biogenesis, biochemical composition, and sources of exosomes, as well as the roles of exosomes as extracellular vesicles in regulation of macrophages to repair IBD.
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Affiliation(s)
- Feifei Ma
- School of Medical Technology, Shangqiu Medical CollegeShangqiu 476100, Henan, P. R. China
| | - Shiheng Zhang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, P. R. China
| | - Francis Atim Akanyibah
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, P. R. China
| | - Weibin Zhang
- School of Medical Technology, Shangqiu Medical CollegeShangqiu 476100, Henan, P. R. China
| | - Kangjing Chen
- School of Medical Technology, Shangqiu Medical CollegeShangqiu 476100, Henan, P. R. China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, P. R. China
- Directorate of University Health Services, University of Cape CoastCape Coast CC0959347, Ghana
| | - Changkun Lyu
- School of Medical Technology, Shangqiu Medical CollegeShangqiu 476100, Henan, P. R. China
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, P. R. China
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7
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Moradimotlagh A, Chen S, Koohbor S, Moon KM, Foster LJ, Reiner N, Nandan D. Leishmania infection upregulates and engages host macrophage Argonaute 1, and system-wide proteomics reveals Argonaute 1-dependent host response. Front Immunol 2023; 14:1287539. [PMID: 38098491 PMCID: PMC10720368 DOI: 10.3389/fimmu.2023.1287539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/26/2023] [Indexed: 12/17/2023] Open
Abstract
Leishmania donovani, an intracellular protozoan parasite, is the causative agent of visceral leishmaniasis, the most severe form of leishmaniasis in humans. It is becoming increasingly clear that several intracellular pathogens target host cell RNA interference (RNAi) pathways to promote their survival. Complexes of Argonaute proteins with small RNAs are core components of the RNAi. In this study, we investigated the potential role of host macrophage Argonautes in Leishmania pathogenesis. Using Western blot analysis of Leishmania donovani-infected macrophages, we show here that Leishmania infection selectively increased the abundance of host Argonaute 1 (Ago1). This increased abundance of Ago1 in infected cells also resulted in higher levels of Ago1 in active Ago-complexes, suggesting the preferred use of Ago1 in RNAi in Leishmania-infected cells. This analysis used a short trinucleotide repeat containing 6 (TNRC6)/glycine-tryptophan repeat protein (GW182) protein-derived peptide fused to Glutathione S-transferase as an affinity matrix to capture mature Ago-small RNAs complexes from the cytosol of non-infected and Leishmania-infected cells. Furthermore, Ago1 silencing significantly reduced intracellular survival of Leishmania, demonstrating that Ago1 is essential for Leishmania pathogenesis. To investigate the role of host Ago1 in Leishmania pathogenesis, a quantitative whole proteome approach was employed, which showed that expression of several previously reported Leishmania pathogenesis-related proteins was dependent on the level of macrophage Ago1. Together, these findings identify Ago1 as the preferred Argonaute of RNAi machinery in infected cells and a novel and essential virulence factor by proxy that promotes Leishmania survival.
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Affiliation(s)
- Atieh Moradimotlagh
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Stella Chen
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sara Koohbor
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Neil Reiner
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Devki Nandan
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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8
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Vetter L, Bajalan A, Ahamed MT, Scasso C, Shafeeq S, Andersson B, Ribacke U. Starvation induces changes in abundance and small RNA cargo of extracellular vesicles released from Plasmodium falciparum infected red blood cells. Sci Rep 2023; 13:18423. [PMID: 37891207 PMCID: PMC10611735 DOI: 10.1038/s41598-023-45590-6] [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: 08/30/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
The lethal malaria parasite Plasmodium falciparum needs to constantly respond and adapt to changes within the human host in order to survive and transmit. One such change is composed of nutritional limitation, which is augmented with increased parasite loads and intimately linked to severe disease development. Extracellular vesicles released from infected red blood cells have been proposed as important mediators of disease pathogenesis and intercellular communication but whether important for the parasite response to nutritional availability is unknown. Therefore, we investigated the abundance and small RNA cargo of extracellular vesicles released upon short-term nutritional starvation of P. falciparum in vitro cultures. We show that primarily ring-stage parasite cultures respond to glucose and amino acid deprivation with an increased release of extracellular vesicles. Small RNA sequencing of these extracellular vesicles further revealed human miRNAs and parasitic tRNA fragments as the main constituent biotypes. Short-term starvations led to alterations in the transcriptomic profile, most notably in terms of the over-represented biotypes. These data suggest a potential role for extracellular vesicles released from P. falciparum infected red blood cells in the response to nutritional perturbations, their potential as prognostic biomarkers and point towards an evolutionary conserved role among protozoan parasites.
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Affiliation(s)
- Leonie Vetter
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Amanj Bajalan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Mohammad Tanvir Ahamed
- Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Tomtebodavägen 18, SE-17177, Solna, Sweden
| | - Caterina Scasso
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Sulman Shafeeq
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden
| | - Ulf Ribacke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-17165, Solna, Sweden.
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-75237, Uppsala, Sweden.
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9
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Fernandez‐Becerra C, Xander P, Alfandari D, Dong G, Aparici‐Herraiz I, Rosenhek‐Goldian I, Shokouhy M, Gualdron‐Lopez M, Lozano N, Cortes‐Serra N, Karam PA, Meneghetti P, Madeira RP, Porat Z, Soares RP, Costa AO, Rafati S, da Silva A, Santarém N, Fernandez‐Prada C, Ramirez MI, Bernal D, Marcilla A, Pereira‐Chioccola VL, Alves LR, Portillo HD, Regev‐Rudzki N, de Almeida IC, Schenkman S, Olivier M, Torrecilhas AC. Guidelines for the purification and characterization of extracellular vesicles of parasites. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e117. [PMID: 38939734 PMCID: PMC11080789 DOI: 10.1002/jex2.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 08/21/2023] [Accepted: 09/14/2023] [Indexed: 06/29/2024]
Abstract
Parasites are responsible for the most neglected tropical diseases, affecting over a billion people worldwide (WHO, 2015) and accounting for billions of cases a year and responsible for several millions of deaths. Research on extracellular vesicles (EVs) has increased in recent years and demonstrated that EVs shed by pathogenic parasites interact with host cells playing an important role in the parasite's survival, such as facilitation of infection, immunomodulation, parasite adaptation to the host environment and the transfer of drug resistance factors. Thus, EVs released by parasites mediate parasite-parasite and parasite-host intercellular communication. In addition, they are being explored as biomarkers of asymptomatic infections and disease prognosis after drug treatment. However, most current protocols used for the isolation, size determination, quantification and characterization of molecular cargo of EVs lack greater rigor, standardization, and adequate quality controls to certify the enrichment or purity of the ensuing bioproducts. We are now initiating major guidelines based on the evolution of collective knowledge in recent years. The main points covered in this position paper are methods for the isolation and molecular characterization of EVs obtained from parasite-infected cell cultures, experimental animals, and patients. The guideline also includes a discussion of suggested protocols and functional assays in host cells.
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Affiliation(s)
- Carmen Fernandez‐Becerra
- ISGlobal, Barcelona Institute for Global HealthHospital Clínic‐Universitatde BarcelonaBarcelonaSpain
- IGTP Institut d'Investigació Germans Trias i PujolBadalona (Barcelona)Spain
- CIBERINFECISCIII‐CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIIMadridSpain
| | - Patrícia Xander
- Departamento de Ciências FarmacêuticasLaboratório de Imunologia Celular e Bioquímica de Fungos e ProtozoáriosDepartamento de Ciências FarmacêuticasInstituto de Ciências AmbientaisQuímicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP)São PauloBrazil
| | - Daniel Alfandari
- Department of Biomolecular SciencesWeizmann Institute of Science (WIS)RehovotIsrael
| | - George Dong
- The Research Institute of the McGill University Health CentreMcGill UniversityMontréalQuébecCanada
| | - Iris Aparici‐Herraiz
- ISGlobal, Barcelona Institute for Global HealthHospital Clínic‐Universitatde BarcelonaBarcelonaSpain
| | | | - Mehrdad Shokouhy
- Department of Immunotherapy and Leishmania Vaccine ResearchPasteur Institute of IranTehranIran
| | - Melisa Gualdron‐Lopez
- ISGlobal, Barcelona Institute for Global HealthHospital Clínic‐Universitatde BarcelonaBarcelonaSpain
| | - Nicholy Lozano
- Departamento de Ciências FarmacêuticasLaboratório de Imunologia Celular e Bioquímica de Fungos e ProtozoáriosDepartamento de Ciências FarmacêuticasInstituto de Ciências AmbientaisQuímicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP)São PauloBrazil
| | - Nuria Cortes‐Serra
- ISGlobal, Barcelona Institute for Global HealthHospital Clínic‐Universitatde BarcelonaBarcelonaSpain
| | - Paula Abou Karam
- Department of Biomolecular SciencesWeizmann Institute of Science (WIS)RehovotIsrael
| | - Paula Meneghetti
- Departamento de Ciências FarmacêuticasLaboratório de Imunologia Celular e Bioquímica de Fungos e ProtozoáriosDepartamento de Ciências FarmacêuticasInstituto de Ciências AmbientaisQuímicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP)São PauloBrazil
| | - Rafael Pedro Madeira
- Departamento de Ciências FarmacêuticasLaboratório de Imunologia Celular e Bioquímica de Fungos e ProtozoáriosDepartamento de Ciências FarmacêuticasInstituto de Ciências AmbientaisQuímicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP)São PauloBrazil
| | - Ziv Porat
- Flow Cytometry UnitLife Sciences Core Facilities, WISRehovotIsrael
| | | | - Adriana Oliveira Costa
- Departamento de Análises Clínicas e ToxicológicasFaculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG)Belo HorizonteMinas GeraisBrasil
| | - Sima Rafati
- Department of Immunotherapy and Leishmania Vaccine ResearchPasteur Institute of IranTehranIran
| | - Anabela‐Cordeiro da Silva
- Host‐Parasite Interactions GroupInstitute of Research and Innovation in HealthUniversity of PortoPortoPortugal
- Department of Biological SciencesFaculty of PharmacyUniversity of PortoPortoPortugal
| | - Nuno Santarém
- Host‐Parasite Interactions GroupInstitute of Research and Innovation in HealthUniversity of PortoPortoPortugal
- Department of Biological SciencesFaculty of PharmacyUniversity of PortoPortoPortugal
| | | | - Marcel I. Ramirez
- EVAHPI ‐ Extracellular Vesicles and Host‐Parasite Interactions Research Group Laboratório de Biologia Molecular e Sistemática de TripanossomatideosInstituto Carlos Chagas‐FiocruzCuritibaParanáBrasil
| | - Dolores Bernal
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències BiològiquesUniversitat de ValènciaBurjassotValenciaSpain
| | - Antonio Marcilla
- Àrea de Parasitologia, Departament de Farmàcia i Tecnologia Farmacèutica i ParasitologiaUniversitat de ValènciaBurjassotValenciaSpain
| | - Vera Lucia Pereira‐Chioccola
- Laboratório de Biologia Molecular de Parasitas e Fungos, Centro de Parasitologia e MicologiaInstituto Adolfo Lutz (IAL)São PauloBrasil
| | - Lysangela Ronalte Alves
- Laboratório de Regulação da Expressão GênicaInstituto Carlos ChagasFiocruz ParanáCuritibaBrazil
- Research Center in Infectious DiseasesDivision of Infectious Disease and Immunity CHU de Quebec Research CenterDepartment of MicrobiologyInfectious Disease and ImmunologyFaculty of MedicineUniversity LavalQuebec CityQuebecCanada
| | - Hernando Del Portillo
- ISGlobal, Barcelona Institute for Global HealthHospital Clínic‐Universitatde BarcelonaBarcelonaSpain
- IGTP Institut d'Investigació Germans Trias i PujolBadalona (Barcelona)Spain
- ICREA Institució Catalana de Recerca i Estudis Avanc¸ats (ICREA)BarcelonaSpain
| | - Neta Regev‐Rudzki
- Department of Biomolecular SciencesWeizmann Institute of Science (WIS)RehovotIsrael
| | - Igor Correia de Almeida
- Department of Biological SciencesBorder Biomedical Research CenterThe University of Texas at El PasoEl PasoTexasUSA
| | - Sergio Schenkman
- Departamento de MicrobiologiaImunologia e Parasitologia, UNIFESPSão PauloBrazil
| | - Martin Olivier
- The Research Institute of the McGill University Health CentreMcGill UniversityMontréalQuébecCanada
| | - Ana Claudia Torrecilhas
- Departamento de Ciências FarmacêuticasLaboratório de Imunologia Celular e Bioquímica de Fungos e ProtozoáriosDepartamento de Ciências FarmacêuticasInstituto de Ciências AmbientaisQuímicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP)São PauloBrazil
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10
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Sharma M, Lozano-Amado D, Chowdhury D, Singh U. Extracellular Vesicles and Their Impact on the Biology of Protozoan Parasites. Trop Med Infect Dis 2023; 8:448. [PMID: 37755909 PMCID: PMC10537256 DOI: 10.3390/tropicalmed8090448] [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: 08/07/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Extracellular vesicles (EVs) are lipid-membrane-bound structures produced naturally by all cells and have a variety of functions. EVs act as vehicles for transporting important molecular signals from one cell to another. Several parasites have been shown to secrete EVs, and their biological functions have been extensively studied. EVs have been shown to facilitate communication with the host cells (such as modulation of the host's immune system or promoting attachment and invasion into the host cells) or for communication between parasitic cells (e.g., transferring drug-resistance genes or factors modulating stage conversion). It is clear that EVs play an important role in host-parasite interactions. In this review, we summarized the latest research on the EVs secreted by protozoan parasites and their role in host-parasite and parasite-parasite communications.
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Affiliation(s)
- Manu Sharma
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.S.); (D.L.-A.); (D.C.)
| | - Daniela Lozano-Amado
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.S.); (D.L.-A.); (D.C.)
| | - Debabrata Chowdhury
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.S.); (D.L.-A.); (D.C.)
| | - Upinder Singh
- Division of Infectious Diseases, School of Medicine, Stanford University, Stanford, CA 94305, USA; (M.S.); (D.L.-A.); (D.C.)
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
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11
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Siddiq A, Dong G, Balan B, Harrison LG, Jex A, Olivier M, Allain T, Buret AG. A thermo-resistant and RNase-sensitive cargo from Giardia duodenalis extracellular vesicles modifies the behaviour of enterobacteria. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e109. [PMID: 38938375 PMCID: PMC11080815 DOI: 10.1002/jex2.109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 06/29/2024]
Abstract
Extracellular vesicles (EVs) recently emerged as important players in the pathophysiology of parasitic infections. While the protist parasite Giardia duodenalis can produce EVs, their role in giardiasis remains obscure. Giardia can disrupt gut microbiota biofilms and transform commensal bacteria into invasive pathobionts at sites devoid of colonizing trophozoites via unknown mechanisms. We hypothesized that Giardia EVs could modify gut bacterial behaviour via a novel mode of trans-kingdom communication. Our findings indicate that Giardia EVs exert bacteriostatic effects on Escherichia coli HB101 and Enterobacter cloacae TW1, increasing their swimming motility. Giardia EVs also decreased the biofilm-forming ability of E. coli HB101 but not by E. cloacae TW1, supporting the hypothesis that these effects are, at least in part, bacteria-selective. E. coli HB101 and E. cloacae TW1 exhibited increased adhesion/invasion onto small intestine epithelial cells when exposed to Giardia EVs. EVs labelled with PKH67 revealed colocalization with E. coli HB101 and E. cloacae TW1 bacterial cells. Small RNA sequencing revealed a high abundance of ribosomal RNA (rRNA)- and transfer RNA (tRNA)-derived small RNAs, short-interfering RNAs (siRNAs) and micro-RNAs (miRNAs) within Giardia EVs. Proteomic analysis of EVs uncovered the presence of RNA chaperones and heat shock proteins that can facilitate the thermal stability of EVs and its sRNA cargo, as well as protein-modifying enzymes. In vitro, RNase heat-treatment assays showed that total RNAs in EVs, but not proteins, are responsible for modulating bacterial swimming motility and biofilm formation. G. duodenalis small RNAs of EVs, but not proteins, were responsible for the increased bacterial adhesion to intestinal epithelial cells induced upon exposure to Giardia EVs. Together, the findings indicate that Giardia EVs contain a heat-stable, RNase-sensitive cargo that can trigger the development of pathobiont characteristics in Enterobacteria, depicting a novel trans-kingdom cross-talk in the gut.
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Affiliation(s)
- Affan Siddiq
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Inflammation Research NetworkUniversity of CalgaryCalgaryAlbertaCanada
- Host‐Parasite InteractionsUniversity of CalgaryCalgaryAlbertaCanada
| | - George Dong
- Department of Microbiology and Immunology, The Research Institute of the McGill University Health Centre, Program in Infectious Diseases and Immunology in Global HeathMontréalQCCanada
| | - Balu Balan
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneAustralia
- The University of MelbourneMelbourneAustralia
| | - Luke G. Harrison
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Inflammation Research NetworkUniversity of CalgaryCalgaryAlbertaCanada
- Host‐Parasite InteractionsUniversity of CalgaryCalgaryAlbertaCanada
| | - Aaron Jex
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneAustralia
- The University of MelbourneMelbourneAustralia
| | - Martin Olivier
- Department of Microbiology and Immunology, The Research Institute of the McGill University Health Centre, Program in Infectious Diseases and Immunology in Global HeathMontréalQCCanada
| | - Thibault Allain
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Inflammation Research NetworkUniversity of CalgaryCalgaryAlbertaCanada
- Host‐Parasite InteractionsUniversity of CalgaryCalgaryAlbertaCanada
| | - Andre G. Buret
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Inflammation Research NetworkUniversity of CalgaryCalgaryAlbertaCanada
- Host‐Parasite InteractionsUniversity of CalgaryCalgaryAlbertaCanada
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12
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Zheng J, Hu X, Zeng Y, Zhang B, Sun Z, Liu X, Zheng W, Chai Y. Review of the advances in lipid anchors-based biosensors for the isolation and detection of exosomes. Anal Chim Acta 2023; 1263:341319. [PMID: 37225343 DOI: 10.1016/j.aca.2023.341319] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/26/2023]
Abstract
Exosomes are nanoparticles with a bilayer lipid structure that carry cargo from their cells of origin. These vesicles are vital to disease diagnosis and therapeutics; however, conventional isolation and detection techniques are generally complicated, time-consuming, and costly, thus hampering the clinical applications of exosomes. Meanwhile, sandwich-structured immunoassays for exosome isolation and detection rely on the specific binding of membrane surface biomarkers, which may be limited by the type and amount of target protein present. Recently, lipid anchors inserted into the membranes of vesicles through hydrophobic interactions have been adopted as a new strategy for extracellular vesicle manipulation. By combining nonspecific and specific binding, the performance of biosensors can be improved variously. This review presents the reaction mechanisms and properties of lipid anchors/probes, as well as advances in the development of biosensors. The combination of signal amplification methods with lipid anchors is discussed in detail to provide insights into the design of convenient and sensitive detection techniques. Finally, the advantages, challenges, and future directions of lipid anchor-based exosome isolation and detection methods are highlighted from the perspectives of research, clinical use, and commercialization.
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Affiliation(s)
- Junyuan Zheng
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
| | - Xiaoxiang Hu
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
| | - Yuping Zeng
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
| | - Binmao Zhang
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
| | - Zhonghao Sun
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
| | - Xiaowei Liu
- Department of Management, Shenzhen University, Shenzhen, 518055, China.
| | - Weidong Zheng
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen, 518055, China.
| | - Yujuan Chai
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
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13
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Natali L, Luna Pizarro G, Moyano S, de la Cruz-Thea B, Musso J, Rópolo AS, Eichner N, Meister G, Musri MM, Feliziani C, Touz MC. The Exosome-like Vesicles of Giardia Assemblages A, B, and E Are Involved in the Delivering of Distinct Small RNA from Parasite to Parasite. Int J Mol Sci 2023; 24:ijms24119559. [PMID: 37298511 DOI: 10.3390/ijms24119559] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 06/12/2023] Open
Abstract
The genetically related assemblages of the intestinal protozoa parasite Giardia lamblia are morphologically indistinguishable and are often derived from specific hosts. The Giardia assemblages are separated by large genetic distances, which might account for their relevant biological and pathogenic differences. In this work, we analyzed the RNAs cargo released into exosomal-like vesicles (ElVs) by the assemblages A and B, which differentially infect humans, and the assemblage E, which infects hoofed animals. The RNA sequencing analysis revealed that the ElVs of each assemblage contained distinct small RNA (sRNA) biotypes, suggesting a preference for specific packaging in each assemblage. These sRNAs were classified into three categories, ribosomal-small RNAs (rsRNAs), messenger-small RNAs (msRNAs), and transfer-small RNAs (tsRNAs), which may play a regulatory role in parasite communication and contribute to host-specificity and pathogenesis. Uptake experiments showed, for the first time, that ElVs were successfully internalized by the parasite trophozoites. Furthermore, we observed that the sRNAs contained inside these ElVs were first located below the plasma membrane but then distributed along the cytoplasm. Overall, the study provides new insights into the molecular mechanisms underlying the host-specificity and pathogenesis of G. lamblia and highlights the potential role of sRNAs in parasite communication and regulation.
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Affiliation(s)
- Lautaro Natali
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Gabriel Luna Pizarro
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Sofía Moyano
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Benjamin de la Cruz-Thea
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Juliana Musso
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Andrea S Rópolo
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Norbert Eichner
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Melina M Musri
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Constanza Feliziani
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - María C Touz
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, Consejo Nacional de Investigaciones Científicas y Técnicas (INIMEC-CONICET), Universidad Nacional de Córdoba, Córdoba 5016, Argentina
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14
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Sharma M, Zhang H, Ehrenkaufer G, Singh U. Stress Response in Entamoeba histolytica Is Associated with Robust Processing of tRNA to tRNA Halves. mBio 2023; 14:e0345022. [PMID: 36809068 PMCID: PMC10127584 DOI: 10.1128/mbio.03450-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/18/2023] [Indexed: 02/23/2023] Open
Abstract
tRNA-derived fragments have been reported in many different organisms and have diverse cellular roles, such as regulating gene expression, inhibiting protein translation, silencing transposable elements, and modulating cell proliferation. In particular, tRNA halves, a class of tRNA fragments produced by the cleavage of tRNAs in the anti-codon loop, have been widely reported to accumulate under stress and regulate translation in cells. Here, we report the presence of tRNA-derived fragments in Entamoeba, with tRNA halves being the most abundant. We further established that tRNA halves accumulate in the parasites upon different stress stimuli such as oxidative stress, heat shock, and serum starvation. We also observed differential expression of tRNA halves during developmental changes of trophozoite-to-cyst conversion, with various tRNA halves accumulating during early encystation. In contrast to other systems, the stress response does not appear to be mediated by a few specific tRNA halves, as multiple tRNAs appear to be processed during the various stresses. Furthermore, we identified some tRNA-derived fragments associated with Entamoeba Argonaute proteins, EhAgo2-2 and EhAgo2-3, which have a preference for different tRNA-derived fragment species. Finally, we show that tRNA halves are packaged inside extracellular vesicles secreted by amoebas. The ubiquitous presence of tRNA-derived fragments, their association with the Argonaute proteins, and the accumulation of tRNA halves during multiple different stresses, including encystation, suggest a nuanced level of gene expression regulation mediated by different tRNA-derived fragments in Entamoeba. IMPORTANCE In the present study, we report for the first time the presence of tRNA-derived fragments in Entamoeba. tRNA-derived fragments were identified by bioinformatics analyses of small-RNA sequencing data sets from the parasites and also confirmed experimentally. We found that tRNA halves accumulated in parasites exposed to environmental stress or during the developmental process of encystation. We also found that shorter tRNA-derived fragments are bound to Entamoeba Argonaute proteins, indicating that they may have a potential role in the Argonaute-mediated RNA-interference pathway, which mediates robust gene silencing in Entamoeba. We noticed that in response to heat shock, the protein translation levels were elevated in the parasites. This effect was reversed in the presence of an analog of leucine, which also reduced the levels of the tRNA halves in the stressed cells. Our results suggest that tRNA-derived fragments in Entamoeba have a possible role in regulating gene expression during environmental stress.
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Affiliation(s)
- Manu Sharma
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Hanbang Zhang
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Gretchen Ehrenkaufer
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Upinder Singh
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
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15
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Weber JI, Rodrigues AV, Valério-Bolas A, Nunes T, Carvalheiro M, Antunes W, Alexandre-Pires G, da Fonseca IP, Santos-Gomes G. Insights on Host-Parasite Immunomodulation Mediated by Extracellular Vesicles of Cutaneous Leishmania shawi and Leishmania guyanensis. Cells 2023; 12:1101. [PMID: 37190011 PMCID: PMC10137031 DOI: 10.3390/cells12081101] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/23/2023] [Accepted: 04/01/2023] [Indexed: 05/17/2023] Open
Abstract
Leishmaniasis is a parasitic disease caused by different species of Leishmania and transmitted through the bite of sand flies vector. Macrophages (MΦ), the target cells of Leishmania parasites, are phagocytes that play a crucial role in the innate immune microbial defense and are antigen-presenting cells driving the activation of the acquired immune response. Exploring parasite-host communication may be key in restraining parasite dissemination in the host. Extracellular vesicles (EVs) constitute a group of heterogenous cell-derived membranous structures, naturally produced by all cells and with immunomodulatory potential over target cells. This study examined the immunogenic potential of EVs shed by L. shawi and L. guyanensis in MΦ activation by analyzing the dynamics of major histocompatibility complex (MHC), innate immune receptors, and cytokine generation. L. shawi and L. guyanensis EVs were incorporated by MΦ and modulated innate immune receptors, indicating that EVs cargo can be recognized by MΦ sensors. Moreover, EVs induced MΦ to generate a mix of pro- and anti-inflammatory cytokines and favored the expression of MHCI molecules, suggesting that EVs antigens can be present to T cells, activating the acquired immune response of the host. Since nano-sized vesicles can be used as vehicles of immune mediators or immunomodulatory drugs, parasitic EVs can be exploited by bioengineering approaches for the development of efficient prophylactic or therapeutic tools for leishmaniasis.
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Affiliation(s)
- Juliana Inês Weber
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Armanda Viana Rodrigues
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Ana Valério-Bolas
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Telmo Nunes
- Microscopy Center, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Manuela Carvalheiro
- Research Institute for Medicines, iMed, Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Wilson Antunes
- Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), 1849-012 Lisboa, Portugal
| | - Graça Alexandre-Pires
- CIISA, Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Av. Universidade Técnica, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 2825-466 Setúbal, Portugal
| | - Isabel Pereira da Fonseca
- CIISA, Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Av. Universidade Técnica, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 2825-466 Setúbal, Portugal
| | - Gabriela Santos-Gomes
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, 1349-008 Lisboa, Portugal
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16
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Kusakisako K, Nakao R, Katakura K. Detection of parasite-derived tRNA and rRNA fragments in the peripheral blood of mice experimentally infected with Leishmania donovani and Leishmania amazonensis using next-generation sequencing analysis. Parasitol Int 2023; 93:102716. [PMID: 36464229 DOI: 10.1016/j.parint.2022.102716] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
All prokaryotes and eukaryotes, including parasites, release extracellular vesicles or exosomes that contain selected proteins, lipids, nucleic acids, glycoconjugates, and metabolites. Leishmania exosomes are highly enriched in small RNAs derived from the rRNAs and tRNAs of the protozoan parasite species. Here, using plasma exosomes isolated by a kit and next-generation sequencing, we report the detection of fragments of parasite-derived rRNAs and tRNAs in the peripheral plasma samples of mice experimentally infected with Leishmania donovani and Leishmania amazonensis, the causative agents of Old World visceral leishmaniasis and New World disseminated cutaneous leishmaniasis, respectively. Detected RNA molecules of 28S rRNA, 5.8S rRNA, tRNA-Glu, and tRNA-Thr were common to both plasma samples of mice inoculated with L. donovani and L. amazonensis, whereas tRNA-Ile and tRNA-Trp were only detected in L. amazonensis-infected mice. The detected rRNAs and tRNA isotypes were matched with the exosomal components reported in a previous key study. Our preliminary results suggested that parasite-derived small RNAs were circulating in the blood of mice infected with Leishmania species, providing a better understanding of the roles of exosomal components in leishmaniasis and also new insights into exosome-based biomarkers for Leishmania infection.
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Affiliation(s)
- Kodai Kusakisako
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Ken Katakura
- Laboratory of Parasitology, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan.
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17
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Cruz Camacho A, Alfandari D, Kozela E, Regev-Rudzki N. Biogenesis of extracellular vesicles in protozoan parasites: The ESCRT complex in the trafficking fast lane? PLoS Pathog 2023; 19:e1011140. [PMID: 36821560 PMCID: PMC9949670 DOI: 10.1371/journal.ppat.1011140] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Extracellular vesicles (EVs) provide a central mechanism of cell-cell communication. While EVs are found in most organisms, their pathogenesis-promoting roles in parasites are of particular interest given the potential for medical insight and consequential therapeutic intervention. Yet, a key feature of EVs in human parasitic protozoa remains elusive: their mechanisms of biogenesis. Here, we survey the current knowledge on the biogenesis pathways of EVs secreted by the four main clades of human parasitic protozoa: apicomplexans, trypanosomatids, flagellates, and amoebae. In particular, we shine a light on findings pertaining to the Endosomal Sorting Complex Required for Transport (ESCRT) machinery, as in mammals it plays important roles in EV biogenesis. This review highlights the diversity in EV biogenesis in protozoa, as well as the related involvement of the ESCRT system in these unique organisms.
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Affiliation(s)
- Abel Cruz Camacho
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Alfandari
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ewa Kozela
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Neta Regev-Rudzki
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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18
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Rangel-Ramírez VV, González-Sánchez HM, Lucio-García C. Exosomes: from biology to immunotherapy in infectious diseases. Infect Dis (Lond) 2023; 55:79-107. [PMID: 36562253 DOI: 10.1080/23744235.2022.2149852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Exosomes are extracellular vesicles derived from the endosomal compartment, which are released by all kinds of eukaryotic and prokaryotic organisms. These vesicles contain a variety of biomolecules that differ both in quantity and type depending on the origin and cellular state. Exosomes are internalized by recipient cells, delivering their content and thus contributing to cell-cell communication in health and disease. During infections exosomes may exert a dual role, on one hand, they can transmit pathogen-related molecules mediating further infection and damage, and on the other hand, they can protect the host by activating the immune response and reducing pathogen spread. Selective packaging of pathogenic components may mediate these effects. Recently, quantitative analysis of samples by omics technologies has allowed a deep characterization of the proteins, lipids, RNA, and metabolite cargoes of exosomes. Knowledge about the content of these vesicles may facilitate their therapeutic application. Furthermore, as exosomes have been detected in almost all biological fluids, pathogenic or host-derived components can be identified in liquid biopsies, making them suitable for diagnosis and prognosis. This review attempts to organize the recent findings on exosome composition and function during viral, bacterial, fungal, and protozoan infections, and their contribution to host defense or to pathogen spread. Moreover, we summarize the current perspectives and future directions regarding the potential application of exosomes for prophylactic and therapeutic purposes.
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Affiliation(s)
| | | | - César Lucio-García
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
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19
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Kalita E, Panda M, Rao A, Prajapati VK. Exploring the role of secretory proteins in the human infectious diseases diagnosis and therapeutics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 133:231-269. [PMID: 36707203 DOI: 10.1016/bs.apcsb.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Secretory proteins are playing important role during the host-pathogen interaction to develop the infection or protection into the cell. Pathogens developing infectious disease to human being are taken up by host macrophages or number of immune cells, play an important role in physiological, developmental and immunological function. At the same time, infectious agents are also secreting various proteins to neutralize the resistance caused by host cells and also helping the pathogens to develop the infection. Secretory proteins (secretome) are only developed at the time of host-pathogen interaction, therefore they become very important to develop the targeted and potential therapeutic strategies. Pathogen specific secretory proteins released during interaction with host cell provide opportunity to develop point of care and rapid diagnostic kits. Proteins secreted by pathogens at the time of interaction with host cell have also been found as immunogenic in nature and numbers of vaccines have been developed to control the spread of human infectious diseases. This chapter highlights the importance of secretory proteins in the development of diagnostic and therapeutic strategies to fight against human infectious diseases.
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Affiliation(s)
- Elora Kalita
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Mamta Panda
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Abhishek Rao
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India.
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20
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Dai Y, Chen Y, Hu Y, Zhang L. Current knowledge and future perspectives on exosomes in the field of regenerative medicine: a bibliometric analysis. Regen Med 2023; 18:123-136. [PMID: 36325823 DOI: 10.2217/rme-2022-0141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Objective: This study aimed to use bibliometric analysis to qualitatively and quantitatively evaluate the research of exosomes in the field of regenerative medicine and to provide research hotspots and trends in this field. Materials & methods: Bibliometric analysis and data presentation were performed by VOSviewer and Microsoft Excel. Results: China was the major contributor to research in this field and enjoys a high reputation in academia. The highest contributing institution is Shanghai Jiao Tong University. Research hotspots included exosome-mediated neurovascular regeneration, exosome mechanism research, exosome-mediated cartilage regeneration and repair and exosome-mediated cardiac regeneration. Research was trending in the treatment of osteoarthritis, knee disease and cartilage regeneration and repair. Conclusion: This study provides a panoramic view of the application of exosomes in regenerative medicine.
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Affiliation(s)
- Yuxuan Dai
- Department of Plastic Surgery, China-Japan Union Hospital of Jilin University, Changchun, 130000, China
| | - Yu Chen
- Division of Thyroid Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Yiming Hu
- Department of Plastic & Aesthetic Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Lianbo Zhang
- Department of Plastic Surgery, China-Japan Union Hospital of Jilin University, Changchun, 130000, China
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21
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Tong F, Tang G, Wang X. Characteristics of Human and Microbiome RNA Profiles in Saliva. RNA Biol 2023; 20:398-408. [PMID: 37401028 PMCID: PMC10321209 DOI: 10.1080/15476286.2023.2229596] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/08/2023] [Accepted: 06/17/2023] [Indexed: 07/05/2023] Open
Abstract
Saliva is a convenient non-invasive source of liquid biopsy to monitor human health and diagnose diseases. In particular, extracellular vesicles (EVs) in saliva can potentially reveal clinically relevant information for systemic health. Recent studies have shown that RNA in saliva EVs could be exploited as biomarkers for disease diagnosis. However, there is no standardized protocol for profiling RNA in saliva EV nor clear guideline on selecting saliva fractions for biomarker analysis. To address these issues, we established a robust protocol for small RNA profiling from fractionated saliva. With this method, we performed comprehensive small RNA sequencing of four saliva fractions, including cell-free saliva (CFS), EV-depleted saliva (EV-D), exosome (EXO), and microvesicle (MV) from ten healthy volunteers. By comparing the expression profiles of total RNA from these fractions, we found that MV was most enriched in microbiome RNA (76.2% of total reads on average), whereas EV-D was notably enriched in human RNA (70.3% of total reads on average). As for human RNA composition, CFS and EV-D were both enriched in snoRNA and tRNA compared with the two EV fractions (EXO and MV, P < 0.05). Interestingly, EXO and MV had highly correlated expression profiles for various noncoding RNAs such as miRNA, tRNA, and yRNA. Our study revealed unique characteristics of circulating RNAs in various saliva fractions, which provides a guideline on preparing saliva samples to study specific RNA biomarkers of interest.
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Affiliation(s)
- Fangjia Tong
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, Chicago, IL, USA
| | - Gongyu Tang
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, Chicago, IL, USA
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, USA
| | - Xiaowei Wang
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, Chicago, IL, USA
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22
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Macrophage Mitochondrial Biogenesis and Metabolic Reprogramming Induced by Leishmania donovani Require Lipophosphoglycan and Type I Interferon Signaling. mBio 2022; 13:e0257822. [PMID: 36222510 PMCID: PMC9764995 DOI: 10.1128/mbio.02578-22] [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] [Indexed: 11/20/2022] Open
Abstract
Pathogen-specific rewiring of host cell metabolism creates the metabolically adapted microenvironment required for pathogen replication. Here, we investigated the mechanisms governing the modulation of macrophage mitochondrial properties by the vacuolar pathogen Leishmania. We report that induction of oxidative phosphorylation and mitochondrial biogenesis by Leishmania donovani requires the virulence glycolipid lipophosphoglycan, which stimulates the expression of key transcriptional regulators and structural genes associated with the electron transport chain. Leishmania-induced mitochondriogenesis also requires a lipophosphoglycan-independent pathway involving type I interferon (IFN) receptor signaling. The observation that pharmacological induction of mitochondrial biogenesis enables an avirulent lipophosphoglycan-defective L. donovani mutant to survive in macrophages supports the notion that mitochondrial biogenesis contributes to the creation of a metabolically adapted environment propitious to the colonization of host cells by the parasite. This study provides novel insight into the complex mechanism by which Leishmania metacyclic promastigotes alter host cell mitochondrial biogenesis and metabolism during the colonization process. IMPORTANCE To colonize host phagocytes, Leishmania metacyclic promastigotes subvert host defense mechanisms and create a specialized intracellular niche adapted to their replication. This is accomplished through the action of virulence factors, including the surface coat glycoconjugate lipophosphoglycan. In addition, Leishmania induces proliferation of host cell mitochondria as well as metabolic reprogramming of macrophages. These metabolic alterations are crucial to the colonization process of macrophages, as they may provide metabolites required for parasite growth. In this study, we describe a new key role for lipophosphoglycan in the stimulation of oxidative phosphorylation and mitochondrial biogenesis. We also demonstrate that host cell pattern recognition receptors Toll-like receptor 4 (TLR4) and endosomal TLRs mediate these Leishmania-induced alterations of host cell mitochondrial biology, which also require type I IFN signaling. These findings provide new insight into how Leishmania creates a metabolically adapted environment favorable to their replication.
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23
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Amatuzzi RF, Zamith-Miranda D, Munhoz da Rocha IF, Lucena ACR, de Toledo Martins S, Streit R, Staats CC, Trentin G, Almeida F, Rodrigues ML, Nosanchuk JD, Alves LR. Caspofungin Affects Extracellular Vesicle Production and Cargo in Candida auris. J Fungi (Basel) 2022; 8:990. [PMID: 36294557 PMCID: PMC9605528 DOI: 10.3390/jof8100990] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/15/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022] Open
Abstract
Antifungal resistance has become more frequent, either due to the emergence of naturally resistant species or the development of mechanisms that lead to resistance in previously susceptible species. Among these fungal species of global threat, Candida auris stands out for commonly being highly resistant to antifungal drugs, and some isolates are pan-resistant. The rate of mortality linked to C. auris infections varies from 28% to 78%. In this study, we characterized C. auris extracellular vesicles (EVs) in the presence of caspofungin, an echinocandin, which is the recommended first line antifungal for the treatment of infections due to this emerging pathogen. Furthermore, we also analyzed the protein and RNA content of EVs generated by C. auris cultivated with or without treatment with caspofungin. We observed that caspofungin led to the increased production of EVs, and treatment also altered the type and quantity of RNA molecules and proteins enclosed in the EVs. There were distinct classes of RNAs in the EVs with ncRNAs being the most identified molecules, and tRNA-fragments (tRFs) were abundant in each of the strains studied. We also identified anti-sense RNAs, varying from 21 to 55 nt in length. The differentially abundant mRNAs detected in EVs isolated from yeast subjected to caspofungin treatment were related to translation, nucleosome core and cell wall. The differentially regulated proteins identified in the EVs produced during caspofungin treatment were consistent with the results observed with the RNAs, with the enriched terms being related to translation and cell wall. Our study adds new information on how an echinocandin can affect the EV pathway, which is associated with the yeast cell being able to evade treatment and persist in the host. The ability of C. auris to efficiently alter the composition of EVs may represent a mechanism for the fungus to mitigate the effects of antifungal agents.
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Affiliation(s)
- Rafaela F. Amatuzzi
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba 81350-010, Brazil
| | - Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Aline C. R. Lucena
- Laboratory for Applied Sciences and Technology in Health, Carlos Chagas Institute, FIOCRUZ PR, Curitiba 81350-010, Brazil
| | - Sharon de Toledo Martins
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba 81350-010, Brazil
| | - Rodrigo Streit
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Brazil
| | - Charley C. Staats
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91509-900, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, Brazil
| | - Gabriel Trentin
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirao Preto 14040-900, Brazil
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirao Preto 14040-900, Brazil
| | - Marcio L. Rodrigues
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba 81350-010, Brazil
- Microbiology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil
| | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Lysangela R. Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ PR, Curitiba 81350-010, Brazil
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24
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Vega-Benedetti AF, Loi E, Zavattari P. DNA methylation alterations caused by Leishmania infection may generate a microenvironment prone to tumour development. Front Cell Infect Microbiol 2022; 12:984134. [PMID: 36105147 PMCID: PMC9465093 DOI: 10.3389/fcimb.2022.984134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/10/2022] [Indexed: 01/10/2023] Open
Abstract
DNA methylation is an epigenetic signature consisting of a methyl group at the 5’ cytosine of CpG dinucleotides. Modifications in DNA methylation pattern have been detected in cancer and infectious diseases and may be associated with gene expression changes. In cancer development DNA methylation aberrations are early events whereas in infectious diseases these epigenetic changes may be due to host/pathogen interaction. In particular, in leishmaniasis, a parasitic disease caused by the protozoan Leishmania, DNA methylation alterations have been detected in macrophages upon infection with Leishmania donovani and in skin lesions from patients with cutaneous leishmaniasis. Interestingly, different types of cancers, such as cutaneous malignant lesions, lymphoma and hepatocellular carcinoma, have been diagnosed in patients with a history of leishmaniasis. In fact, it is known that there exists an association between cancer and infectious diseases. Leishmania infection may increase susceptibility to develop cancer, but the mechanisms involved are not entirely clear. Considering these aspects, in this review we discuss the hypothesis that DNA methylation alterations induced by Leishmania may trigger tumorigenesis in long term infection since these epigenetic modifications may enhance and accumulate during chronic leishmaniasis.
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25
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Yoshimoto R, Ishida F, Yamaguchi M, Tanaka S. The production and secretion of tRNA-derived RNA fragments in the corn smut fungus Ustilago maydis. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:958798. [PMID: 37746175 PMCID: PMC10512261 DOI: 10.3389/ffunb.2022.958798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/18/2022] [Indexed: 09/26/2023]
Abstract
The biogenesis of small non-coding RNAs is a molecular event that contributes to cellular functions. The basidiomycete fungus Ustilago maydis is a biotrophic pathogen parasitizing maize. A hallmark of its genome structure is an absence of RNAi machinery including Dicer and Argonaute proteins, which are responsible for the production of small RNAs in other organisms. However, it remains unclear whether U. maydis produces small RNAs during fungal growth. Here we found that U. maydis cells accumulate approximately 20-30 nucleotides of small RNA fragments during growth in the axenic culture condition. The RNA-seq analysis of these fragments identified that these small RNAs are originated from tRNAs and 5.8S ribosomal RNA. Interestingly, majority of their sequences are generated from tRNAs responsible for asparagine, glutamine and glycine, suggesting a bias of origin. The cleavage of tRNAs mainly occurs at the position near anticodon-stem-loop. We generated the deletion mutants of two genes nuc1 and nuc2 encoding RNase T2, which is a candidate enzyme that cleaves tRNAs. The deletion mutants of two genes largely fail to accumulate tRNA-derived RNA fragments. Nuc1 and tRNA are co-localized at the tip of budding cells and tRNA fragment could be detected in culture supernatant. Our results suggest that specific tRNAs would be cleaved during secretory processes and tRNA fragments might have extracellular functions.
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Affiliation(s)
- Rei Yoshimoto
- Faculty of Agriculture, Setsunan University, Osaka, Japan
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26
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Shokouhy M, Sarvnaz H, Taslimi Y, Lajevardi MS, Habibzadeh S, Mizbani A, Shekari F, Behbahani M, Torrecilhas AC, Rafati S. Isolation, characterization, and functional study of extracellular vesicles derived from Leishmania tarentolae. Front Cell Infect Microbiol 2022; 12:921410. [PMID: 35992172 PMCID: PMC9381964 DOI: 10.3389/fcimb.2022.921410] [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: 04/15/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Leishmania (L.) species are protozoan parasites with a complex life cycle consisting of a number of developmental forms that alternate between the sand fly vector and their host. The non-pathogenic species L. tarentolae is not able to induce an active infection in a human host. It has been observed that, in pathogenic species, extracellular vesicles (EVs) could exacerbate the infection. However, so far, there is no report on the identification, isolation, and characterization of L. tarentolae EVs. In this study, we have isolated and characterized EVs from L. tarentolaeGFP+ (tEVs) along with L. majorGFP+ as a reference and positive control. The EVs secreted by these two species demonstrated similar particle size distribution (approximately 200 nm) in scanning electron microscopy and nanoparticle tracking analysis. Moreover, the said EVs showed similar protein content, and GFP and GP63 proteins were detected in both using dot blot analysis. Furthermore, we could detect Leishmania-derived GP63 protein in THP-1 cells treated with tEVs. Interestingly, we observed a significant increase in the production of IFN-γ, TNF-α, and IL-1β, while there were no significant differences in IL-6 levels in THP-1 cells treated with tEVs following an infection with L. major compared with another group of macrophages that were treated with L. major EVs prior to the infection. Another exciting observation of this study was a significant decrease in parasite load in tEV-treated Leishmania-infected macrophages. In addition, in comparison with another group of Leishmania-infected macrophages which was not exposed to any EVs, tEV managed to increase IFN-γ and decrease IL-6 and the parasite burden. In conclusion, we report for the first time that L. tarentolae can release EVs and provide evidence that tEVs are able to control the infection in human macrophages, making them a great potential platform for drug delivery, at least for parasitic infections.
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Affiliation(s)
- Mehrdad Shokouhy
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Hamzeh Sarvnaz
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Yasaman Taslimi
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Mahya Sadat Lajevardi
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Sima Habibzadeh
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Amir Mizbani
- Department of Health Science and Technology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology Cell Science, Research Center, Royan Institute for Stem Cell Biology and Technology, Academic center tor Education, Culture and Research (ACECR), Tehran, Iran
| | - Mandana Behbahani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Ana Claudia Torrecilhas
- Laboratório de Imunologia Celular e Bioquímica de Fungos e Protozoários, Departamento de Ciências Farmacêuticas, Universidade Federal de São Paulo (UNIFESP), Diadema, Brazil
- *Correspondence: Ana Claudia Torrecilhas, ; Sima Rafati, ;
| | - Sima Rafati
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
- *Correspondence: Ana Claudia Torrecilhas, ; Sima Rafati, ;
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27
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Current Status of Regulatory Non-Coding RNAs Research in the Tritryp. Noncoding RNA 2022; 8:ncrna8040054. [PMID: 35893237 PMCID: PMC9326685 DOI: 10.3390/ncrna8040054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/23/2022] Open
Abstract
Trypanosomatids are protozoan parasites that cause devastating vector-borne human diseases. Gene expression regulation of these organisms depends on post-transcriptional control in responding to diverse environments while going through multiple developmental stages of their complex life cycles. In this scenario, non-coding RNAs (ncRNAs) are excellent candidates for a very efficient, quick, and economic strategy to regulate gene expression. The advent of high throughput RNA sequencing technologies show the presence and deregulation of small RNA fragments derived from canonical ncRNAs. This review seeks to depict the ncRNA landscape in trypanosomatids, focusing on the small RNA fragments derived from functional RNA molecules observed in RNA sequencing studies. Small RNA fragments derived from canonical ncRNAs (tsRNAs, snsRNAs, sdRNAs, and sdrRNAs) were identified in trypanosomatids. Some of these RNAs display changes in their levels associated with different environments and developmental stages, demanding further studies to determine their functional characterization and potential roles. Nevertheless, a comprehensive and detailed ncRNA annotation for most trypanosomatid genomes is still needed, allowing better and more extensive comparative and functional studies.
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28
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Rada P, Hrdý I, Zdrha A, Narayanasamy RK, Smutná T, Horáčková J, Harant K, Beneš V, Ong SC, Tsai CY, Luo HW, Chiu CH, Tang P, Tachezy J. Double-Stranded RNA Viruses Are Released From Trichomonas vaginalis Inside Small Extracellular Vesicles and Modulate the Exosomal Cargo. Front Microbiol 2022; 13:893692. [PMID: 35602021 PMCID: PMC9114709 DOI: 10.3389/fmicb.2022.893692] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Trichomonas vaginalis is a parasitic protist that infects the human urogenital tract. During the infection, trichomonads adhere to the host mucosa, acquire nutrients from the vaginal/prostate environment, and release small extracellular vesicles (sEVs) that contribute to the trichomonad adherence and modulate the host-parasite communication. Approximately 40–70% of T. vaginalis strains harbor a double-stranded RNA virus called Trichomonasvirus (TVV). Naked TVV particles have the potential to stimulate a proinflammatory response in human cells, however, the mode of TVV release from trichomonads to the environment is not clear. In this report, we showed for the first time that TVV particles are released from T. vaginalis cells within sEVs. The sEVs loaded with TVV stimulated a higher proinflammatory response of human HaCaT cells in comparison to sEVs from TVV negative parasites. Moreover, a comparison of T. vaginalis isogenic TVV plus and TVV minus clones revealed a significant impact of TVV infection on the sEV proteome and RNA cargo. Small EVs from TVV positive trichomonads contained 12 enriched and 8 unique proteins including membrane-associated BspA adhesine, and about a 2.5-fold increase in the content of small regulatory tsRNA. As T. vaginalis isolates are frequently infected with TVV, the release of TVV via sEVs to the environment represents an important factor with the potential to enhance inflammation-related pathogenesis during trichomoniasis.
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Affiliation(s)
- Petr Rada
- Department of Parasitology, Faculty of Science, Charles University, Biotechnology and Biomedicine Center in Vestec (BIOCEV), Vestec, Czechia
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, Biotechnology and Biomedicine Center in Vestec (BIOCEV), Vestec, Czechia
| | - Alois Zdrha
- Department of Parasitology, Faculty of Science, Charles University, Biotechnology and Biomedicine Center in Vestec (BIOCEV), Vestec, Czechia
| | - Ravi Kumar Narayanasamy
- Department of Parasitology, Faculty of Science, Charles University, Biotechnology and Biomedicine Center in Vestec (BIOCEV), Vestec, Czechia
| | - Tamara Smutná
- Department of Parasitology, Faculty of Science, Charles University, Biotechnology and Biomedicine Center in Vestec (BIOCEV), Vestec, Czechia
| | - Jana Horáčková
- Department of Parasitology, Faculty of Science, Charles University, Biotechnology and Biomedicine Center in Vestec (BIOCEV), Vestec, Czechia
| | - Karel Harant
- Department of Parasitology, Faculty of Science, Charles University, Biotechnology and Biomedicine Center in Vestec (BIOCEV), Vestec, Czechia
| | - Vladimír Beneš
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Seow-Chin Ong
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Yu Tsai
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hong-Wei Luo
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Petrus Tang
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, Biotechnology and Biomedicine Center in Vestec (BIOCEV), Vestec, Czechia
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29
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Kumar D, Downs LP, Embers M, Flynt AS, Karim S. Identification of microRNAs in the Lyme Disease Vector Ixodes scapularis. Int J Mol Sci 2022; 23:5565. [PMID: 35628370 PMCID: PMC9141961 DOI: 10.3390/ijms23105565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 02/01/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in many biological processes, including the immune pathways that control bacterial, parasitic, and viral infections. Pathogens probably modify host miRNAs to facilitate successful infection, so they might be useful targets for vaccination strategies. There are few data on differentially expressed miRNAs in the black-legged tick Ixodes scapularis after infection with Borrelia burgdorferi, the causative agent of Lyme disease in the United States. Small RNA sequencing and qRT-PCR analysis were used to identify and validate differentially expressed I. scapularis salivary miRNAs. Small RNA-seq yielded 133,465,828 (≥18 nucleotides) and 163,852,135 (≥18 nucleotides) small RNA reads from Borrelia-infected and uninfected salivary glands for downstream analysis using the miRDeep2 algorithm. As such, 254 miRNAs were identified across all datasets, 25 of which were high confidence and 51 low confidence known miRNAs. Further, 23 miRNAs were differentially expressed in uninfected and infected salivary glands: 11 were upregulated and 12 were downregulated upon pathogen infection. Gene ontology and network analysis of target genes of differentially expressed miRNAs predicted roles in metabolic, cellular, development, cellular component biogenesis, and biological regulation processes. Several Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including sphingolipid metabolism; valine, leucine and isoleucine degradation; lipid transport and metabolism; exosome biogenesis and secretion; and phosphate-containing compound metabolic processes, were predicted as targets of differentially expressed miRNAs. A qRT-PCR assay was utilized to validate the differential expression of miRNAs. This study provides new insights into the miRNAs expressed in I. scapularis salivary glands and paves the way for their functional manipulation to prevent or treat B. burgdorferi infection.
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Affiliation(s)
- Deepak Kumar
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA; (D.K.); (A.S.F.)
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA;
| | - Latoyia P. Downs
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA;
| | - Monica Embers
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA;
| | - Alex Sutton Flynt
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA; (D.K.); (A.S.F.)
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA;
| | - Shahid Karim
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA; (D.K.); (A.S.F.)
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA;
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30
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Li Y, Baptista RP, Mei X, Kissinger JC. Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics. Microb Genom 2022; 8. [PMID: 35536609 PMCID: PMC9465071 DOI: 10.1099/mgen.0.000821] [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] [Indexed: 12/03/2022] Open
Abstract
Small and intermediate-size noncoding RNAs (sRNAs and is-ncRNAs) have been shown to play important regulatory roles in the development of several eukaryotic organisms. However, they have not been thoroughly explored in Cryptosporidium parvum, an obligate zoonotic protist parasite responsible for the diarrhoeal disease cryptosporidiosis. Using Illumina sequencing of a small RNA library, a systematic identification of novel small and is-ncRNAs was performed in C. parvum excysted sporozoites. A total of 79 novel is-ncRNA candidates, including antisense, intergenic and intronic is-ncRNAs, were identified, including 7 new small nucleolar RNAs (snoRNAs). Expression of select novel is-ncRNAs was confirmed by RT-PCR. Phylogenetic conservation was analysed using covariance models (CMs) in related Cryptosporidium and apicomplexan parasite genome sequences. A potential new type of small ncRNA derived from tRNA fragments was observed. Overall, a deep profiling analysis of novel is-ncRNAs in C. parvum and related species revealed structural features and conservation of these novel is-ncRNAs. Covariance models can be used to detect is-ncRNA genes in other closely related parasites. These findings provide important new sequences for additional functional characterization of novel is-ncRNAs in the protist pathogen C. parvum.
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Affiliation(s)
- Yiran Li
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Rodrigo P Baptista
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA.,Present address: Houston Methodist Research Institute, Houston, TX, USA
| | - Xiaohan Mei
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, USA
| | - Jessica C Kissinger
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA.,Department of Genetics, University of Georgia, Athens, GA, USA
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31
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Gu Z, Meng S, Wang Y, Lyu B, Li P, Shang N. A novel bioactive postbiotics: from microbiota-derived extracellular nanoparticles to health promoting. Crit Rev Food Sci Nutr 2022; 63:6885-6899. [PMID: 35179102 DOI: 10.1080/10408398.2022.2039897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In recent years, the emerging concern regarding safety issues associated with live bacterial cells is enhancing the interest in using cell components and metabolites derived from microbiota. Therefore, the term "postbiotics" is increasingly found in food microbiology, food scientific and commercial products. Postbiotics is defined as non-viable microorganisms or their components that provide benefits to the host. Many in vivo and in vitro experiments have shown that beneficial microbiota-generated extracellular nanoparticles (NPs) confer unique health promoting functions to the intestinal local and systemic effects, which can be considered as a novel postbiotics. Meanwhile, the postbiotics-NPs is a protective complex, delivering bioactive components to reach distant tissues and organs at high concentrations. These properties demonstrate that postbiotics-NPs may contribute to the improvement of host health by regulating specific gut microbiota and physiological functions, while the exact mechanisms are not fully elucidated. This review highlights the current understanding of postbiotics-NPs functional properties and mechanisms of health benefits, especially focusing on the interactions in gut microbiota and host, functions in human health and potential applications in future functional food and biomedical fields.
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Affiliation(s)
- Zelin Gu
- Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- College of Engineering, China Agricultural University, Beijing, China
| | - Shuhan Meng
- Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Yu Wang
- Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Bo Lyu
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Pinglan Li
- Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Nan Shang
- College of Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Healthy, China Agricultural University, Beijing, China
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Peng R, Santos HJ, Nozaki T. Transfer RNA-Derived Small RNAs in the Pathogenesis of Parasitic Protozoa. Genes (Basel) 2022; 13:286. [PMID: 35205331 PMCID: PMC8872473 DOI: 10.3390/genes13020286] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 01/25/2023] Open
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are newly identified non-coding small RNAs that have recently attracted attention due to their functional significance in both prokaryotes and eukaryotes. tsRNAs originated from the cleavage of precursor or mature tRNAs by specific nucleases. According to the start and end sites, tsRNAs can be broadly divided into tRNA halves (31-40 nucleotides) and tRNA-derived fragments (tRFs, 14-30 nucleotides). tsRNAs have been reported in multiple organisms to be involved in gene expression regulation, protein synthesis, and signal transduction. As a novel regulator, tsRNAs have also been identified in various protozoan parasites. The conserved biogenesis of tsRNAs in early-branching eukaryotes strongly suggests the universality of this machinery, which requires future research on their shared and potentially disparate biological functions. Here, we reviewed the recent studies of tsRNAs in several representative protozoan parasites including their biogenesis and the roles in parasite biology and intercellular communication. Furthermore, we discussed the remaining questions and potential future works for tsRNAs in this group of organisms.
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Affiliation(s)
| | | | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (R.P.); (H.J.S.)
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Pandey KK, Madhry D, Ravi Kumar YS, Malvankar S, Sapra L, Srivastava RK, Bhattacharyya S, Verma B. Regulatory roles of tRNA-derived RNA fragments in human pathophysiology. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:161-173. [PMID: 34513302 PMCID: PMC8413677 DOI: 10.1016/j.omtn.2021.06.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hundreds of tRNA genes and pseudogenes are encoded by the human genome. tRNAs are the second most abundant type of RNA in the cell. Advancement in deep-sequencing technologies have revealed the presence of abundant expression of functional tRNA-derived RNA fragments (tRFs). They are either generated from precursor (pre-)tRNA or mature tRNA. They have been found to play crucial regulatory roles during different pathological conditions. Herein, we briefly summarize the discovery and recent advances in deciphering the regulatory role played by tRFs in the pathophysiology of different human diseases.
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Affiliation(s)
- Kush Kumar Pandey
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Deeksha Madhry
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Y S Ravi Kumar
- Department of Biotechnology, M.S. Ramaiah, Institute of Technology, MSR Nagar, Bengaluru, India
| | - Shivani Malvankar
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Leena Sapra
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Rupesh K Srivastava
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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Gabriel ÁM, Galué-Parra A, Pereira WLA, Pedersen KW, da Silva EO. Leishmania 360°: Guidelines for Exosomal Research. Microorganisms 2021; 9:2081. [PMID: 34683402 PMCID: PMC8537887 DOI: 10.3390/microorganisms9102081] [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: 09/02/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
Leishmania parasites are a group of kinetoplastid pathogens that cause a variety of clinical disorders while maintaining cell communication by secreting extracellular vesicles. Emerging technologies have been adapted for the study of Leishmania-host cell interactions, to enable the broad-scale analysis of the extracellular vesicles of this parasite. Leishmania extracellular vesicles (LEVs) are spheroidal nanoparticles of polydispersed suspensions surrounded by a layer of lipid membrane. Although LEVs have attracted increasing attention from researchers, many aspects of their biology remain unclear, including their bioavailability and function in the complex molecular mechanisms of pathogenesis. Given the importance of LEVs in the parasite-host interaction, and in the parasite-parasite relationships that have emerged during the evolutionary history of these organisms, the present review provides an overview of the available data on Leishmania, and formulates guidelines for LEV research. We conclude by reporting direct methods for the isolation of specific LEVs from the culture supernatant of the promastigotes and amastigotes that are suitable for a range of different downstream applications, which increases the compatibility and reproducibility of the approach for the establishment of optimal and comparable isolation conditions and the complete characterization of the LEV, as well as the critical immunomodulatory events triggered by this important group of parasites.
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Affiliation(s)
- Áurea Martins Gabriel
- Global Health and Tropical Medicine, GHTM, Institute of Hygiene and Tropical Medicine of NOVA University of Lisbon, IHMT-UNL, 1349-008 Lisbon, Portugal
- Laboratory of Structural Biology of Institute of Biological Sciences of Federal University of Pará, Av. Augusto Correa 01, Belém 66075-110, PA, Brazil; (A.G.-P.); (E.O.d.S.)
| | - Adan Galué-Parra
- Laboratory of Structural Biology of Institute of Biological Sciences of Federal University of Pará, Av. Augusto Correa 01, Belém 66075-110, PA, Brazil; (A.G.-P.); (E.O.d.S.)
| | | | | | - Edilene Oliveira da Silva
- Laboratory of Structural Biology of Institute of Biological Sciences of Federal University of Pará, Av. Augusto Correa 01, Belém 66075-110, PA, Brazil; (A.G.-P.); (E.O.d.S.)
- National Institute of Science and Technology in Structural Biology and Bioimaging, UFRJ, Rio de Janeiro 21941-902, RJ, Brazil
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New Advances in the Research of Resistance to Neoadjuvant Chemotherapy in Breast Cancer. Int J Mol Sci 2021; 22:ijms22179644. [PMID: 34502549 PMCID: PMC8431789 DOI: 10.3390/ijms22179644] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 12/24/2022] Open
Abstract
Breast cancer has an extremely high incidence in women, and its morbidity and mortality rank first among female tumors. With the increasing development of medicine today, the clinical application of neoadjuvant chemotherapy has brought new hope to the treatment of breast cancer. Although the efficacy of neoadjuvant chemotherapy has been confirmed, drug resistance is one of the main reasons for its treatment failure, contributing to the difficulty in the treatment of breast cancer. This article focuses on multiple mechanisms of action and expounds a series of recent research advances that mediate drug resistance in breast cancer cells. Drug metabolizing enzymes can mediate a catalytic reaction to inactivate chemotherapeutic drugs and develop drug resistance. The drug efflux system can reduce the drug concentration in breast cancer cells. The combination of glutathione detoxification system and platinum drugs can cause breast cancer cells to be insensitive to drugs. Changes in drug targets have led to poorer efficacy of HER2 receptor inhibitors. Moreover, autophagy, epithelial–mesenchymal transition, and tumor microenvironment can all contribute to the development of resistance in breast cancer cells. Based on the relevant research on the existing drug resistance mechanism, the current treatment plan for reversing the resistance of breast cancer to neoadjuvant chemotherapy is explored, and the potential drug targets are analyzed, aiming to provide a new idea and strategy to reverse the resistance of neoadjuvant chemotherapy drugs in breast cancer.
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Comparative Molecular and Immunoregulatory Analysis of Extracellular Vesicles from Candida albicans and Candida auris. mSystems 2021; 6:e0082221. [PMID: 34427507 PMCID: PMC8407381 DOI: 10.1128/msystems.00822-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Candida auris is a recently described multidrug-resistant pathogenic fungus that is increasingly responsible for health care-associated outbreaks across the world. Bloodstream infections of this fungus cause death in up to 70% of cases. Aggravating this scenario, the disease-promoting mechanisms of C. auris are poorly understood. Fungi release extracellular vesicles (EVs) that carry a broad range of molecules, including proteins, lipids, carbohydrates, pigments, and RNA, many of which are virulence factors. Here, we carried out a comparative molecular characterization of C. auris and Candida albicans EVs and evaluated their capacity to modulate effector mechanisms of host immune defense. Using proteomics, lipidomics, and transcriptomics, we found that C. auris released EVs with payloads that were significantly different from those of EVs released by C. albicans. EVs released by C. auris potentiated the adhesion of this yeast to an epithelial cell monolayer, while EVs from C. albicans had no effect. C. albicans EVs primed macrophages for enhanced intracellular yeast killing, whereas C. auris EVs promoted survival of the fungal cells. Moreover, EVs from both C. auris and C. albicans induced the activation of bone marrow-derived dendritic cells. Together, our findings show distinct profiles and properties of EVs released by C. auris and by C. albicans and highlight the potential contribution of C. auris EVs to the pathogenesis of this emerging pathogen. IMPORTANCECandida auris is a recently described multidrug-resistant pathogenic fungus that is responsible for outbreaks across the globe, particularly in the context of nosocomial infections. Its virulence factors and pathogenesis are poorly understood. Here, we tested the hypothesis that extracellular vesicles (EVs) released by C. auris are a disease-promoting factor. We describe the production of EVs by C. auris and compare their biological activities against those of the better-characterized EVs from C. albicans. C. auris EVs have immunoregulatory properties, of which some are opposite those of C. albicans EVs. We also explored the cargo and structural components of those vesicles and found that they are remarkably distinct compared to EVs from C. auris’s phylogenetic relative Candida albicans.
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Dias-Lopes G, Zabala-Peñafiel A, de Albuquerque-Melo BC, Souza-Silva F, Menaguali do Canto L, Cysne-Finkelstein L, Alves CR. Axenic amastigotes of Leishmania species as a suitable model for in vitro studies. Acta Trop 2021; 220:105956. [PMID: 33979642 DOI: 10.1016/j.actatropica.2021.105956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/26/2022]
Abstract
Leishmania spp. are etiological agents of infection diseases, which in some cases can be fatal. The main forms of their biological cycle, promastigotes and amastigotes, can be maintained in vitro. While promastigotes are easier to maintain, amastigotes are more complex and can be obtained through different ways, including infection assays of tissues or in vitro cells, and differentiation from promastigotes to axenic amastigotes. Several protocols have been proposed for in vitro differentiation for at least 12 Leishmania spp. of both subgenera, Leishmania and Viannia. In this review we propose a critical summary of axenic amastigotes induction, as well as the impact of these strategies on metabolic pathways and regulatory networks analyzed by omics approaches. The parameters used by different research groups show considerable variations in temperature, pH and induction stages, as highlighted here for Leishmania (Viannia) braziliensis. Therefore, a consensus on strategies for inducing amastigogenesis is necessary to improve accuracy and even define stage-specific biomarkers. In fact, the axenic amastigote model has contributed to elucidate several aspects of the parasite cycle, however, since it does not reproduce the intracellular environment, its use requires several precautions. In addition, we present a discussion about using axenic amastigotes for drug screening, suggesting the need of a more sensitive methodology to verify cell viability in these tests. Collectively, this review explores the advantages and limitations found in studies with axenic amastigotes, done for more than 30 years, and discuss the gaps that impair their use as a suitable model for in vitro studies.
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Yuan Y, Zhao J, Chen M, Liang H, Long X, Zhang B, Chen X, Chen Q. Understanding the Pathophysiology of Exosomes in Schistosomiasis: A New Direction for Disease Control and Prevention. Front Immunol 2021; 12:634138. [PMID: 34220800 PMCID: PMC8242937 DOI: 10.3389/fimmu.2021.634138] [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] [Received: 11/27/2020] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
Schistosomiasis is a parasitic disease endemic to freshwater areas of Southeast Asia, Africa, and South America that is capable of causing serious damage to the internal organs. Recent studies have linked exosomes to the progression of schistosomiasis. These structures are important mediators for intercellular communication, assist cells to exchange proteins, lipids, and genetic material and have been shown to play critical roles during host–parasite interactions. This review aims to discuss the pathophysiology of exosomes in schistosomiasis and their roles in regulating the host immune response. Understanding how exosomes are involved in the pathogenesis of schistosomiasis may provide new perspectives in diagnosing and treating this neglected disease.
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Affiliation(s)
- Yue Yuan
- Division of Gastroenterology, Department of Internal Medicine at Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Jianping Zhao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Min Chen
- Division of Gastroenterology, Department of Internal Medicine at Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Huifang Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Xin Long
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Qian Chen
- Division of Gastroenterology, Department of Internal Medicine at Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
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Li Z, Stanton BA. Transfer RNA-Derived Fragments, the Underappreciated Regulatory Small RNAs in Microbial Pathogenesis. Front Microbiol 2021; 12:687632. [PMID: 34079534 PMCID: PMC8166272 DOI: 10.3389/fmicb.2021.687632] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 01/20/2023] Open
Abstract
In eukaryotic organisms, transfer RNA (tRNA)-derived fragments have diverse biological functions. Considering the conserved sequences of tRNAs, it is not surprising that endogenous tRNA fragments in bacteria also play important regulatory roles. Recent studies have shown that microbes secrete extracellular vesicles (EVs) containing tRNA fragments and that the EVs deliver tRNA fragments to eukaryotic hosts where they regulate gene expression. Here, we review the literature describing microbial tRNA fragment biogenesis and how the fragments secreted in microbial EVs suppress the host immune response, thereby facilitating chronic infection. Also, we discuss knowledge gaps and research challenges for understanding the pathogenic roles of microbial tRNA fragments in regulating the host response to infection.
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Affiliation(s)
- Zhongyou Li
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
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40
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Transcriptional profiles of genes potentially involved in extracellular vesicle biogenesis in Schistosoma japonicum. Acta Trop 2021; 217:105851. [PMID: 33524382 DOI: 10.1016/j.actatropica.2021.105851] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 01/16/2023]
Abstract
Schistosomiasis is a severe chronic disease caused by parasitic worms of the genus Schistosoma. Recent studies indicate that schistosomes can secrete extracellular vesicles (EVs), which play important regulatory roles in many biological processes. However, the mechanisms underlying EV biogenesis in schistosomes are poorly understood. In this study, we performed bioinformatic analyses and identified several genes putatively involved in EV biogenesis in Schistosoma japonicum, which were then confirmed by PCR. Quantitative transcriptional profiles of the selected genes indicated that they were differentially expressed in male and female worms as well as in the different developmental stages of S. japonicum. Thus, the highest expression of VAMP3 was detected in cercariae, whereas that of ARF6 was detected in eggs. RAB11A and the Syntenin-encoding gene SDCBP were highly expressed in 14-day schistosomula and VPS4A and RAB27A were highly expressed in 35-day-old adult schistosomes. The expression of RAB11A, CHMP4C, VPS4A, and SDCBP was higher in male worms, whereas that of ARF6, VAMP3, and RAB27A was higher in female worms. Our results are expected to provide important clues for understanding the role of EV biogenesis in S. japonicum development.
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41
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Gut microbiota-microRNA interactions in ankylosing spondylitis. Autoimmun Rev 2021; 20:102827. [PMID: 33864943 DOI: 10.1016/j.autrev.2021.102827] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/17/2021] [Indexed: 12/20/2022]
Abstract
Ankylosing spondylitis (AS) is a chronic autoimmune inflammatory disability that is part of the rheumatic disease group of spondyloarthropathies. AS commonly influences the joints of the axial skeleton. The contributions to AS pathogenesis of genetic susceptibility (particularly HLA-B27 and ERAP-1) and epigenetic modifications, like non-coding RNAs, as well as environmental factors, have been investigated over the last few years. But the fundamental etiology of AS remains elusive to date. The evidence summarized here indicates that in the immunopathogenesis of AS, microRNAs and the gut microbiome perform critical functions. We discuss significant advances in the immunological mechanisms underlying AS and address potential cross-talk between the gut microbiome and host microRNAs. This critical interaction implicates a co-evolutionary symbiotic link between host immunity and the gut microbiome.
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42
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Dong G, Wagner V, Minguez-Menendez A, Fernandez-Prada C, Olivier M. Extracellular vesicles and leishmaniasis: Current knowledge and promising avenues for future development. Mol Immunol 2021; 135:73-83. [PMID: 33873096 DOI: 10.1016/j.molimm.2021.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/23/2021] [Accepted: 04/01/2021] [Indexed: 02/09/2023]
Abstract
Extracellular vesicles (EVs) are small, membrane-bound "delivery trucks" that are present in the extracellular environment, including biological fluids. EVs are capable of inducing changes in the physiological status of neighboring cells through the transfer of key macromolecules, and are thought to play a role in a number of pathological processes. Leishmaniasis, caused by the protozoan parasite Leishmania, is an important example. The biology of Leishmania EVs has been studied in detail, and findings point to their role in exacerbation of disease and potential involvement in the perpetuation of drug resistance. Furthermore, the use of EVs for development of vaccines has been explored, as well as their potential use in a number of fields as biomarkers of disease and drug resistance. Here we discuss the latest findings on EVs, with a particular focus on Leishmania, as well as potential avenues for their future development and clinical applications.
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Affiliation(s)
- George Dong
- Infectious Diseases and Immunology in Global Health Program (IDIGH), The Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Victoria Wagner
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, QC, Canada; The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, Université de Montréal, QC, Canada
| | | | - Christopher Fernandez-Prada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, QC, Canada; The Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, Université de Montréal, QC, Canada.
| | - Martin Olivier
- Infectious Diseases and Immunology in Global Health Program (IDIGH), The Research Institute of the McGill University Health Centre, Montréal, QC, Canada; Departments of Medicine, Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, QC, Canada.
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43
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Torres AG, Martí E. Toward an Understanding of Extracellular tRNA Biology. Front Mol Biosci 2021; 8:662620. [PMID: 33937338 PMCID: PMC8082309 DOI: 10.3389/fmolb.2021.662620] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Extracellular RNAs (exRNAs) including abundant full length tRNAs and tRNA fragments (tRFs) have recently garnered attention as a promising source of biomarkers and a novel mediator in cell-to-cell communication in eukaryotes. Depending on the physiological state of cells, tRNAs/tRFs are released to the extracellular space either contained in extracellular vesicles (EVs) or free, through a mechanism that is largely unknown. In this perspective article, we propose that extracellular tRNAs (ex-tRNAs) and/or extracellular tRFs (ex-tRFs) are relevant paracrine signaling molecules whose activity depends on the mechanisms of release by source cells and capture by recipient cells. We speculate on how ex-tRNA/ex-tRFs orchestrate the effects in target cells, depending on the type of sequence and the mechanisms of uptake. We further propose that tRNA modifications may be playing important roles in ex-tRNA biology.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eulàlia Martí
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Epidemiología y Salud Pública, Madrid, Spain
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44
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Shi J, Zhang Y, Tan D, Zhang X, Yan M, Zhang Y, Franklin R, Shahbazi M, Mackinlay K, Liu S, Kuhle B, James ER, Zhang L, Qu Y, Zhai Q, Zhao W, Zhao L, Zhou C, Gu W, Murn J, Guo J, Carrell DT, Wang Y, Chen X, Cairns BR, Yang XL, Schimmel P, Zernicka-Goetz M, Cheloufi S, Zhang Y, Zhou T, Chen Q. PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nat Cell Biol 2021; 23:424-436. [PMID: 33820973 PMCID: PMC8236090 DOI: 10.1038/s41556-021-00652-7] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 02/23/2021] [Indexed: 02/06/2023]
Abstract
Although high-throughput RNA sequencing (RNA-seq) has greatly advanced small non-coding RNA (sncRNA) discovery, the currently widely used complementary DNA library construction protocol generates biased sequencing results. This is partially due to RNA modifications that interfere with adapter ligation and reverse transcription processes, which prevent the detection of sncRNAs bearing these modifications. Here, we present PANDORA-seq (panoramic RNA display by overcoming RNA modification aborted sequencing), employing a combinatorial enzymatic treatment to remove key RNA modifications that block adapter ligation and reverse transcription. PANDORA-seq identified abundant modified sncRNAs-mostly transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs)-that were previously undetected, exhibiting tissue-specific expression across mouse brain, liver, spleen and sperm, as well as cell-specific expression across embryonic stem cells (ESCs) and HeLa cells. Using PANDORA-seq, we revealed unprecedented landscapes of microRNA, tsRNA and rsRNA dynamics during the generation of induced pluripotent stem cells. Importantly, tsRNAs and rsRNAs that are downregulated during somatic cell reprogramming impact cellular translation in ESCs, suggesting a role in lineage differentiation.
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Affiliation(s)
- Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Yunfang Zhang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Dongmei Tan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
| | - Xudong Zhang
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Menghong Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
- Pudong Medical Center, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Zhang
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Reuben Franklin
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, USA
| | - Marta Shahbazi
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Kirsty Mackinlay
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Shichao Liu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Emma R James
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Liwen Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yongcun Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qiwei Zhai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Wenxin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Changcheng Zhou
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Weifeng Gu
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, USA
| | - Jernej Murn
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, USA
| | - Jingtao Guo
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Douglas T Carrell
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sihem Cheloufi
- Department of Biochemistry, Stem Cell Center, University of California, Riverside, Riverside, CA, USA.
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- The Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA.
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45
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Yang J, Pan B, Zeng F, He B, Gao Y, Liu X, Song Y. Magnetic Colloid Antibodies Accelerate Small Extracellular Vesicles Isolation for Point-of-Care Diagnostics. NANO LETTERS 2021; 21:2001-2009. [PMID: 33591201 DOI: 10.1021/acs.nanolett.0c04476] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Small extracellular vesicles (sEVs) are increasingly recognized as noninvasive diagnostic markers for many diseases. Hence, it is highly desirable to isolate sEVs rapidly for downstream molecular analyses. However, conventional methods for sEV isolation (such as ultracentrifugation and immune-based isolation) are time-consuming and expensive and require large sample volumes. Herein, we developed artificial magnetic colloid antibodies (MCAs) via surface imprinting technology for rapid isolation and analysis of sEVs. This approach enabled the rapid, purification-free, and low-cost isolation of sEVs based on size and shape recognition. The MCAs presented a higher capture yield in 20 min with more than 3-fold enrichment of sEVs compared with the ultracentrifugation method in 4 h. Moreover, the MCAs also proposed a reusability benefiting from the high stability of the organosilica recognition layer. By combining with volumetric bar-chart chip technology, this work provides a sensitive, rapid, and easy-to-use sEV detection platform for point-of-care (POC) diagnostics.
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Affiliation(s)
- Jingjing Yang
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Nanjing University, Nanjing 210023, China
| | - Bei Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Fei Zeng
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Nanjing University, Nanjing 210023, China
| | - Bangshun He
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Yanfeng Gao
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Nanjing University, Nanjing 210023, China
| | - Xinli Liu
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Nanjing University, Nanjing 210023, China
| | - Yujun Song
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Nanjing University, Nanjing 210023, China
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46
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Abstract
Trichomonas vaginalis is an anaerobic/microaerophilic protist parasite which causes trichomoniasis, one of the most prevalent sexually transmitted diseases worldwide. T. vaginalis not only is important as a human pathogen but also is of great biological interest because of its peculiar cell biology and metabolism, in earlier times fostering the erroneous notion that this microorganism is at the root of eukaryotic evolution. This review summarizes the major advances in the last five years in the T. vaginalis field with regard to genetics, molecular biology, ecology, and pathogenicity of the parasite.
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Affiliation(s)
- David Leitsch
- Department of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
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47
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Wang ZS, Zhou HC, Wei CY, Wang ZH, Hao X, Zhang LH, Li JZ, Wang ZL, Wang H. Global survey of miRNAs and tRNA-derived small RNAs from the human parasitic protist Trichomonas vaginalis. Parasit Vectors 2021; 14:87. [PMID: 33514387 PMCID: PMC7844918 DOI: 10.1186/s13071-020-04570-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/28/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Small non-coding RNAs play critical regulatory roles in post-transcription. However, their characteristics in Trichomonas vaginalis, the causative agent of human sexually transmitted trichomoniasis, still remain to be determined. METHODS Small RNA transcriptomes from Trichomonas trophozoites were deep sequenced using the Illumina NextSeq 500 system and comprehensively analyzed to identify Trichomonas microRNAs (miRNAs) and transfer RNA (tRNA)-derived small RNAs (tsRNAs). The tsRNA candidates were confirmed by stem-loop quantitative reverse transcription-PCR, and motifs to guide the cleavage of tsRNAs were predicted using the GLAM2 algorithm. RESULTS The miRNAs were found to be present in T. vaginalis but at an extremely low abundance (0.0046%). Three categories of endogenous Trichomonas tsRNAs were identified, namely 5'tritsRNAs, mid-tritsRNAs and 3'tritsRNAs, with the 5'tritsRNAs constituting the dominant category (67.63%) of tsRNAs. Interestingly, the cleavage site analysis verified both conventional classes of tRNA-derived fragments (tRFs) and tRNA-halves in tritsRNAs, indicating the expression of tRNA-halves in the non-stress condition. A total of 25 tritsRNAs were experimentally confirmed, accounting for 78.1% of all tested candidates. Three motifs were predicted to guide the production of tritsRNAs. The results prove the expression of tRFs and tRNA-halves in the T. vaginalis transcriptome. CONCLUSIONS This is the first report of genome-wide investigation of small RNAs, particularly tsRNAs and miRNAs, from Trichomonas parasites. Our findings demonstrate the expression profile of tsRNAs in T. vaginalis, while miRNA was barely detected. These results may promote further research aimed at gaining a better understanding of the evolution of small non-coding RNA in T. vaginalis and their functions in the pathogenesis of trichomoniasis.
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Affiliation(s)
- Zhen-Sheng Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China.,NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Hong-Chang Zhou
- School of Medicine, Huzhou University and Huzhou Central Hospital, Huzhou, 313000, Zhejiang province, China
| | - Chun-Yan Wei
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China
| | - Zhi-Hua Wang
- Department of Immunology, Guilin Medical University, Guilin, 541000, Guangxi province, China
| | - Xiao Hao
- Blood Chamber, Blood Station of Jinan, Jinan, 250000, Shandong province, China
| | - Lian-Hui Zhang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China
| | - Jing-Zhong Li
- NHC Key Laboratory of Echinococcosis Prevention and Control, #21 linkuo North Road, Chengguan District, Lhasa, 850000, Tibet Autonomous Region, People's Republic of China
| | - Zeng-Lei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
| | - Heng Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing, 100005, People's Republic of China.
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48
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Joshi B, Singh B, Nadeem A, Askarian F, Wai SN, Johannessen M, Hegstad K. Transcriptome Profiling of Staphylococcus aureus Associated Extracellular Vesicles Reveals Presence of Small RNA-Cargo. Front Mol Biosci 2021; 7:566207. [PMID: 33521050 PMCID: PMC7838569 DOI: 10.3389/fmolb.2020.566207] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial extracellular vesicles (EVs) have a vital role in bacterial pathogenesis. However, to date, the small RNA-cargo of EVs released by the opportunistic pathogen Staphylococcus aureus has not been characterized. Here, we shed light on the association of small RNAs with EVs secreted by S. aureus MSSA476 cultured in iron-depleted bacteriologic media supplemented with a subinhibitory dosage of vancomycin to mimic infection condition. Confocal microscopy analysis on intact RNase-treated EVs indicated that RNA is associated with EV particles. Transcriptomic followed by bioinformatics analysis of EV-associated RNA revealed the presence of potential gene regulatory small RNAs and high levels of tRNAs. Among the EV-associated enriched small RNAs were SsrA, RsaC and RNAIII. Our finding invites new insights into the potential role of EV-associated RNA as a modulator of host-pathogen interaction.
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Affiliation(s)
- Bishnu Joshi
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Bhupender Singh
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Aftab Nadeem
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Fatemeh Askarian
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway.,Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Sun Nyunt Wai
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Mona Johannessen
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Department of Medical Biology, Research Group for Host-Microbe Interactions, UiT The Arctic University of Norway, Tromsø, Norway.,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North-Norway, Tromsø, Norway
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miRNA profile of extracellular vesicles isolated from saliva of Haemaphysalis longicornis tick. Acta Trop 2020; 212:105718. [PMID: 32971070 DOI: 10.1016/j.actatropica.2020.105718] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/19/2020] [Accepted: 09/19/2020] [Indexed: 12/19/2022]
Abstract
Extracellular vesicles (EVs) play a key role in host-parasite interactions. Previous studies have shown that parasites can release microRNA (miRNA) containing EVs, which can transfer their contents to host cells and regulate gene expression in recipient cells. However, a little is known about the secretion of EVs by the ticks. This study was therefore, carried out to examine the saliva of ticks for the presence of miRNA containing EVs. Vesicles were purified from saliva of partially engorged Haemaphysalis longicornis ticks. Transmission electron microscopy (TEM) was carried out to confirm that vesicles within saliva were EVs based on size and morphology. Total RNA was extracted from EVs and was analyzed by deep sequencing to determine miRNA profile. TEM analysis confirmed the presence of extracellular vesicle-like structures within tick saliva. RNA-seq analysis showed that tick-derived EVs contained small non-coding RNA populations including miRNAs. The analysis of tick-derived EVs identified 36 known miRNAs, 34 novel miRNAs and 842 novel Piwi-interacting RNAs (piRNA). The results of this study provide evidence that EVs containing miRNAs can be secreted by the ticks and suggest that vesicles could transfer these miRNAs to modulate host cell functions.
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50
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Artuyants A, Campos TL, Rai AK, Johnson PJ, Dauros-Singorenko P, Phillips A, Simoes-Barbosa A. Extracellular vesicles produced by the protozoan parasite Trichomonas vaginalis contain a preferential cargo of tRNA-derived small RNAs. Int J Parasitol 2020; 50:1145-1155. [DOI: 10.1016/j.ijpara.2020.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022]
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