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Li X, Ding J, Zhang X, Zhang X, Jiang X, Chen R, Cheng Y, Sun Y, Wan J, Zhang Y, Cao J, Han S. MicroRNAs in opisthorchiids and their definitive hosts: Current Status and Perspectives. Mol Biochem Parasitol 2024; 260:111636. [PMID: 38880486 DOI: 10.1016/j.molbiopara.2024.111636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
Opisthorchis felineus, Opisthorchis viverrini, and Clonorchis sinensis (family Opisthorchiidae) are parasitic flatworms that pose serious threats to humans in certain countries and cause opisthorchiasis/clonorchiasis. Opisthorchiid flukes parasitize the biliary tract of the host, causing cholangitis, cholecystitis, cholelithiasis and cholangiocarcinoma. In this review, we primarily focus on recent microRNAs (miRNAs) studies of opisthorchiid flukes and their definitive hosts. Many miRNAs are conserved and expressed in a developmentally stage specific manner in the three opisthorchiid flukes, which play important roles in the growth and development of Opisthorchiidae spp., as well as host-pathogen interactions. Some miRNAs might be potential biomarkers related to carcinogenesis of cholangiocarcinoma. Therefore, this review provides the basis for further investigating the roles of miRNAs in opisthorchiid flukes and their definitive hosts, as well as promoting the development of novel approaches to prevent and treat opisthorchiasis/clonorchiasis.
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Affiliation(s)
- Xiang Li
- Central Laboratory, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jian Ding
- West Coast New Area Center for Disease Prevention and Control, Qingdao, China
| | - Xiaoli Zhang
- Department of Parasitology, Harbin Medical University, Harbin, China
| | - Xueli Zhang
- Department of Parasitology, Harbin Medical University, Harbin, China
| | - Xu Jiang
- Department of Parasitology, Harbin Medical University, Harbin, China
| | - Rui Chen
- Department of orthopaedics, Affiliated Wuxi No. 2 Hospital, Wuxi, China
| | - Yang Cheng
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yifan Sun
- Department of Clinical Laboratory, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jie Wan
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yu Zhang
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianping Cao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, (Chinese Center for Tropical Diseases Research), Shanghai 200025, China.
| | - Su Han
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China; Department of Parasitology, Harbin Medical University, Harbin, China.
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Pereira I, Paludo GP, Hidalgo C, Stoore C, Baquedano MS, Cabezas C, Cancela M, Ferreira HB, Bastías M, Riveros A, Meneses C, Sáenz L, Paredes R. Weighted gene co-expression network analysis reveals immune evasion related genes in Echinococcus granulosus sensu stricto. Exp Biol Med (Maywood) 2024; 249:10126. [PMID: 38510493 PMCID: PMC10954194 DOI: 10.3389/ebm.2024.10126] [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: 07/10/2023] [Accepted: 11/22/2023] [Indexed: 03/22/2024] Open
Abstract
Cystic echinococcosis (CE) is a zoonotic disease caused by the tapeworm Echinococcus granulosus sensu lato (s.l). In the intermediate host, this disease is characterized by the growth of cysts in viscera such as liver and lungs, inside of which the parasite develops to the next infective stage known as protoscoleces. There are records that the infected viscera affect the development and morphology of E. granulosus s.l. protoscolex in hosts such as buffalo or humans. However, the molecular mechanisms that drive these differences remains unknown. Weighted gene co-expression network analysis (WGCNA) using a set of RNAseq data obtained from E. granulosus sensu stricto (s.s.) protoscoleces found in liver and lung cysts reveals 34 modules in protoscoleces of liver origin, of which 12 have differential co-expression from protoscoleces of lung origin. Three of these twelve modules contain hub genes related to immune evasion: tegument antigen, tegumental protein, ubiquitin hydrolase isozyme L3, COP9 signalosome complex subunit 3, tetraspanin CD9 antigen, and the methyl-CpG-binding protein Mbd2. Also, two of the twelve modules contain only hypothetical proteins with unknown orthology, which means that there are a group of unknown function proteins co-expressed inside the protoscolex of liver CE cyst origin. This is the first evidence of gene expression differences in protoscoleces from CE cysts found in different viscera, with co-expression networks that are exclusive to protoscoleces from liver CE cyst samples. This should be considered in the control strategies of CE, as intermediate hosts can harbor CE cysts in liver, lungs, or both organs simultaneously.
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Affiliation(s)
- Ismael Pereira
- Laboratorio de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Universidad de Chile, Santiago, Chile
| | - Gabriela Prado Paludo
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazi
| | - Christian Hidalgo
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Sede Santiago Centro, Santiago, Chile
| | - Caroll Stoore
- Laboratorio de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - María Soledad Baquedano
- Laboratorio de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Carolina Cabezas
- Laboratorio de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Martín Cancela
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazi
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazi
| | - Macarena Bastías
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Aníbal Riveros
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Leonardo Sáenz
- Laboratorio de Vacunas Veterinarias, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Rodolfo Paredes
- Laboratorio de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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Celik F, Tektemur A, Simsek S. miRNA based biomarkers for the early diagnosis of Echinococcus granulosus in experimentally infected dogs. Vet Parasitol 2023; 324:110075. [PMID: 38000178 DOI: 10.1016/j.vetpar.2023.110075] [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: 08/17/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023]
Abstract
Cystic echinococcosis, which is caused by the Echinococcus granulosus. Carnivores, as final hosts, contain adult tapeworms in the small intestine, and a variety of mammals, including humans, harbor the metacestod. This study was designed to investigate the miRNA-based biomarkers for early and accurate diagnosis of E. granulosus in experimentally infected dogs. A liver with an obvious hydatid cyst was obtained from a slaughterhouse and then protoscoleces were collected. Following, viable protoscoleces were administred to three experimental dogs (ED1, ED2 and ED3) and another uninfected control dog (UCD) was kept as control without infection. Stool samples of all groups were collected during 50 days from the beginning of the experimental infection and stored at - 80 °C till work. Total miRNA was isolated from all individual stool samples. The qRT-PCR method was used to determine the differences in the expression levels of E. granulosus specific miRNAs which were egr-let-7-5p, egr-miR-2b-5p, egr-miR-71-5p and egr-miR-125-5p. All miRNAs were found to be expressed from the first day in all infected dogs. In the stool samples of the UCD, the egr-miR-71-5p was detected, while the other miRNAs (egr-let-7-5p, egr-miR-2b-5p, egr-miR-125-5p) were not expressed. The expression of egr-let-7-5p and egr-miR-125-5p was significantly increased in ED1 compared to UCD on all days. In particular, for the first time, the expression levels of egr-let-7-5p and egr-miR-125-5p increased significantly between days 15 and 19. Similarly, the increase in let-7-5p and miR-125-5p expression was statistically significant in ED2. In ED3, egr-let-7-5p, egr-miR2b-5p and egr-miR-125-5p expressions were significantly increased on all days. In particular, egr-let-7-5p expression levels increased significantly for the first time between days 15 and 19. In addition, egr-mir-125-5p expression levels were found to increase at a high level for the first time on day 16. In conclusion, especially egr-let-7-5p and egr-miR-125-5p can be used as early diagnostic biomarkers in dogs infected with E. granulosus.
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Affiliation(s)
- Figen Celik
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, 23119 Elazig, Turkey
| | - Ahmet Tektemur
- Department of Medical Biology, Faculty of Medicine, University of Firat, 23119 Elazig, Turkey
| | - Sami Simsek
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, 23119 Elazig, Turkey.
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Grecco A, Macchiaroli N, Pérez MG, Casulli A, Cucher MA, Rosenzvit MC. microRNA silencing in a whole worm cestode model provides insight into miR-71 function. Int J Parasitol 2023; 53:699-710. [PMID: 37699506 DOI: 10.1016/j.ijpara.2023.08.002] [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: 04/11/2023] [Revised: 06/13/2023] [Accepted: 08/05/2023] [Indexed: 09/14/2023]
Abstract
Parasites belonging to the class Cestoda include zoonotic species such as Echinococcus spp. and Taenia spp. that cause morbidity and mortality in endemic areas, mainly affecting pastoral and rural communities in low income countries but also upper middle income countries. Cestodes show remarkable developmental plasticity, implying tight regulation of gene expression throughout their complex life cycles. Despite the recent availability of genomic data for cestodes, little progress was made on postgenomic functional studies. MicroRNAs (miRNAs) are key components of gene regulatory systems that guide diverse developmental processes in multicellular organisms. miR-71 is a highly expressed miRNA in cestodes, which is absent in vertebrates and targets essential parasite genes, representing a potential key player in understanding the role of miRNAs in cestodes biology. Here we used transfection with antisense oligonucleotides to perform whole worm miRNA knockdown in tetrathyridia of Mesocestoides vogae (syn. Mesocestoides corti), a laboratory model of cestodes. We believe this is the first report of miRNA knockdown at the organism level in these parasites. Our results showed that M. vogae miR-71 is involved in the control of strobilation in vitro and in the establishment of murine infection. In addition, we identified miR-71 targets in M. vogae, several of them being de-repressed upon miR-71 knockdown. This study provides new knowledge on gene expression regulation in cestodes and suggests that miRNAs could be evaluated as new selective therapeutic targets for treating Neglected Tropical Diseases prioritised by the World Health Organization.
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Affiliation(s)
- Andrés Grecco
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Natalia Macchiaroli
- Laboratorio de Genómica y Bioinformática de Patógenos, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Matías Gastón Pérez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Adriano Casulli
- WHO Collaborating Centre for the Epidemiology, Detection and Control of Cystic and Alveolar Echinococcosis. Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy; European Reference Laboratory for Parasites. Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marcela Alejandra Cucher
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mara Cecilia Rosenzvit
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina.
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Regmi R, Newman TE, Khentry Y, Kamphuis LG, Derbyshire MC. Genome-wide identification of Sclerotinia sclerotiorum small RNAs and their endogenous targets. BMC Genomics 2023; 24:582. [PMID: 37784009 PMCID: PMC10544508 DOI: 10.1186/s12864-023-09686-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Several phytopathogens produce small non-coding RNAs of approximately 18-30 nucleotides (nt) which post-transcriptionally regulate gene expression. Commonly called small RNAs (sRNAs), these small molecules were also reported to be present in the necrotrophic pathogen Sclerotinia sclerotiorum. S. sclerotiorum causes diseases in more than 400 plant species, including the important oilseed crop Brassica napus. sRNAs can further be classified as microRNAs (miRNAs) and short interfering RNAs (siRNAs). Certain miRNAs can activate loci that produce further sRNAs; these secondary sRNA-producing loci are called 'phased siRNA' (PHAS) loci and have only been described in plants. To date, very few studies have characterized sRNAs and their endogenous targets in S. sclerotiorum. RESULTS We used Illumina sequencing to characterize sRNAs from fungal mycelial mats of S. sclerotiorum spread over B. napus leaves. In total, eight sRNA libraries were prepared from in vitro, 12 h post-inoculation (HPI), and 24 HPI mycelial mat samples. Cluster analysis identified 354 abundant sRNA clusters with reads of more than 100 Reads Per Million (RPM). Differential expression analysis revealed upregulation of 34 and 57 loci at 12 and 24 HPI, respectively, in comparison to in vitro samples. Among these, 25 loci were commonly upregulated. Altogether, 343 endogenous targets were identified from the major RNAs of 25 loci. Almost 88% of these targets were annotated as repeat element genes, while the remaining targets were non-repeat element genes. Fungal degradome reads confirmed cleavage of two transposable elements by one upregulated sRNA. Altogether, 24 milRNA loci were predicted with both mature and milRNA* (star) sequences; these are both criteria associated previously with experimentally verified miRNAs. Degradome sequencing data confirmed the cleavage of 14 targets. These targets were related to repeat element genes, phosphate acetyltransferases, RNA-binding factor, and exchange factor. A PHAS gene prediction tool identified 26 possible phased interfering loci with 147 phasiRNAs from the S. sclerotiorum genome, suggesting this pathogen might produce sRNAs that function similarly to miRNAs in higher eukaryotes. CONCLUSIONS Our results provide new insights into sRNA populations and add a new resource for the study of sRNAs in S. sclerotiorum.
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Affiliation(s)
- Roshan Regmi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia
- Present address: Microbiome for One Systems Health, CSIRO, Urrbrae, South Australia, Australia
| | - Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia
| | - Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
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Irehan B, Celik F, Koroglu E, Tektemur A, Simsek S. Molecular characterization of cattle and sheep isolates of Echinococcus granulosus from elazig province in Turkey and expression analysis of the non-coding RNAs, egr-miR-7, egr-miR-71 and egr-miR-96. Exp Parasitol 2023:108551. [PMID: 37257717 DOI: 10.1016/j.exppara.2023.108551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/29/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
Cystic Echinococcosis (CE) is a common zoonotic disease seen in human and animals worldwide, caused by the larval form of Echinococcus granulosus. In this study, E. granulosus s.l. species and haplotypes were determined in hydatid cysts isolated from cattle and sheep, and the expression levels of egr-miR-7, egr-miR-71 and egr-miR-96 miRNAs were compared in different cyst structures. A total of 82 (cattle, n = 41; sheep, n = 41) hydatid cyst isolates (germinal membranes and/or protoscoleces) were collected from a slaughterhouse in Elazig province of Turkey. After mt-CO1 gene sequences were made, 81 out of 82 hydatid cyst isolates were determined as E. granulosus s.s. (G1 and G3), while an isolate of cattle origin was determined as Echinococcus canadensis (G6/7). A total of 26 nucleotide polymorphisms and 29 haplotype groups were identified in the samples. miRNA expressions in germinal membranes of sterile cysts and germinal membrane and protoscoleces of fertile cysts were investigated by qRT-PCR and Real Time PCR analyses. It was determined that miRNAs were expressed at high levels in 79.31% of the 29 haplotype groups and at low levels in the remaining 10.34%. In 10 fertile samples of sheep origin, egr-miR-7, egr-miR-71 and egr-miR-96 miRNAs were found to be 44, 168, and 351-fold higher in expression, respectively, in the germinal membrane compared to the protoscoleces. Especially egr-miR-96 may have the potential to be used as biomarkers in the diagnosis of active CE.
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Affiliation(s)
- Bunyamin Irehan
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, Elazig, Turkey
| | - Figen Celik
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, Elazig, Turkey
| | - Ergun Koroglu
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, Elazig, Turkey
| | - Ahmet Tektemur
- Department of Medical Biology, Faculty of Medicine, University of Firat, Elazig, Turkey
| | - Sami Simsek
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, Elazig, Turkey.
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Bioinformatics analysis and experimental verification of Notch signalling pathway-related miRNA-mRNA subnetwork in extracellular vesicles during Echinococcus granulosus encystation. Parasit Vectors 2022; 15:272. [PMID: 35906657 PMCID: PMC9338502 DOI: 10.1186/s13071-022-05391-8] [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: 04/28/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
Background Encystation of the protoscoleces (PSCs) of Echinococcus granulosus is the main cause of secondary hydatid dissemination in the intermediate host. Extracellular vesicles (EVs) can transfer miRNAs into parasite cells to regulate mRNA expression. However, loading of developmental pathway-related miRNAs, such as those related to the Notch signalling pathway in EVs is unclear. Thus, we screened the miRNA-mRNA subnetwork involved in the Notch pathway during E. granulosus encystation in vitro and assessed changes in expression in the parasite and EVs. Methods mRNAs and miRNAs differentially expressed (DE) between PSCs and microcysts (MCs) were screened using high-throughput sequencing. DE mRNAs obtained from transcriptome analysis were intersected with mRNAs predicted to be targets of the conserved DE miRNAs of a small RNA library. DE miRNA functions were analysed using public databases, and a miRNA–mRNA subnetwork related to the Notch pathway was established. Notch pathway-related mRNA and miRNA expression of worms and EVs at different times was verified. Results In total, 1445 DE mRNAs between MCs and PSCs were screened after the intersection between 1586 DE mRNAs from the transcriptome and 9439 target mRNAs predicted using 39 DE miRNAs from the small RNA library. The DE mRNAs were clustered into 94 metabolic pathways, including the Notch pathway. Five DE miRNAs, including the most significantly expressed new DE miRNA, egr-new-mir0694-3p, corresponding to four target mRNAs (EgrG_000892700, EgrG_001029400, EgrG_001081400 and EgrG_000465800) were all enriched in the Notch pathway. The expression of the above mRNAs and miRNAs was consistent with the results of high-throughput sequencing, and the expression of each miRNA in EVs was verified. Annotated as ADAM17/TACE in the Notch pathway, EgrG_000892700 was down-regulated during PSC encystation. egr-miR-4989-3p and egr-miR-277a-3p expression in EVs after encystation was nearly five times that in EVs before encystation, which might regulate the expression of EgrG_000892700. Conclusions Five miRNAs corresponding to four target mRNAs may be involved in regulating the Notch pathway during the PSC encystation. EVs may regulate the expression of EgrG_000892700 in PSCs because of continuous targeting of egr-miR-4989-3p and egr-miR-277a-3p and participate in the regulation the Notch pathway. The study might expand new ideas for blocking the secondary infection of E. granulosus PSCs via EVs miRNAs. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05391-8.
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Sun Y, Kou Y, He X, Yan Y, Guo X, Yang X, He N, Cho WC, Kutyrev I, Harandi MF, Kandil OM, Wang X, Song H, Zheng Y. Efficient delivery of Echinococcus multilocularis miRNAs using chitosan nanoparticles. Biomed Pharmacother 2022; 150:112945. [PMID: 35405393 DOI: 10.1016/j.biopha.2022.112945] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022] Open
Abstract
Alveolar echinococcosis caused by Echinococcus multilocularis is an important zoonotic disease, a great threat to human health due to limited interventions. microRNAs are a type of small non-coding RNA that plays a key role in many diseases and is considered as a potential therapeutic target for control of parasitic diseases. However, naked miRNAs are difficult to enter into cells and are easily degraded in both external and internal environments. Chitosan (CS) has recently been used as a promising vehicle for delivery of nucleic acids. Therefore, we prepared miRNA-bearing CS nanoparticles and investigated the physicochemical properties as well as the delivery efficiency. We found that CS nanoparticles was relatively stable, offered miRNA strong protection from degradation and had low cytotoxicity with no significant effects on cell proliferation and apoptosis. CS nanoparticles were shown to be easily absorbed by cells and have remarkable liver tropism. Furthermore, CS nanoparticles were used to efficiently deliver E. multilocularis miR-4989 in vitro and in vivo and caused a significant reduction in the expression of UBE2N in the liver, a potential target of emu-miR-4989, at both mRNA and protein levels. Our data demonstrate that CS nanoparticles can act as a vehicle for efficient liver-targeted delivery of miRNAs and for development of miRNA-based therapeutics against E. multilocularis infection.
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Affiliation(s)
- Yue Sun
- School of Chemistry and Chemical Engineering, School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, Gansu, China; State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, China
| | - Yongjie Kou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, China
| | - Xuedong He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, China
| | - Yuting Yan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, China
| | - Xiaola Guo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, China
| | - Xing Yang
- Department of Medical Microbiology and Immunology, School of Basic Medicine, Dali University, Dali 671000, Yunnan, China
| | - Naipu He
- School of Chemistry and Chemical Engineering, School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, Gansu, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Ivan Kutyrev
- Institute of General and Experimental Biology, Siberian Branch of Russian Academy of Sciences, Sakhyanovoi st. 6, 670047 Ulan-Ude, Russia; Institute of Biology, Irkutsk State University, Irkutsk 664025, Russia
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman 7616914115, Iran
| | - Omnia M Kandil
- Depterment of Parasitology and Animal Disease, Veterinary Research Institute, National Research Centre, Giza 12622, Egypt
| | - Xiaoqiang Wang
- School of Chemistry and Chemical Engineering, School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, Gansu, China.
| | - Houhui Song
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou 311300, China.
| | - Yadong Zheng
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou 311300, China.
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9
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Yang S, Du X, Wang C, Zhang T, Xu S, Zhu Y, Lv Y, Zhao Y, Zhu M, Guo L, Zhao W. Coding and Noncoding RNA Expression Profiles of Spleen CD4 + T Lymphocytes in Mice with Echinococcosis. CONTRAST MEDIA & MOLECULAR IMAGING 2022; 2022:9742461. [PMID: 35480082 PMCID: PMC9012641 DOI: 10.1155/2022/9742461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022]
Abstract
Cystic echinococcosis (CE) is a severe and neglected zoonotic disease that poses health and socioeconomic hazards. So far, the prevention and treatment of CE are far from meeting people's ideal expectations. Therefore, to gain insight into the prevention and diagnosis of CE, we explored the changes in RNA molecules and the biological processes and pathways involved in these RNA molecules as E. granulosus infects the host. Interferon (IFN)-γ, interleukin (IL)-2, IL-4, IL-6, IL-10, IL-17A, and tumor necrosis factor (TNF)-α levels in peripheral blood serum of E. granulosus infected and uninfected female BALB/c mice were measured using the cytometric bead array mouse Th1/Th2/Th17 cytokine kit. mRNA, microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA) profiles of spleen CD4+ T cells from the two groups of mice were analyzed using high-throughput sequencing and bioinformatics. The levels of IFN-γ, IL-2, IL-4, IL-6, IL-10, IL-17A, and TNF-α were significantly higher in the serum of the CE mice than in control mice (P < 0.01). In total, 1,758 known mRNAs, 37 miRNAs, 175 lncRNAs, and 22 circRNAs were differentially expressed between infected and uninfected mice (|fold change| ≥ 0.585, P < 0.05). These differentially expressed molecules are involved in chromosome composition, DNA/RNA metabolism, and gene expression in cell composition, biological function, and cell function. Moreover, closely related to the JAK/STAT signaling pathways, mitogen-activated protein kinase signaling pathways, P53 signaling pathways, PI3K/AKT signaling pathways, cell cycle, and metabolic pathways. E. granulosus infection significantly increased the levels of IFN-γ, IL-2, IL-4, IL-6, IL-10, IL-17A, and TNF-α in mouse peripheral blood of mice and significantly changed expression levels of various coding and noncoding RNAs. Further study of these trends and pathways may help clarify the pathogenesis of CE and provide new insights into the prevention and treatment of this disease.
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Affiliation(s)
- Songhao Yang
- Key Laboratory of Prevention and Control of Common Infectious Diseases of Ningxia Hui Autonomous Region, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Department of Medical Genetics and Cell Biology, School of Basic Medical Science of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
| | - Xiancai Du
- Key Laboratory of Prevention and Control of Common Infectious Diseases of Ningxia Hui Autonomous Region, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Department of Medical Genetics and Cell Biology, School of Basic Medical Science of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
| | - Chan Wang
- Key Laboratory of Prevention and Control of Common Infectious Diseases of Ningxia Hui Autonomous Region, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Department of Medical Genetics and Cell Biology, School of Basic Medical Science of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
| | - Tingrui Zhang
- Key Laboratory of Prevention and Control of Common Infectious Diseases of Ningxia Hui Autonomous Region, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Department of Medical Genetics and Cell Biology, School of Basic Medical Science of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
| | - Shimei Xu
- Key Laboratory of Prevention and Control of Common Infectious Diseases of Ningxia Hui Autonomous Region, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Center of Scientific Technology of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
| | - Yazhou Zhu
- Key Laboratory of Prevention and Control of Common Infectious Diseases of Ningxia Hui Autonomous Region, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Department of Medical Genetics and Cell Biology, School of Basic Medical Science of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
| | - Yongxue Lv
- Key Laboratory of Prevention and Control of Common Infectious Diseases of Ningxia Hui Autonomous Region, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Department of Medical Genetics and Cell Biology, School of Basic Medical Science of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
| | - Yinqi Zhao
- Key Laboratory of Prevention and Control of Common Infectious Diseases of Ningxia Hui Autonomous Region, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Center of Scientific Technology of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
| | - Mingxing Zhu
- Key Laboratory of Prevention and Control of Common Infectious Diseases of Ningxia Hui Autonomous Region, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Department of Medical Genetics and Cell Biology, School of Basic Medical Science of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Center of Scientific Technology of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
| | - Lingna Guo
- Key Laboratory of Prevention and Control of Common Infectious Diseases of Ningxia Hui Autonomous Region, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Center of Scientific Technology of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
| | - Wei Zhao
- Key Laboratory of Prevention and Control of Common Infectious Diseases of Ningxia Hui Autonomous Region, Ningxia Hui Autonomous Region 750004, Yinchuan, China
- Department of Medical Genetics and Cell Biology, School of Basic Medical Science of Ningxia Medical University, Ningxia Hui Autonomous Region 750004, Yinchuan, China
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10
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Du X, Zhu M, Zhang T, Wang C, Tao J, Yang S, Zhu Y, Zhao W. The Recombinant Eg.P29-Mediated miR-126a-5p Promotes the Differentiation of Mouse Naive CD4 + T Cells via DLK1-Mediated Notch1 Signal Pathway. Front Immunol 2022; 13:773276. [PMID: 35211114 PMCID: PMC8861942 DOI: 10.3389/fimmu.2022.773276] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/18/2022] [Indexed: 12/12/2022] Open
Abstract
Cystic echinococcosis (CE) is a zoonotic parasitic disease spread worldwide caused by Echinococcus granulosus (Eg), which sometimes causes serious damage; however, in many cases, people are not aware that they are infected. A number of recombinant vaccines based on Eg are used to evaluate their effectiveness against the infection. Our previous report showed that recombinant Eg.P29 (rEg.P29) has a marvelous immunoprotection and can induce Th1 immune response. Furthermore, data of miRNA microarray in mice spleen CD4+ T cells showed that miR-126a-5p was significantly elevated 1 week after immunization by using rEg.P29. Therefore, in this perspective, we discussed the role of miR-126a-5p in the differentiation of naive CD4+ T cells into Th1/Th2 under rEg.P29 immunization and determined the mechanisms associated with delta-like 1 homolog (DLK1) and Notch1 signaling pathway. One week after P29 immunization of mice, we found that miR-126a-5p was significantly increased and DLK1 expression was decreased, while Notch1 pathway activation was enhanced and Th1 response was significantly stronger. The identical conclusion was obtained by overexpression of mmu-miR-126a-5p in primary naive CD4+ T cells in mice. Intriguingly, mmu-miR-126a-5p was significantly raised in serum from mice infected with protoscolex in the early stages of infection and markedly declined in the late stages of infection, while has-miR-126-5p expression was dramatically reduced in serum from CE patients. Taken together, we show that miR-126a-5p functions as a positive regulator of Notch1-mediated differentiation of CD4+ T cells into Th1 through downregulating DLK1 in vivo and in vitro. Hsa-miR-126-5p is potentially a very promising diagnostic biomarker for CE.
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Affiliation(s)
- Xiancai Du
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Mingxing Zhu
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China.,Center of Scientific Technology of Ningxia Medical University, Yinchuan, China
| | - Tingrui Zhang
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Chan Wang
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Jia Tao
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Songhao Yang
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Yazhou Zhu
- School of Basic Medical Science of Ningxia Medical University, Yinchuan, China.,Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China
| | - Wei Zhao
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan, China.,Center of Scientific Technology of Ningxia Medical University, Yinchuan, China
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11
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Pereira I, Hidalgo C, Stoore C, Baquedano MS, Cabezas C, Bastías M, Riveros A, Meneses C, Cancela M, Ferreira HB, Sáenz L, Paredes R. Transcriptome analysis of Echinococcus granulosus sensu stricto protoscoleces reveals differences in immune modulation gene expression between cysts found in cattle and sheep. Vet Res 2022; 53:8. [PMID: 35090558 PMCID: PMC8796354 DOI: 10.1186/s13567-022-01022-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/03/2021] [Indexed: 11/22/2022] Open
Abstract
Cystic Echinococcosis (CE), a zoonotic parasitic disease, is caused by the cestode Echinococcus granulosus sensu lato. CE inflicts severe damage in cattle, sheep, and human hosts worldwide. Fertile CE cysts are characterized by the presence of viable protoscoleces. These parasite forms are studied with minimal contamination with host molecules. Hosts, cattle and sheep, show differences in their CE cyst fertility. The effect of the host in protoscolex transcriptome is not known. We genotyped and performed transcriptomic analysis on sheep protoscoleces obtained from liver and lung CE cysts. The transcriptomic data of Echinococcus granulosus sensu stricto protoscoleces from 6 lung CE cysts and 6 liver CE cysts were Collected. For host comparison analysis, 4 raw data files belonging to Echinococcus granulosus sensu stricto protoscoleces from cattle liver CE cysts were obtained from the NCBI SRA database. Principal component and differential expression analysis did not reveal any statistical differences between protoscoleces obtained from liver or lung cysts, either within the same sheep or different sheep hosts. Conversely, there are significant differences between cattle and sheep protoscolex samples. We found differential expression of immune-related genes. In cattle, 7 genes were upregulated in protoscoleces from liver cysts. In sheep, 3 genes were upregulated in protoscoleces from liver and lung CE cysts. Noteworthy, are the differential expression of antigen B, tegument antigen, and arginase-2 in samples obtained from sheep CE cysts, and basigin in samples from cattle CE cysts. These findings suggest that the host species is an important factor involved in the differential expression of immune related genes, which in turn is possibly related to the fertility of Echinococcus granulosus sensu stricto cysts.
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Affiliation(s)
- Ismael Pereira
- Laboratorio de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, 8820808, Santiago, Chile
| | - Christian Hidalgo
- Instituto de Ciencias Agroalimentarias, Animales y Ambientales (ICA3), Universidad de O'Higgins, San Fernando, Chile
| | - Caroll Stoore
- Laboratorio de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - María Soledad Baquedano
- Laboratorio de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Carolina Cabezas
- Laboratorio de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Macarena Bastías
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Aníbal Riveros
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Martín Cancela
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Leonardo Sáenz
- Laboratorio de Vacunas Veterinarias, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Rodolfo Paredes
- Laboratorio de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
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12
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Örsten S, Baysal İ, Yabanoglu-Ciftci S, Ciftci T, Ünal E, Akıncı D, Akyön Y, Akhan O. Can parasite-derived microRNAs differentiate active and inactive cystic echinococcosis patients? Parasitol Res 2021; 121:191-196. [PMID: 34811587 DOI: 10.1007/s00436-021-07382-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/11/2021] [Indexed: 11/28/2022]
Abstract
Cystic Echinococcosis (CE) is a neglected zoonotic disease caused by the metacestode form of Echinococcus granulosus sensu lato. Non-invasive imaging techniques, especially ultrasound, are primarily used for CE diagnosis. MicroRNAs (miRNAs) are small, non-coding RNA molecules that act as post-transcriptional regulators in various biological processes. After identification of parasite-derived miRNAs, these miRNAs are considered to be potential biomarkers for diagnosis and follow-up. The focus of this research is to compare the expression profiles of certain parasite-derived miRNAs in CE patients with active and inactive cysts as well as healthy controls. Parasite-derived miRNAs, egr-let-7-5p, egr-miR-71a-5p, and egr-miR-9-5p, of inactive CE patients were found to be differentially expressed with 3.74-, 2.72-, and 20.78-fold change (p < 0.05), respectively, when compared with active CE patients. In this study, we evaluated for the first time the expression profile of three parasite-derived miRNAs in the serum of CE patients to determine their potential to distinguish between active and inactive CE. It was concluded that serum levels of parasite-derived miRNAs, egr-let-7-5p and egr-miR-9-5p, could be promising new potential biomarkers for stage-specific diagnosis of CE. Further studies are needed with larger sample set to validate discriminating potential of these miRNAs.
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Affiliation(s)
- Serra Örsten
- Vocational School of Health Services, Hacettepe University, Ankara, Turkey.
| | - İpek Baysal
- Vocational School of Health Services, Hacettepe University, Ankara, Turkey
| | | | - Türkmen Ciftci
- Department of Radiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Emre Ünal
- Department of Radiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Devrim Akıncı
- Department of Radiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Yakut Akyön
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Okan Akhan
- Department of Radiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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13
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Alizadeh Z, Mahami-Oskouei M, Spotin A, Ahmadpour E, Cai P, Sandoghchian Shotorbani S, Pashazadeh F, Ansari F, Mohammadi H. MicroRNAs in helminth parasites: a systematic review. Curr Mol Med 2021; 22:779-808. [PMID: 34749620 DOI: 10.2174/1566524021666211108114009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/05/2021] [Accepted: 06/10/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) are about 22-nucleotide, small, non-coding RNAs that control gene expression post-transcriptionally. Helminth parasites usually express a unique repertoire of genes, including miRNAs, across different developmental stages with subtle regulatory mechanisms. OBJECTIVE There is a necessity to investigate the involvement of miRNAs in the development of parasites, host-parasite interaction, immune evasion and their abilities to govern infection in hosts. miRNAs present in helminth parasites have been summarized in the current systematic review (SR). METHODS Electronic databases, including PubMed, Scopus, ProQuest, Embase, and Google Scholar search engine, were searched to identify helminth miRNA studies published from February 1993 till December 2019. Only the published articles in English were included in the study. RESULTS A total of 1769 articles were preliminarily recorded. Following the strict inclusion and exclusion criteria, 105 studies were included in this SR. Most of these studies focused on the identification of miRNAs in helminth parasites and/or probing of differentially expressed host miRNA profiles in specific relevant tissues, while 12 studies aimed to detect parasite-derived miRNAs in host circulating system and 15 studies characterized extracellular vesicles (EV)-derived miRNAs secreted by parasites. CONCLUSION In the current SR, information regarding all miRNAs expressed in helminth parasites has been comprehensively provided and the utility of helminth parasites-derived miRNAs in diagnosis and control of parasitic infections has been discussed. Furthermore, functional studies on helminth-derived miRNAs have also been presented.
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Affiliation(s)
- Zahra Alizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Adel Spotin
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Ehsan Ahmadpour
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Pengfei Cai
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane. Australia
| | | | - Fariba Pashazadeh
- Research Center for Evidence-Based Medicine, Health Management and Safety Promotion Research Institute, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Fereshteh Ansari
- Research Center for Evidence-Based Medicine, Health Management and Safety Promotion Research Institute, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Hamed Mohammadi
- Non-Communicable Diseases Research Center, Alborz University of Medical Science, Karaj. Iran
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14
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Kamenetzky L, Maldonado LL, Cucher MA. Cestodes in the genomic era. Parasitol Res 2021; 121:1077-1089. [PMID: 34665308 DOI: 10.1007/s00436-021-07346-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/10/2021] [Indexed: 12/20/2022]
Abstract
The first cestode genomes were obtained by an international consortium led by the Wellcome Sanger Institute that included representative institutions from countries where the sequenced parasites have been studied for decades, in part because they are etiological agents of endemic diseases (Argentina, Uruguay, Mexico, Canada, UK, Germany, Switzerland, Ireland, USA, Japan, and China). After this, several complete genomes were obtained reaching 16 species to date. Cestode genomes have smaller relative size compared to other animals including free-living flatworms. Moreover, the features genome size and repeat content seem to differ in the two analyzed orders. Cyclophyllidean species have smaller genomes and with fewer repetitive content than Diphyllobothriidean species. On average, cestode genomes have 13,753 genes with 6 exons per gene and 41% GC content. More than 5,000 shared cestode proteins were accurately annotated by the integration of gene predictions and transcriptome evidence being more than 40% of these proteins of unknown function. Several gene losses and reduction of gene families were found and could be related to the extreme parasitic lifestyle of these species. The application of cutting-edge sequencing technology allowed the characterization of the terminal sequences of chromosomes that possess unique characteristics. Here, we review the current status of knowledge of complete cestode genomes and place it within a comparative genomics perspective. Multidisciplinary work together with the implementation of new technologies will provide valuable information that can certainly improve our chances to finally eradicate or at least control diseases caused by cestodes.
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Affiliation(s)
- Laura Kamenetzky
- iB3, Instituto de Biociencias, Departamento de Fisiología Y Biología Molecular Y Celular, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Biotecnología y Biología traslacional, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
| | - Lucas L Maldonado
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Research On Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina
| | - Marcela A Cucher
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Research On Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina
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15
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Taghipour A, Ghaffarifar F, Horton J, Dalimi A, Sharifi Z. Silybum marianum ethanolic extract: in vitro effects on protoscolices of Echinococcus granulosus G1 strain with emphasis on other Iranian medicinal plants. Trop Med Health 2021; 49:71. [PMID: 34496975 PMCID: PMC8424884 DOI: 10.1186/s41182-021-00363-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cystic echinococcosis (CE), is a parasitic zoonosis caused by Echinococcus granulosus (E. granulosus) larvae in liver and lungs of both humans and animals. Surgical intervention is the mainstay for CE treatment, using scolicidal agents that inactivate live protoscolices. This study evaluated the scolicidal effects of Silybum marianum ethanolic extract and its combination with albendazole in vitro for the first time. Moreover, in a literature review, we investigated the effects of a wide range of Iranian medicinal plants on protoscolices of E. granulosus. METHODS S. marianum ethanolic extract was prepared and high-performance liquid chromatography (HPLC) analysis was used to establish the proportions of its component compounds in the extract. Cytotoxicity was evaluated in mouse macrophage cells (J774A.1 cell line) using MTT method. Next, the scolicidal activity of the extract alone and combined with albendazole was tested as triplicate at various concentrations incubated for 5, 10, 20, 30, and 60 min. Finally, protoscolex viability was determined using 0.1% eosin as a vital stain. PCR-RFLP and DNA sequencing techniques were used to characterize the genotype of E. granulosus. RESULTS HPLC analysis showed that S. marianum ethanolic extract contained mostly silydianin (14.41%), isosilybin A (10.50%), and silychristin (10.46%). The greatest scolicidal effects were obtained with the combination of S. marianum with albendazole (79%), S. marianum ethanolic extract alone (77%) and albendazole (69%), at a concentration of 500 μg/ml for 60 min, respectively (P < 0.05). Molecular analysis showed that all the cysts used were G1 genotype. CONCLUSION The data suggest that S. marianum ethanolic extract is a potential scolicide in vitro; however, further investigations are required to determine its efficacy in vivo.
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Affiliation(s)
- Ali Taghipour
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Ghaffarifar
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | | | - Abdolhossein Dalimi
- Department of Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zohreh Sharifi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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16
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Faridi A, Mansouri M, Macchiaroli N, Afgar A, Mousavi SM, Rosenzvit MC, Harandi MF. MicroRNA profile of the strobilated worms of Echinococcus granulosus derived from in vivo and in vitro systems by using high-throughput approach. Parasitol Res 2021; 120:3203-3214. [PMID: 34351489 DOI: 10.1007/s00436-021-07251-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 07/13/2021] [Indexed: 11/26/2022]
Abstract
MicroRNAs are critical gene regulators at the post-transcriptional level and play essential roles in numerous developmental processes in metazoan parasites including the causative agent of cystic echinococcosis, Echinococcus granulosus. The molecular basis of different patterns of E. granulosus development in the canine definitive host and in in vitro culture systems is poorly understood. In the present study, miRNA transcriptomes of the strobilated worms derived from experimental infection in the definitive host were compared with those from diphasic culture system after 60-day protoscoleces cultivation. Total RNA was extracted from in vivo- and in vitro-derived strobilated worms. Small RNA libraries were constructed, and deep sequencing was performed. Subsequently, differential miRNA expressions and target predictions were obtained, and pathway analysis was performed by gene ontology and KEGG. Seven miRNAs were differentially expressed between the in vivo- and in vitro-derived worms. In addition, we reported 13 novel miRNA candidates and 42 conserved miRNAs. Four out of five top miRNAs with the highest read counts were shared between the in vivo and in vitro-derived worms, i.e., egr-miR-10a-5p, egr-let-7-5p, egr-bantam-3p, and egr-miR-71-5p. Target prediction of the differential miRNAs between the two systems showed significant differences in the membrane-enclosed lumen, membrane part, and an intrinsic component of the membrane. Findings of KEGG analysis indicated that differentially expressed miRNAs were involved in hippo, MAPK, and WNT signaling pathways. The study demonstrated a significant difference in miRNA transcriptomes and related signaling pathways between the two systems, suggesting the importance of host-parasite interplay in the fate of protoscoleces development in in vivo and in vitro systems.
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Affiliation(s)
- Ashkan Faridi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Natalia Macchiaroli
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología Y Parasitología Médica (IMPaM), Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Laboratorio de Genómica Y Bioinformática de Patógenos, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología Y Biología Molecular Y Celular, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Seyed Mohammad Mousavi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mara C Rosenzvit
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología Y Parasitología Médica (IMPaM), Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran.
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17
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Mu Y, McManus DP, Gordon CA, Cai P. Parasitic Helminth-Derived microRNAs and Extracellular Vesicle Cargos as Biomarkers for Helminthic Infections. Front Cell Infect Microbiol 2021; 11:708952. [PMID: 34249784 PMCID: PMC8267863 DOI: 10.3389/fcimb.2021.708952] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022] Open
Abstract
As an adaption to their complex lifecycles, helminth parasites garner a unique repertoire of genes at different developmental stages with subtle regulatory mechanisms. These parasitic worms release differential components such as microRNAs (miRNAs) and extracellular vesicles (EVs) as mediators which participate in the host-parasite interaction, immune regulation/evasion, and in governing processes associated with host infection. MiRNAs are small (~ 22-nucleotides) non-coding RNAs that regulate gene expression at the post-transcriptional level, and can exist in stable form in bodily fluids such as serum/plasma, urine, saliva and bile. In addition to reports focusing on the identification of miRNAs or in the probing of differentially expressed miRNA profiles in different development stages/sexes or in specific tissues, a number of studies have focused on the detection of helminth-derived miRNAs in the mammalian host circulatory system as diagnostic biomarkers. Extracellular vesicles (EVs), small membrane-surrounded structures secreted by a wide variety of cell types, contain rich cargos that are important in cell-cell communication. EVs have attracted wide attention due to their unique functional relevance in host-parasite interactions and for their potential value in translational applications such as biomarker discovery. In the current review, we discuss the status and potential of helminth parasite-derived circulating miRNAs and EV cargos as novel diagnostic tools.
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Affiliation(s)
- Yi Mu
- Molecular Parasitology Laboratory, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Donald P McManus
- Molecular Parasitology Laboratory, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Catherine A Gordon
- Molecular Parasitology Laboratory, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Pengfei Cai
- Molecular Parasitology Laboratory, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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18
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Eroglu F, Dokur M, Ulu Y. MicroRNA profile in immune response of alveolar and cystic echinococcosis patients. Parasite Immunol 2021; 43:e12817. [PMID: 33410199 DOI: 10.1111/pim.12817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 11/27/2022]
Abstract
It is known that miRNAs are effective in immune response in the diagnosis and treatment of many infectious diseases. However, the miRNAs profile is unknown in Alveolar and Cystic Echinococcosis which can be fatal if left untreated. The miRNAs profile that activates the T and B cells forming the immune system in Alveolar and Cystic Echinococcosis patients was investigated in this study. A total of 50 liver tissue samples were obtained from Alveolar and Cystic Echinococcosis patients in Kilis State Hospital Pathology Laboratory in southeast of Turkey. The circulating cell-free miRNAs were evaluated by a quantitative real-time polymerase chain reaction, statistically calculated within ΔΔCt values and fold changes were evaluated by Welch T test, in which P < .05 was considered to be significant. Twenty-five microRNAs, including let-7a-5p, let-7c, let-7e-5p, miR-15b-5p, miR16, miR-17-5p, miR-23a-5p, miR-24-3p, miR-25-3p, miR-26a-3p, miR-26b-3p, miR-29b-3p, miR-29c-3p, miR-30a-5p, miR-30b-5p, miR-30c-5p, miR-30d-5p, miR-30e-5p, miR-98-5p, miR-101-3p, miR-106b-5p, miR-125b-5p, miR-142-5p, miR-222-3p and miR-223-3p, were found as down-regulated in Alveolar and Cystic Echinococcosis patients than control groups. Twelve miRNAs, including miR-15a-5p, miR-21-5p, miR-27a-3p, miR-29a-3p, miR-146a-5p, miR-181a-5p, miR-181b-5p, miR-181d, miR-181c-5p, miR-195-5p, miR-214-3p and miR-365-3p, were found as up-regulated in Alveolar and Cystic Echinococcosis patients than healthy person. It has been shown that T- and B-cell activities are related in the progressive of both Alveolar and Cystic Echinococcosis in this study. The miRNA panel activated by T and B cells may be important for exploring the mechanisms underlying early development in Alveolar and Cystic Echinococcosis providing novel information that may be used to discover new therapeutics for these diseases.
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Affiliation(s)
- Fadime Eroglu
- Faculty of Medicine, Department of Parasitology, Aksaray University, Aksaray, Turkey.,FaBiyosit Microbiology-Biotechnology R&D Co., Adana, Turkey
| | - Mehmet Dokur
- Faculty of Medicine, Department of Emergency Medicine, Biruni University, Istanbul, Turkey
| | - Yüksel Ulu
- Department of Medical Pathology, Kilis State Hospital, Kilis, Turkey.,Department of Medical Pathology, Istanbul Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
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19
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Ma X, He K, Shi Z, Li M, Li F, Chen XX. Large-Scale Annotation and Evolution Analysis of MiRNA in Insects. Genome Biol Evol 2021; 13:6255746. [PMID: 33905491 PMCID: PMC8126727 DOI: 10.1093/gbe/evab083] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2021] [Indexed: 12/22/2022] Open
Abstract
Insects are among the most diverse and successful groups of animals and exhibit great morphological diversity and complexity. The innovation of wings and metamorphosis are some examples of the fascinating biological evolution of insects. Most microRNAs (miRNAs) contribute to canalization by conferring robustness to gene networks and thus increase the heritability of important phenotypes. Though previous studies have demonstrated how miRNAs regulate important phenotypes, little is still known about miRNA evolution in insects. Here, we used both small RNA-seq data and homology searching methods to annotate the miRNA repertoires of 152 arthropod species, including 135 insects and 17 noninsect arthropods. We identified 16,212 miRNA genes, and classified them into highly conserved (62), insect-conserved (90), and lineage-specific (354) miRNA families. The phylogenetic relationship of miRNA binary presence/absence dynamics implies that homoplastic loss of conserved miRNA families tends to occur in far-related morphologically simplified taxa, including scale insects (Coccoidea) and twisted-wing insects (Strepsiptera), leading to inconsistent phylogenetic tree reconstruction. The common ancestor of Insecta shares 62 conserved miRNA families, of which five were rapidly gained in the early winged-insects (Pterygota). We also detected extensive miRNA losses in Paraneoptera that are correlated with morphological reduction, and miRNA gains in early Endopterygota around the time holometabolous metamorphosis appeared. This was followed by abundant miRNA gains in Hymenoptera and Lepidoptera. In summary, we provide a comprehensive data set and a detailed evolutionary analysis of miRNAs in insects. These data will be important for future studies on miRNA functions associated with insect morphological innovation and trait biodiversity.
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Affiliation(s)
- Xingzhou Ma
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,College of Plant Protection, Nanjing Agricultural University, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmin Shi
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Meizhen Li
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xue-Xin Chen
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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20
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Expression profiling of Echinococcus multilocularis miRNAs throughout metacestode development in vitro. PLoS Negl Trop Dis 2021; 15:e0009297. [PMID: 33750964 PMCID: PMC8016320 DOI: 10.1371/journal.pntd.0009297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/01/2021] [Accepted: 03/08/2021] [Indexed: 12/30/2022] Open
Abstract
The neglected zoonotic disease alveolar echinococcosis (AE) is caused by the metacestode stage of the tapeworm parasite Echinococcus multilocularis. MicroRNAs (miRNAs) are small non-coding RNAs with a major role in regulating gene expression in key biological processes. We analyzed the expression profile of E. multilocularis miRNAs throughout metacestode development in vitro, determined the spatial expression of miR-71 in metacestodes cultured in vitro and predicted miRNA targets. Small cDNA libraries from different samples of E. multilocularis were sequenced. We confirmed the expression of 37 miRNAs in E. multilocularis being some of them absent in the host, such as miR-71. We found a few miRNAs highly expressed in all life cycle stages and conditions analyzed, whereas most miRNAs showed very low expression. The most expressed miRNAs were miR-71, miR-9, let-7, miR-10, miR-4989 and miR-1. The high expression of these miRNAs was conserved in other tapeworms, suggesting essential roles in development, survival, or host-parasite interaction. We found highly regulated miRNAs during the different transitions or cultured conditions analyzed, which might suggest a role in the regulation of developmental timing, host-parasite interaction, and/or in maintaining the unique developmental features of each developmental stage or condition. We determined that miR-71 is expressed in germinative cells and in other cell types of the germinal layer in E. multilocularis metacestodes cultured in vitro. MiRNA target prediction of the most highly expressed miRNAs and in silico functional analysis suggested conserved and essential roles for these miRNAs in parasite biology. We found relevant targets potentially involved in development, cell growth and death, lifespan regulation, transcription, signal transduction and cell motility. The evolutionary conservation and expression analyses of E. multilocularis miRNAs throughout metacestode development along with the in silico functional analyses of their predicted targets might help to identify selective therapeutic targets for treatment and control of AE. Alveolar echinococcosis (AE) is a zoonotic disease caused by the metacestode stage of the helminth parasite Echinococcus multilocularis. Current treatment requires surgery and/or prolonged drug therapy. Thus, novel strategies for the treatment of AE are needed. MicroRNAs (miRNAs), a class of small ~22-nucleotide (nt) non-coding RNAs with a major role in regulating gene expression, have been suggested as potential therapeutic targets for treatment and control of helminth parasite infections. In this work, we analyzed the expression profile of E. multilocularis miRNAs throughout metacestode development in vitro. We predicted functional roles for highly expressed miRNAs and found that they could be involved in essential roles for survival and development in the host. We determined that E. multilocularis miR-71, a highly expressed miRNA that is absent in the human host, is expressed in germinative cells and in other cell types of the germinal layer in E. multilocularis metacestodes cultured in vitro. Germinative cells are a relevant cell type to target for anti-echinococcosis drug development. MiRNAs that are absent in the human host, involved in essential functions, highly expressed and/or expressed in germinative cells in E. multilocularis metacestodes may represent selective therapeutic targets for treatment and control of AE.
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21
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Deping C, Bofan J, Yaogang Z, Mingquan P. microRNA-125b-5p is a promising novel plasma biomarker for alveolar echinococcosis in patients from the southern province of Qinghai. BMC Infect Dis 2021; 21:246. [PMID: 33678159 PMCID: PMC7938541 DOI: 10.1186/s12879-021-05940-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/28/2021] [Indexed: 02/06/2023] Open
Abstract
Background Alveolar echinococcosis (AE) is caused by parasitic infection by Echinococcus multilocularis. Its diagnosis is usually based on clinical symptoms, ultrasound, and other imaging methods. MicroRNAs (miRNAs) play important roles in disease processes and can exist in a highly stable cell-free form in body fluids. It is important to identify specific, sensitive diagnostic markers for early diagnosis and evaluation of AE. In this study, we examined hsa-miR-125b-5p as a potential plasma biomarker of E. multilocularis infection. Methods Plasma samples from patients with AE and healthy individuals were screened for the presence of five miRNAs using miRNA chips. We used quantitative polymerase chain reaction to measure miRNA expression levels in plasma and liver tissue samples from patients with AE. Results hsa-miR-125b-5p was stably upregulated in the plasma and liver tissue samples from patients with AE. Conclusions The results suggest that hsa-miR-125b-5p may be a promising biomarker for early, non-invasive diagnosis of AE.
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Affiliation(s)
- Cao Deping
- Department of Human Parasitology, Guilin Medical College, Guilin, 541101, Guangxi Zhuang Autonomous, China.
| | - Jiang Bofan
- The Department of Pathogenic Biology of Qinghai University Medical College, Xining, 810001, Qinghai Province, China
| | - Zhang Yaogang
- The Echinococcosis Key Laboratory of Affiliated Hospital of Qinghai University, Xining, 810001, Qinghai Province, China
| | - Pang Mingquan
- The Echinococcosis Key Laboratory of Affiliated Hospital of Qinghai University, Xining, 810001, Qinghai Province, China
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22
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Differential expression of microRNAs and tRNA fragments mediate the adaptation of the liver fluke Fasciola gigantica to its intermediate snail and definitive mammalian hosts. Int J Parasitol 2021; 51:405-414. [PMID: 33513403 DOI: 10.1016/j.ijpara.2020.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023]
Abstract
The tropical liver fluke Fasciola gigantica affects livestock and humans in many Asian countries, large parts of Africa, and parts of Europe. Despite the public health and economic impacts of F. gigantica, understanding of F. gigantica biology and how the complex lifecycle of this liver fluke is transcriptionally regulated remain unknown. Here, we tested the hypothesis that the regulatory small non-coding RNAs (sncRNAs), microRNAs (miRNAs) and tRNA-derived fragments (tRFs) play roles in the adaptation of F. gigantica to its intermediate and definitive hosts. We sequenced sncRNAs of eight lifecycle stages of F. gigantica. In total, 56 miRNAs from 33 conserved families and four Fasciola-specific miRNAs were identified. Expression analysis of miRNAs suggested clear stage-related patterns. By leveraging the existing transcriptomic data, we predicted a miRNA-based regulation of metabolism, transport, growth and developmental processes. Also, by comparing miRNA complement of F. gigantica with that of Fasciola hepatica, we detected a high level of conservation and identified differences in some miRNAs, which can be used to distinguish the two species. Moreover, we found that tRFs at each lifecycle stage were predominantly derived by tRNA-Lys and tRNA-Gly at 5' half sites, but relatively high expression was related to the buffalo-infecting stages. Taken together, we provided a comprehensive overview of the dynamic transcriptional changes of small RNAs that occur during the developmental stages of F. gigantica. This global analysis of F. gigantica lifecycle stages revealed new roles of miRNAs and tRFs in parasite development and will facilitate future research into understanding of fasciolosis pathobiology.
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23
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Faridi A, Afgar A, Mousavi SM, Nasibi S, Mohammadi MA, Farajli Abbasi M, Fasihi Harandi M. Intestinal Expression of miR-130b, miR-410b, and miR-98a in Experimental Canine Echinococcosis by Stem-Loop RT-qPCR. Front Vet Sci 2020; 7:507. [PMID: 33005638 PMCID: PMC7480022 DOI: 10.3389/fvets.2020.00507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022] Open
Abstract
Echinococcus granulosus is a zoonotic cestode dwelling in the small intestine of canid definitive hosts. Intermediate hosts are a wide range of domestic and wild ungulates. Human infection with the larval stage causes cystic echinococcosis. Understanding the nature and extent of molecular mechanisms involved in host–parasite interactions helps to answer some very basic questions in the biology of cestode parasites with significant implications in the management and control of cystic echinococcosis. Little is known on the miRNAs expression in the intestinal tissues of dogs infected with E. granulosus. In the present study, expression of a selected profile of miRNAs was evaluated in experimental canine echinococcosis. MiRNAs were extracted from 20 different parts of small intestinal tract of two sibling 3-months-old mix-breed dogs. Complementary DNA was specifically synthesized using an optimized stem-loop system. Intestinal expression of four miRNAs (cfa-let7g, cfa-miR-98, cfamiR-410, cfa-miR-130b) was evaluated using RT-qPCR. The results of the study indicate a significant difference between test and control dogs in cfamiR-130b, cfa-miR-98, and cfa-miR-410 (P ≤ 0.05); however, there was no significant difference for cfa-let7g. The most upregulated miRNAs were cfamiR-130b and cfa-miR-98. An increasing trend for cfa-let7g and a declining trend for cfa-miR-98, cfa-miR-410, and cfamiR-130b were found toward the distal segments of the small intestine. Our study revealed that cfa-miR-98, cfa-miR-410, and cfamiR-130b are involved in the definitive host response in canine echinococcosis. The study provides new information on the molecular basis of interactions between E. granulosus and dogs in terms of miRNA expression and showed that E. granulosus infection could increase the expression of some pro-inflammatory miRNAs at the cellular level in the definitive host.
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Affiliation(s)
- Ashkan Faridi
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran.,Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Seyed Mohammad Mousavi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Saeid Nasibi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Ali Mohammadi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Farajli Abbasi
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
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24
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Zhang X, Gong W, Cao S, Yin J, Zhang J, Cao J, Shen Y. Comprehensive Analysis of Non-coding RNA Profiles of Exosome-Like Vesicles From the Protoscoleces and Hydatid Cyst Fluid of Echinococcus granulosus. Front Cell Infect Microbiol 2020; 10:316. [PMID: 32793506 PMCID: PMC7387405 DOI: 10.3389/fcimb.2020.00316] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/25/2020] [Indexed: 12/31/2022] Open
Abstract
Cystic echinococcosis is a worldwide chronic zoonotic disease that threatens human health and animal husbandry. Exosome-like vesicles (ELVs) have emerged recently as mediators in the parasite-parasite intercommunication and parasite-host interactions. Exosome-like vesicles from parasites can transfer non-coding RNAs (ncRNAs) into host cells to regulate their gene expression; however, the ncRNAs profiles of the ELVs from Echinococcus granulosus remain unknown. Here, we isolated protoscolece (PSC)-ELVs and hydatid fluid (HF)-ELVs from the culture medium for E. granulosus PSCs in vitro and the HF of fertile sheep cysts, respectively. The microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) profiles of the two types of ELVs were analyzed using high-throughput sequencing, and their functions were predicted using Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis. In PSC-ELVs and HF-ELVs, 118 and 58 miRNAs were identified, respectively, among which 53 miRNAs were present in both ELVs, whereas 65 and 5 miRNAs were unique to PSC-ELVs and HF-ELVs, respectively; 2,361 and 1,254 lncRNAs were identified in PSC-ELVs and HF-ELVs, respectively, among which 1,004 lncRNAs were present in both ELVs, whereas 1,357 and 250 lncRNAs were unique to PSC-ELVs and HF-ELVs, respectively. Intriguingly, the spilled PSCs from cysts excrete ELVs with higher numbers of and higher expression levels of miRNAs and circRNAs than HF-ELVs. The miRNA sequencing data were validated by quantitative reverse transcription-polymerase chain reaction. Furthermore, the target lncRNAs and mRNAs regulated by the 20 most abundant miRNAs were screened, and a ceRNA regulatory network containing 5 miRNAs, 41 lncRNAs, and 23 mRNAs was constructed, which provided new ideas and the molecular basis for further clarification of the function and mechanism of E. granulosus ELVs ncRNAs in the parasite-host interactions. Egr-miR-125-5p and egr-miR-10a-5p, sharing identical seed sites with host miRNAs, were predicted to mediate inflammatory response, collagen catabolic process, and mitogen-activated protein kinase cascade during parasite infections. In conclusion, for the first time, we identified the ncRNAs profiles in PSC-ELVs and HF-ELVs that might be involved in host immunity and pathogenesis, and enriched the ncRNAs data of E. granulosus. These results provided valuable resources for further analysis of the regulatory potential of ncRNAs, especially miRNAs, in both types of ELVs at the parasite-host interface.
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Affiliation(s)
- Xiaofan Zhang
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Wenci Gong
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Shengkui Cao
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Jianhai Yin
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Jing Zhang
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Jianping Cao
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
| | - Yujuan Shen
- Chinese Center for Disease Control and Prevention, National Institute of Parasitic Diseases, Shanghai, China.,Chinese Center for Tropical Diseases Research, Shanghai, China.,Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China.,WHO Collaborating Centre for Tropical Diseases, Shanghai, China.,National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Shanghai, China
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25
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Bai Y, Zhang Z, Jin L, Zhu Y, Zhao L, Shi B, Li J, Guo G, Guo B, McManus DP, Wang S, Zhang W. Dynamic Changes in the Global Transcriptome and MicroRNAome Reveal Complex miRNA-mRNA Regulation in Early Stages of the Bi-Directional Development of Echinococcus granulosus Protoscoleces. Front Microbiol 2020; 11:654. [PMID: 32373094 PMCID: PMC7188192 DOI: 10.3389/fmicb.2020.00654] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/23/2020] [Indexed: 12/27/2022] Open
Abstract
Background Cystic echinococcosis is a life-threatening disease caused by the larval stages of the dog tapeworm Echinococcus granulosus. Protoscoleces (PSCs) of this worm have the ability of bi-directional development to either larval cysts or strobilar adult worms. However, the molecular mechanisms underlying this development process are unknown. Results RNA and small RNAs sequencing was employed to characterize the gene and miRNA expression at 0–24 h and 7–14 days in the bi-directional development of PSCs. A total of 963 genes and 31 miRNAs were differentially expressed in the early development of PSCs to adult worms whereas 972 genes and 27 miRNAs were differentially expressed in the early development of PSCs to cysts. Pairwise comparison between the two developmental patterns showed that 172 genes and 15 miRNAs were differentially expressed at three time-points. Most of these genes were temporally changed at 24 h or 7 days. GO enrichment analysis revealed that the differentially expressed genes in early adult worm development are associated with nervous system development and carbohydrate metabolic process; whereas, the differentially expressed genes in early cystic development are associated with transmembrane transporter activity and nucleoside triphosphatase activity. In addition, miR-71 and miR-219 regulated genes are likely involved in oxidation reduction in adult worm development. Conclusion The early stages of bi-directional development in E. granulosus PSCs are controlled by miRNAs and genes likely associated with nervous system development and carbohydrate metabolic process. ATP-dependent transporter genes are associated with cystic development. These results may be important for exploring the mechanisms underlying early development in E. granulosus providing novel information that can be used to discover new therapeutics for controlling cystic echinococcosis.
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Affiliation(s)
- Yun Bai
- Central Laboratory, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Zhuangzhi Zhang
- Veterinary Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Lei Jin
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Yongqiang Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Li Zhao
- Veterinary Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Baoxin Shi
- Veterinary Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Jun Li
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Gang Guo
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Baoping Guo
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Donald P McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Shengyue Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China.,National Research Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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26
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He Z, Yan T, Yuan Y, Yang D, Yang G. miRNAs and lncRNAs in Echinococcus and Echinococcosis. Int J Mol Sci 2020; 21:ijms21030730. [PMID: 31979099 PMCID: PMC7037763 DOI: 10.3390/ijms21030730] [Citation(s) in RCA: 14] [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: 10/28/2019] [Revised: 01/16/2020] [Accepted: 01/19/2020] [Indexed: 01/04/2023] Open
Abstract
Echinococcosis are considered to be potentially lethal zoonotic diseases that cause serious damage to hosts. The metacestode of Echinococcus multilocularis and E. granulosus can result in causing the alveolar and cystic echinococcoses, respectively. Recent studies have shown that non-coding RNAs are widely expressed in Echinococcus spp. and hosts. In this review, the two main types of non-coding RNAs—long non-coding RNAs (lncRNAs) and microRNAs (miRNAs)—and the wide-scale involvement of these molecules in these parasites and their hosts were discussed. The expression pattern of miRNAs in Echinococcus spp. is species- and developmental stage-specific. Furthermore, common miRNAs were detected in three Echinococcus spp. and their intermediate hosts. Here, we primarily focus on recent insights from transcriptome studies, the expression patterns of miRNAs and lncRNAs, and miRNA-related databases and techniques that are used to investigate miRNAs in Echinococcus and echinococcosis. This review provides new avenues for screening therapeutic and diagnostic markers.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
| | - Ya Yuan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Correspondence: ; Tel.: +86-028-8278-3043
| | - Guangyou Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China;
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Library Preparation for Small RNA Transcriptome Sequencing in Patients Affected by Cerebral Cavernous Malformations. Methods Mol Biol 2020; 2152:467-478. [PMID: 32524574 DOI: 10.1007/978-1-0716-0640-7_35] [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: 01/12/2023]
Abstract
Small RNA sequencing by Illumina's Next Generation technology has revolutionized the transcriptome analysis by facilitating massive parallel sequencing of RNA molecules at low cost. Illumina's Next Generation RNA sequencing is ideal for profiling small RNA (microRNAs, snoRNAs, and piRNAs) libraries in the identification of novel biomarkers for better clinical diagnosis. This method offers significant advantages when compared to microarray analysis with the ability to identify novel transcripts, higher sensitivity, specificity, and detection of rare and low-abundance transcripts. Small RNAs, including microRNAs and snoRNAs, belong to the class of small non-coding RNAs with 50-200 nucleotides in length and are involved in post-transcriptional regulation of gene expression. Executing Illumina's Next Generation Sequencing technology, we have recently deciphered microRNAs and snoRNAs expressed in cerebral cavernous malformations (CCMs). Small RNA library preparation is a prerequisite step prior to RNA sequencing for the identification of microRNAs and snoRNAs. Here, we describe stepwise small RNA library preparation starting from total RNA isolated from CCMs patient until library validation using the Illumina® TruSeq® Small RNA Sample preparation kit. We believe this method will shed light into the functional identification of other novel small non-coding RNAs in CCMs that awaits discovery.
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Pérez MG, Spiliotis M, Rego N, Macchiaroli N, Kamenetzky L, Holroyd N, Cucher MA, Brehm K, Rosenzvit MC. Deciphering the role of miR-71 in Echinococcus multilocularis early development in vitro. PLoS Negl Trop Dis 2019; 13:e0007932. [PMID: 31881019 PMCID: PMC6957206 DOI: 10.1371/journal.pntd.0007932] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 01/13/2020] [Accepted: 11/17/2019] [Indexed: 01/25/2023] Open
Abstract
Echinococcosis represents a major public health problem worldwide and is considered a neglected disease by the World Health Organization. The etiological agents are Echinococcus tapeworms, which display elaborate developmental traits that imply a complex control of gene expression. MicroRNAs (miRNAs), a class of small regulatory RNAs, are involved in the regulation of many biological processes such as development and metabolism. They act through the repression of messenger RNAs (mRNAs) usually by binding to the 3’ untranslated region (3’UTR). Previously, we described the miRNome of several Echinococcus species and found that miRNAs are highly expressed in all life cycle stages, suggesting an important role in gene expression regulation. However, studying the role of miRNAs in helminth biology remains a challenge. To develop methodology for functional analysis of miRNAs in tapeworms, we performed miRNA knockdown experiments in primary cell cultures of Echinococcus multilocularis, which mimic the development of metacestode vesicles from parasite stem cells in vitro. First, we analysed the miRNA repertoire of E. multilocularis primary cells by small RNA-seq and found that miR-71, a bilaterian miRNA absent in vertebrate hosts, is one of the top five most expressed miRNAs. Using genomic information and bioinformatic algorithms for miRNA binding prediction, we found a high number of potential miR-71 targets in E. multilocularis. Inhibition of miRNAs can be achieved by transfection of antisense oligonucleotides (anti-miRs) that block miRNA function. To this end, we evaluated a variety of chemically modified anti-miRs for miR-71 knockdown. Electroporation of primary cells with 2’-O-methyl modified anti-miR-71 led to significantly reduced miR-71 levels. Transcriptomic analyses showed that several predicted miR-71 targets were up-regulated in anti-miR-treated primary cells, including genes potentially involved in parasite development, host parasite interaction, and several genes of as yet unknown function. Notably, miR-71-silenced primary cell cultures showed a strikingly different phenotype from control cells and did not develop into fully mature metacestodes. These findings indicate an important function of miR-71 in Echinococcus development and provide, for the first time, methodology to functionally study miRNAs in a tapeworm. Echinococcosis, caused by the larval stages of tapeworms of the genus Echinococcus, is a neglected disease that affects millions of people world-wide. These parasites show elaborate developmental features that rely on a complex control of gene expression. microRNAs are small molecules which have been discovered in the last decades and control gene expression in animals, plants and viruses. microRNAs are highly expressed in several tapeworms but their biological function in these parasites is unknown. Assuming that microRNAs will be important for parasite development, we analysed the function of these molecules in Echinococcus multilocularis, employing an in vitro model that mimics the first developmental transitions which occur in the human host. By artificially decreasing the concentration of the highest expressed microRNA, we observed phenotypic alterations and inhibition of development. In addition, we identified possible mRNA molecules targeted by microRNAs and found that some of these are known for being involved in developmental processes in other organisms. This work provides novel methodology to study microRNA function in tapeworms. Furthermore, highly expressed parasite microRNAs that are absent in the host but fulfil an important role in parasite developmental processes can serve as selective drug targets against the underlying diseases.
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Affiliation(s)
- Matías Gastón Pérez
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Markus Spiliotis
- University of Würzburg, Institute for Hygiene and Microbiology, Consultant Laboratory for Echinococcosis, Würzburg, Germany
| | - Natalia Rego
- Institut Pasteur de Montevideo, Unidad de Bioinformática, Montevideo, Uruguay
| | - Natalia Macchiaroli
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Laura Kamenetzky
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Marcela Alejandra Cucher
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Klaus Brehm
- University of Würzburg, Institute for Hygiene and Microbiology, Consultant Laboratory for Echinococcosis, Würzburg, Germany
- * E-mail: (KB); (MCR)
| | - Mara Cecilia Rosenzvit
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
- * E-mail: (KB); (MCR)
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Mortezaei S, Afgar A, Mohammadi MA, Mousavi SM, Sadeghi B, Harandi MF. The effect of albendazole sulfoxide on the expression of miR-61 and let-7 in different in vitro developmental stages of Echinococcus granulosus. Acta Trop 2019; 195:97-102. [PMID: 31051116 DOI: 10.1016/j.actatropica.2019.04.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 04/16/2019] [Accepted: 04/29/2019] [Indexed: 12/30/2022]
Abstract
Albendazole, as the main anti-echinococcal benzimidazole, has demonstrated safe and effective therapeutic outcomes in the treatment of echinococcosis. The emergence of resistance or reduced response to albendazole sulfoxide (ABZ_SOX) and other benzimidazoles have been demonstrated in several parasitic helminths of medical and veterinary importance. As the genetic makeup and miRNA profile of helminths affects their response to albendazole sulfoxide, the present study was conducted to investigate the expression of miRNAs in different developmental stages of Echinococcus granulosus exposed to albendazole sulfoxide in vitro. Different developmental stages of the helminth were obtained from in vitro cultured E. granulosus in monophasic and diphasic media. In both ABZ-SOX-treated and control parasites miRNAs were extracted from microcysts, intact protoscoleces and strobilated worms with one and three segments. Expression of two miRNAs, let-7 and miR-61 was evaluated using RT-qPCR for each stage. Results of the present study revealed significant differential expression of both let-7 and miR-61 at different drug concentrations. A significant difference of let-7 expression was observed between the strobilated and metacestode stages of E. granulosus exposed to ABZ-SOX. In the treated protoscoleces, let-7 expression was significantly reduced in the presence of ABZ-SOX at 1000 μg/ml concentration. In contrast higher expression levels were documented in the segmented worms. In the microcysts exposed to different drug concentrations a significant decline of miR-61 expression was demonstrated. Also, a significant increase in expression of miR-61 was observed in one proglottid worms as well as the protoscoleces. Under high drug concentration or long-term exposure of the protoscoleces to ABZ-SOX significantly higher miR-61 expression was observed compared to the controls. Our findings suggested that under in vitro benzimidazole exposure the expression of two E. granulosus miRNAs were significantly affected in the microcyst stage. This study presents the first evidence of the nature of benzimidazole effects on miRNA expression in platyhelminths.
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Fromm B, Tosar JP, Aguilera F, Friedländer MR, Bachmann L, Hejnol A. Evolutionary Implications of the microRNA- and piRNA Complement of Lepidodermella squamata (Gastrotricha). Noncoding RNA 2019; 5:E19. [PMID: 30813358 PMCID: PMC6468455 DOI: 10.3390/ncrna5010019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023] Open
Abstract
Gastrotrichs-'hairy bellies'-are microscopic free-living animals inhabiting marine and freshwater habitats. Based on morphological and early molecular analyses, gastrotrichs were placed close to nematodes, but recent phylogenomic analyses have suggested their close relationship to flatworms (Platyhelminthes) within Spiralia. Small non-coding RNA data on e.g., microRNAs (miRNAs) and PIWI-interacting RNAs (piRNA) may help to resolve this long-standing question. MiRNAs are short post-transcriptional gene regulators that together with piRNAs play key roles in development. In a 'multi-omics' approach we here used small-RNA sequencing, available transcriptome and genomic data to unravel the miRNA- and piRNA complements along with the RNAi (RNA interference) protein machinery of Lepidodermella squamata (Gastrotricha, Chaetonotida). We identified 52 miRNA genes representing 35 highly conserved miRNA families specific to Eumetazoa, Bilateria, Protostomia, and Spiralia, respectively, with overall high similarities to platyhelminth miRNA complements. In addition, we found four large piRNA clusters that also resemble flatworm piRNAs but not those earlier described for nematodes. Congruently, transcriptomic annotation revealed that the Lepidodermella protein machinery is highly similar to flatworms, too. Taken together, miRNA, piRNA, and protein data support a close relationship of gastrotrichs and flatworms.
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Affiliation(s)
- Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden.
| | - Juan Pablo Tosar
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
- Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo 11400, Uruguay.
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160_C, Concepción 3349001, Chile.
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway.
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden.
| | - Lutz Bachmann
- Research group Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, 0318 Oslo, Norway.
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway.
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31
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Macchiaroli N, Cucher M, Kamenetzky L, Yones C, Bugnon L, Berriman M, Olson PD, Rosenzvit MC. Identification and expression profiling of microRNAs in Hymenolepis. Int J Parasitol 2019; 49:211-223. [PMID: 30677390 DOI: 10.1016/j.ijpara.2018.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 02/08/2023]
Abstract
Tapeworms (cestodes) of the genus Hymenolepis are the causative agents of hymenolepiasis, a neglected zoonotic disease. Hymenolepis nana is the most prevalent human tapeworm, especially affecting children. The genomes of Hymenolepis microstoma and H. nana have been recently sequenced and assembled. MicroRNAs (miRNAs), a class of small non-coding RNAs, are principle regulators of gene expression at the post-transcriptional level and are involved in many different biological processes. In previous work, we experimentally identified miRNA genes in the cestodes Echinococcus, Taenia and Mesocestoides. However, current knowledge about miRNAs in Hymenolepis is limited. In this work we described for the first known time the expression profile of the miRNA complement in H. microstoma, and discovered miRNAs in H. nana. We found a reduced complement of 37 evolutionarily conserved miRNAs, putatively reflecting their low morphological complexity and parasitic lifestyle. We found high expression of a few miRNAs in the larval stage of H. microstoma that are conserved in other cestodes, suggesting that these miRNAs may have important roles in development, survival and for host-parasite interplay. We performed a comparative analysis of the identified miRNAs across the Cestoda and showed that most of the miRNAs in Hymenolepis are located in intergenic regions, implying that they are independently transcribed. We found a Hymenolepis-specific cluster composed of three members of the mir-36 family. Also, we found that one of the neighboring genes of mir-10 was a Hox gene as in most bilaterial species. This study provides a valuable resource for further experimental research in cestode biology that might lead to improved detection and control of these neglected parasites. The comprehensive identification and expression analysis of Hymenolepis miRNAs can help to identify novel biomarkers for diagnosis and/or novel therapeutic targets for the control of hymenolepiasis.
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Affiliation(s)
- Natalia Macchiaroli
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Marcela Cucher
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence, (sinc(i)), FICH-UNL-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Santa Fe, Argentina
| | - Leandro Bugnon
- Research Institute for Signals, Systems and Computational Intelligence, (sinc(i)), FICH-UNL-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Santa Fe, Argentina
| | - Matt Berriman
- Parasite Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter D Olson
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Mara Cecilia Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina.
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Tarver JE, Taylor RS, Puttick MN, Lloyd GT, Pett W, Fromm B, Schirrmeister BE, Pisani D, Peterson KJ, Donoghue PCJ. Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss. Genome Biol Evol 2018; 10:1457-1470. [PMID: 29788279 PMCID: PMC6007596 DOI: 10.1093/gbe/evy096] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.
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Affiliation(s)
- James E Tarver
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Richard S Taylor
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Mark N Puttick
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
- Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Graeme T Lloyd
- School of Earth and Environment, University of Leeds, United Kingdom
| | - Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - Bettina E Schirrmeister
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Davide Pisani
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Philip C J Donoghue
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
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Stroehlein AJ, Young ND, Gasser RB. Advances in kinome research of parasitic worms - implications for fundamental research and applied biotechnological outcomes. Biotechnol Adv 2018; 36:915-934. [PMID: 29477756 DOI: 10.1016/j.biotechadv.2018.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/15/2018] [Accepted: 02/21/2018] [Indexed: 12/17/2022]
Abstract
Protein kinases are enzymes that play essential roles in the regulation of many cellular processes. Despite expansions in the fields of genomics, transcriptomics and bioinformatics, there is limited information on the kinase complements (kinomes) of most eukaryotic organisms, including parasitic worms that cause serious diseases of humans and animals. The biological uniqueness of these worms and the draft status of their genomes pose challenges for the identification and classification of protein kinases using established tools. In this article, we provide an account of kinase biology, the roles of kinases in diseases and their importance as drug targets, and drug discovery efforts in key socioeconomically important parasitic worms. In this context, we summarise methods and resources commonly used for the curation, identification, classification and functional annotation of protein kinase sequences from draft genomes; review recent advances made in the characterisation of the worm kinomes; and discuss the implications of these advances for investigating kinase signalling and developing small-molecule inhibitors as new anti-parasitic drugs.
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Affiliation(s)
- Andreas J Stroehlein
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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34
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Gutierrez-Loli R, Orrego MA, Sevillano-Quispe OG, Herrera-Arrasco L, Guerra-Giraldez C. MicroRNAs in Taenia solium Neurocysticercosis: Insights as Promising Agents in Host-Parasite Interaction and Their Potential as Biomarkers. Front Microbiol 2017; 8:1905. [PMID: 29033926 PMCID: PMC5626859 DOI: 10.3389/fmicb.2017.01905] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are short, endogenous, non-coding, single-stranded RNAs involved in post-transcriptional gene regulation. Although, several miRNAs have been identified in parasitic helminths, there is little information about their identification and function in Taenia. Furthermore, the impact of miRNAs in neurocysticercosis, the brain infection caused by larvae of Taenia solium is still unknown. During chronic infection, T. solium may activate numerous mechanisms aimed to modulate host immune responses. Helminthic miRNAs might also have effects on host mRNA expression and thus play an important role regulating host-parasite interactions. Also, the diagnosis of this disease is difficult and it usually requires neuroimaging and confirmatory serology. Since miRNAs are stable when released, they can be detected in body fluids and therefore have potential to diagnose infection, determine parasite burden, and ascertain effectiveness of treatment or disease progression, for instance. This review discusses the potential roles of miRNAs in T. solium infection, including regulation of host-parasite relationships and their eventual use as diagnostic or disease biomarkers. Additionally, we summarize the bioinformatics resources available for identification of T. solium miRNAs and prediction of their targets.
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Affiliation(s)
- Renzo Gutierrez-Loli
- Neurocysticercosis Lab, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Miguel A Orrego
- Neurocysticercosis Lab, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Oscar G Sevillano-Quispe
- Neurocysticercosis Lab, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Luis Herrera-Arrasco
- Neurocysticercosis Lab, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Cristina Guerra-Giraldez
- Neurocysticercosis Lab, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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35
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Fromm B, Ovchinnikov V, Høye E, Bernal D, Hackenberg M, Marcilla A. On the presence and immunoregulatory functions of extracellular microRNAs in the trematode Fasciola hepatica. Parasite Immunol 2017; 39. [PMID: 27809346 DOI: 10.1111/pim.12399] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/28/2016] [Indexed: 12/16/2022]
Abstract
Liver flukes represent a paraphyletic group of endoparasitic flatworms that significantly affect man either indirectly due to economic damage on livestock or directly as pathogens. A range of studies have focussed on how these macroscopic organisms can evade the immune system and live inside a hostile environment such as the mammalian liver and bile ducts. Recently, microRNAs, a class of short noncoding gene regulators, have been proposed as likely candidates to play roles in this scenario. MicroRNAs (miRNAs) are key players in development and pathogenicity and are highly conserved between metazoans: identical miRNAs can be found in flatworms and mammalians. Interestingly, miRNAs are enriched in extracellular vesicles (EVs) which are secreted by most cells. EVs constitute an important mode of parasite/host interaction, and recent data illustrate that miRNAs play a vital part. We have demonstrated the presence of miRNAs in the EVs of the trematode species Dicrocoelium dendriticum and Fasciola hepatica (Fhe) and identified potential immune-regulatory miRNAs with targets in the host. After our initial identification of miRNAs expressed by F. hepatica, an assembled genome and additional miRNA data became available. This has enabled us to update the known complement of miRNAs in EVs and speculate on potential immune-regulatory functions that we review here.
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Affiliation(s)
- B Fromm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway
| | - V Ovchinnikov
- Department of Human and Animal Genetics, The Federal Research Center, Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - E Høye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway
| | - D Bernal
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - M Hackenberg
- Facultad de Ciencias, Departamento de Genética, Universidad de Granada, Granada, Spain.,Laboratorio de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, Granada, Spain
| | - A Marcilla
- Área de Parasitología, Departamento de Farmacia y Tecnologia Farmacéutica y Parasitología, Universitat de València, Burjassot, Valencia, Spain.,Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics, Health Research Institute-La Fe, Universitat de Valencia, Valencia, Spain
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Pérez MG, Macchiaroli N, Lichtenstein G, Conti G, Asurmendi S, Milone DH, Stegmayer G, Kamenetzky L, Cucher M, Rosenzvit MC. microRNA analysis of Taenia crassiceps cysticerci under praziquantel treatment and genome-wide identification of Taenia solium miRNAs. Int J Parasitol 2017; 47:643-653. [DOI: 10.1016/j.ijpara.2017.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 12/14/2022]
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Biological significance of phosphoenolpyruvate carboxykinase in a cestode parasite, Raillietina echinobothrida and effect of phytoestrogens on the enzyme from the parasite and its host, Gallus domesticus. Parasitology 2017; 144:1264-1274. [PMID: 28485262 DOI: 10.1017/s0031182017000518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphoenolpyruvate carboxykinase (PEPCK) is involved in glycolysis in the cestode parasite, Raillietina echinobothrida; whereas, it executes a gluconeogenic role in its host, Gallus domesticus. Because of its differing primary function in the cestode parasite and its host, this enzyme is regarded as a plausible anthelmintic target. Hence, the biological significance of PEPCK in the parasite was analysed using siRNA against PEPCK from R. echinobothrida (RePEPCK). In order to find out the functional differences between RePEPCK and GdPEPCK (PEPCK from its host, G. domesticus), PEPCK genes from both sources were cloned, over-expressed, characterized, and some properties of the purified enzymes were compared. RePEPCK and GdPEPCK showed a standard Michaelis-Menten kinetics with K mapp of 46.9 and 22.9 µ m, respectively, for phosphoenolpyruvate and K mapp of 15.4 µ m for oxaloacetate in GdPEPCK decarboxylation reaction. Here, we report antagonist behaviours of recombinant PEPCKs derived from the parasite and its host. In search of possible modulators for PEPCK, few phytoestrogens were examined on the purified enzymes and their inhibitory constants were determined and discussed. This study stresses the potential of these findings to validate PEPCK as the anthelmintic drug target for parasitism management.
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Macchiaroli N, Maldonado LL, Zarowiecki M, Cucher M, Gismondi MI, Kamenetzky L, Rosenzvit MC. Genome-wide identification of microRNA targets in the neglected disease pathogens of the genus Echinococcus. Mol Biochem Parasitol 2017; 214:91-100. [PMID: 28385564 DOI: 10.1016/j.molbiopara.2017.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/30/2017] [Accepted: 04/01/2017] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in biological processes such as development. MiRNAs silence target mRNAs by binding to complementary sequences in the 3'untranslated regions (3'UTRs). The parasitic helminths of the genus Echinococcus are the causative agents of echinococcosis, a zoonotic neglected disease. In previous work, we performed a comprehensive identification and characterization of Echinococcus miRNAs. However, current knowledge about their targets is limited. Since target prediction algorithms rely on complementarity between 3'UTRs and miRNA sequences, a major limitation is the lack of accurate sequence information of 3'UTR for most species including parasitic helminths. We performed RNA-seq and developed a pipeline that integrates the transcriptomic data with available genomic data of this parasite in order to identify 3'UTRs of Echinococcus canadensis. The high confidence set of 3'UTRs obtained allowed the prediction of miRNA targets in Echinococcus through a bioinformatic approach. We performed for the first time a comparative analysis of miRNA targets in Echinococcus and Taenia. We found that many evolutionarily conserved target sites in Echinococcus and Taenia may be functional and under selective pressure. Signaling pathways such as MAPK and Wnt were among the most represented pathways indicating miRNA roles in parasite growth and development. Genome-wide identification and characterization of miRNA target genes in Echinococcus provide valuable information to guide experimental studies in order to understand miRNA functions in the parasites biology. miRNAs involved in essential functions, especially those being absent in the host or showing sequence divergence with respect to host orthologs, might be considered as novel therapeutic targets for echinococcosis control.
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Affiliation(s)
- Natalia Macchiaroli
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Lucas L Maldonado
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Magdalena Zarowiecki
- Parasite Genomics Group, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Marcela Cucher
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | | | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Mara Cecilia Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina.
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Basika T, Macchiaroli N, Cucher M, Espínola S, Kamenetzky L, Zaha A, Rosenzvit M, Ferreira HB. Identification and profiling of microRNAs in two developmental stages of the model cestode parasite Mesocestoides corti. Mol Biochem Parasitol 2016; 210:37-49. [DOI: 10.1016/j.molbiopara.2016.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 12/21/2022]
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40
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MicroRNA discovery in the human parasite Echinococcus multilocularis from genome-wide data. Genomics 2016; 107:274-80. [DOI: 10.1016/j.ygeno.2016.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/06/2016] [Accepted: 04/18/2016] [Indexed: 11/17/2022]
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41
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Jiang S, Li X, Wang X, Ban Q, Hui W, Jia B. MicroRNA profiling of the intestinal tissue of Kazakh sheep after experimental Echinococcus granulosus infection, using a high-throughput approach. ACTA ACUST UNITED AC 2016; 23:23. [PMID: 27235195 PMCID: PMC4884269 DOI: 10.1051/parasite/2016023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/30/2016] [Indexed: 12/15/2022]
Abstract
Cystic echinococcosis (CE), caused by infection with the larval stage of the cestode Echinococcus granulosus, is a chronic zoonosis, to which sheep are highly susceptible. Previously, we found that Kazakh sheep with different MHC haplotypes differed in CE infection. Sheep with haplotype MHCMvaIbc-SacIIab-Hin1Iab were resistant to CE infection, while their counterparts without this haplotype were not. MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at the post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. To identify microRNA controlling resistance to CE in the early stage of infection, microRNA profiling was conducted in the intestinal tissue of sheep with resistant and non-resistant MHC haplotypes after peroral infection with E. granulosus eggs. A total of 351 known and 186 novel miRNAs were detected in the resistant group, against 353 known and 129 novel miRNAs in the non-resistant group. Among these miRNAs, 83 known miRNAs were significantly differentially expressed, including 75 up-regulated and 8 down-regulated miRNAs. Among these known microRNAs, miR-21-3p, miR-542-5p, miR-671, miR-134-5p, miR-26b, and miR-27a showed a significantly higher expression in CE-resistant sheep compared to the CE-non-resistant library, with the FC > 3. Functional analysis showed that they were NF-kB pathway-responsive miRNAs, which are involved in the inflammation process. The results suggest that these microRNAs may play important roles in the response of intestinal tissue to E. granulosus.
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Affiliation(s)
- Song Jiang
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Xin Li
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Xuhai Wang
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
| | - Qian Ban
- Center for Stem Cell and Translational Medicine, School of Life Sciences, Anhui University, Road Jiulong, Hefei 230000, Anhui, PR China
| | - Wenqiao Hui
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China - Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agriculture Sciences, Road Nongkenan, Hefei 230031, Anhui, PR China
| | - Bin Jia
- College of Animal Science and Technology, Shihezi University, Road Beisi, Shihezi 832003, Xinjiang, PR China
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Cai P, Gobert GN, McManus DP. MicroRNAs in Parasitic Helminthiases: Current Status and Future Perspectives. Trends Parasitol 2016; 32:71-86. [DOI: 10.1016/j.pt.2015.09.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/04/2015] [Accepted: 09/11/2015] [Indexed: 01/08/2023]
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43
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Lorenzatto KR, Kim K, Ntai I, Paludo GP, Camargo de Lima J, Thomas PM, Kelleher NL, Ferreira HB. Top Down Proteomics Reveals Mature Proteoforms Expressed in Subcellular Fractions of the Echinococcus granulosus Preadult Stage. J Proteome Res 2015; 14:4805-14. [PMID: 26465659 DOI: 10.1021/acs.jproteome.5b00642] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Echinococcus granulosus is the causative agent of cystic hydatid disease, a neglected zoonosis responsible for high morbidity and mortality. Several molecular mechanisms underlying parasite biology remain poorly understood. Here, E. granulosus subcellular fractions were analyzed by top down and bottom up proteomics for protein identification and characterization of co-translational and post-translational modifications (CTMs and PTMs, respectively). Nuclear and cytosolic extracts of E. granulosus protoscoleces were fractionated by 10% GELFrEE and proteins under 30 kDa were analyzed by LC-MS/MS. By top down analysis, 186 proteins and 207 proteoforms were identified, of which 122 and 52 proteoforms were exclusively detected in nuclear and cytosolic fractions, respectively. CTMs were evident as 71% of the proteoforms had methionine excised and 47% were N-terminal acetylated. In addition, in silico internal acetylation prediction coupled with top down MS allowed the characterization of 9 proteins differentially acetylated, including histones. Bottom up analysis increased the overall number of identified proteins in nuclear and cytosolic fractions to 154 and 112, respectively. Overall, our results provided the first description of the low mass proteome of E. granulosus subcellular fractions and highlighted proteoforms with CTMs and PTMS whose characterization may lead to another level of understanding about molecular mechanisms controlling parasitic flatworm biology.
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Affiliation(s)
- Karina R Lorenzatto
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Kyunggon Kim
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Ioanna Ntai
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Gabriela P Paludo
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Jeferson Camargo de Lima
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
| | - Paul M Thomas
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrique B Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Avenida Bento Gonçalves, 9500 Porto Alegre, Rio Grande do Sul, Brazil
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44
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Fromm B, Billipp T, Peck LE, Johansen M, Tarver JE, King BL, Newcomb JM, Sempere LF, Flatmark K, Hovig E, Peterson KJ. A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annu Rev Genet 2015; 49:213-42. [PMID: 26473382 DOI: 10.1146/annurev-genet-120213-092023] [Citation(s) in RCA: 364] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although microRNAs (miRNAs) are among the most intensively studied molecules of the past 20 years, determining what is and what is not a miRNA has not been straightforward. Here, we present a uniform system for the annotation and nomenclature of miRNA genes. We show that less than a third of the 1,881 human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase entries, are robustly supported as miRNA genes. Furthermore, we show that the human repertoire of miRNAs has been shaped by periods of intense miRNA innovation and that mature gene products show a very different tempo and mode of sequence evolution than star products. We establish a new open access database--MirGeneDB ( http://mirgenedb.org )--to catalog this set of miRNAs, which complements the efforts of miRBase but differs from it by annotating the mature versus star products and by imposing an evolutionary hierarchy upon this curated and consistently named repertoire.
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Affiliation(s)
- Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research
| | - Tyler Billipp
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755;
| | - Liam E Peck
- Department of Biology and Health Sciences, New England College, Henniker, New Hampshire 03242
| | | | - James E Tarver
- Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland.,School of Earth Sciences, University of Bristol, BS8 1TQ Bristol, United Kingdom
| | - Benjamin L King
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, Maine 04672
| | - James M Newcomb
- Department of Biology and Health Sciences, New England College, Henniker, New Hampshire 03242
| | - Lorenzo F Sempere
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research.,Department of Gastroenterological Surgery.,Institute of Clinical Medicine
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research.,Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, N-0424 Oslo, Norway.,Department of Informatics, University of Oslo, Blindern, N-0318 Oslo, Norway
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755;
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Fontenla S, Dell'Oca N, Smircich P, Tort JF, Siles-Lucas M. The miRnome of Fasciola hepatica juveniles endorses the existence of a reduced set of highly divergent micro RNAs in parasitic flatworms. Int J Parasitol 2015; 45:901-13. [PMID: 26432296 DOI: 10.1016/j.ijpara.2015.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/27/2015] [Accepted: 06/30/2015] [Indexed: 12/20/2022]
Abstract
The liver fluke Fasciola hepatica is a foodborne zoonotic parasite affecting livestock worldwide, with increasing relevance in human health. The first developmental stage that the host meets after ingestion of the parasite is the newly excysted juvenile, that actively transverses the gut wall and migrates to its final location in the liver. The regulation of the early developmental events in newly excysted juveniles is still poorly understood and a relevant target for control strategies. Here we investigated the putative involvement of small regulatory RNAs in the invasion process. The small RNA population of the newly excysted juvenile fall into two classes, one represented by micro (mi)RNAs and a secondary group of larger (32-33 nucleotides) tRNA-derived sequences. We identified 40 different miRNAs, most of those belonging to ancient miRNAs conserved in protostomes and metazoans, notably with a highly predominant miR-125b variant. Remarkably, several protostomian and metazoan conserved families were not detected in consonance with previous reports of drastic miRnome reduction in parasitic flatworms. Additionally, a set of five novel miRNAs was identified, probably associated with specific gene regulation expression needs in F. hepatica. While sequence conservation in mature miRNA is high across the metazoan tree, we observed that flatworm miRNAs are more divergent, suggesting that mutation rates in parasitic flatworms could be high. Finally, the distinctive presence of tRNA-derived sequences, mostly 5' tRNA halves of selected tRNAs in the small RNA population of newly excysted juveniles, raises the possibility that both miRNA and tRNA fragments participate in the regulation of gene expression in this parasite.
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Affiliation(s)
- Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Nicolás Dell'Oca
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Pablo Smircich
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay; Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - José F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UdelaR), Montevideo, Uruguay.
| | - Mar Siles-Lucas
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA), Consejo Superior de Investigaciones Científicas (CSIC), Salamanca, Spain
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Debarba JA, Monteiro KM, Moura H, Barr JR, Ferreira HB, Zaha A. Identification of Newly Synthesized Proteins by Echinococcus granulosus Protoscoleces upon Induction of Strobilation. PLoS Negl Trop Dis 2015; 9:e0004085. [PMID: 26393918 PMCID: PMC4578768 DOI: 10.1371/journal.pntd.0004085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/25/2015] [Indexed: 12/21/2022] Open
Abstract
Background The proteins responsible for the key molecular events leading to the structural changes between the developmental stages of Echinococcus granulosus remain unknown. In this work, azidohomoalanine (AHA)-specific labeling was used to identify proteins expressed by E. granulosus protoscoleces (PSCs) upon the induction of strobilar development. Methodology/Principal Findings The in vitro incorporation of AHA with different tags into newly synthesized proteins (NSPs) by PSCs was analyzed using SDS-PAGE and confocal microscopy. The LC-MS/MS analysis of AHA-labeled NSPs by PSCs undergoing strobilation allowed for the identification of 365 proteins, of which 75 were differentially expressed in comparison between the presence or absence of strobilation stimuli and 51 were expressed exclusively in either condition. These proteins were mainly involved in metabolic, regulatory and signaling processes. Conclusions/Significance After the controlled-labeling of proteins during the induction of strobilar development, we identified modifications in protein expression. The changes in the metabolism and the activation of control and signaling pathways may be important for the correct parasite development and be target for further studies. In the life cycle of the parasite Echinococcus granulosus, hydatid cysts produce the pre-adult form, which has the ability to either differentiate into an adult worm (strobilation) or dedifferentiate into a secondary hydatid cyst. We used different protein tags that allowed for the visualization and purification of proteins produced specifically after the induction of strobilar development to identify proteins that might be involved in this process (temporally controlled and context-dependent). As a result, we found proteins that are involved in important processes during development, such as energy metabolism, control pathways and cellular communication. We believe that these results will be useful for the development of scientific approaches to controlling and preventing cystic hydatid disease.
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Affiliation(s)
- João Antonio Debarba
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Biologia Molecular de Cestódeos, and Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Karina Mariante Monteiro
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Biologia Molecular de Cestódeos, and Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Hercules Moura
- Biological Mass Spectrometry Laboratory, Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John R. Barr
- Biological Mass Spectrometry Laboratory, Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Henrique Bunselmeyer Ferreira
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Biologia Molecular de Cestódeos, and Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Arnaldo Zaha
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Biologia Molecular de Cestódeos, and Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- * E-mail:
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47
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Macchiaroli N, Cucher M, Zarowiecki M, Maldonado L, Kamenetzky L, Rosenzvit MC. microRNA profiling in the zoonotic parasite Echinococcus canadensis using a high-throughput approach. Parasit Vectors 2015; 8:83. [PMID: 25656283 PMCID: PMC4326209 DOI: 10.1186/s13071-015-0686-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/21/2015] [Indexed: 01/08/2023] Open
Abstract
Background microRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. The particular developmental and metabolic characteristics of cestode parasites highlight the importance of studying miRNA gene regulation in these organisms. Here, we perform a comprehensive analysis of miRNAs in the parasitic cestode Echinococcus canadensis G7, one of the causative agents of the neglected zoonotic disease cystic echinococcosis. Methods Small RNA libraries from protoscoleces and cyst walls of E. canadensis G7 and protoscoleces of E. granulosus sensu stricto G1 were sequenced using Illumina technology. For miRNA prediction, miRDeep2 core algorithm was used. The output list of candidate precursors was manually curated to generate a high confidence set of miRNAs. Differential expression analysis of miRNAs between stages or species was estimated with DESeq. Expression levels of selected miRNAs were validated using poly-A RT-qPCR. Results In this study we used a high-throughput approach and found transcriptional evidence of 37 miRNAs thus expanding the miRNA repertoire of E. canadensis G7. Differential expression analysis showed highly regulated miRNAs between life cycle stages, suggesting a role in maintaining the features of each developmental stage or in the regulation of developmental timing. In this work we characterize conserved and novel Echinococcus miRNAs which represent 30 unique miRNA families. Here we confirmed the remarkable loss of conserved miRNA families in E. canadensis, reflecting their low morphological complexity and high adaptation to parasitism. Conclusions We performed the first in-depth study profiling of small RNAs in the zoonotic parasite E. canadensis G7. We found that miRNAs are the preponderant small RNA silencing molecules, suggesting that these small RNAs could be an essential mechanism of gene regulation in this species. We also identified both parasite specific and divergent miRNAs which are potential biomarkers of infection. This study will provide valuable information for better understanding of the complex biology of this parasite and could help to find new potential targets for therapy and/or diagnosis. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-0686-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natalia Macchiaroli
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Paraguay 2155, Piso 13, CP 1121, Buenos Aires, Argentina.
| | - Marcela Cucher
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Paraguay 2155, Piso 13, CP 1121, Buenos Aires, Argentina.
| | - Magdalena Zarowiecki
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Lucas Maldonado
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Paraguay 2155, Piso 13, CP 1121, Buenos Aires, Argentina.
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Paraguay 2155, Piso 13, CP 1121, Buenos Aires, Argentina.
| | - Mara Cecilia Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Paraguay 2155, Piso 13, CP 1121, Buenos Aires, Argentina.
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