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Fernandez‐Becerra C, Xander P, Alfandari D, Dong G, Aparici‐Herraiz I, Rosenhek‐Goldian I, Shokouhy M, Gualdron‐Lopez M, Lozano N, Cortes‐Serra N, Karam PA, Meneghetti P, Madeira RP, Porat Z, Soares RP, Costa AO, Rafati S, da Silva A, Santarém N, Fernandez‐Prada C, Ramirez MI, Bernal D, Marcilla A, Pereira‐Chioccola VL, Alves LR, Portillo HD, Regev‐Rudzki N, de Almeida IC, Schenkman S, Olivier M, Torrecilhas AC. Guidelines for the purification and characterization of extracellular vesicles of parasites. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e117. [PMID: 38939734 PMCID: PMC11080789 DOI: 10.1002/jex2.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 08/21/2023] [Accepted: 09/14/2023] [Indexed: 06/29/2024]
Abstract
Parasites are responsible for the most neglected tropical diseases, affecting over a billion people worldwide (WHO, 2015) and accounting for billions of cases a year and responsible for several millions of deaths. Research on extracellular vesicles (EVs) has increased in recent years and demonstrated that EVs shed by pathogenic parasites interact with host cells playing an important role in the parasite's survival, such as facilitation of infection, immunomodulation, parasite adaptation to the host environment and the transfer of drug resistance factors. Thus, EVs released by parasites mediate parasite-parasite and parasite-host intercellular communication. In addition, they are being explored as biomarkers of asymptomatic infections and disease prognosis after drug treatment. However, most current protocols used for the isolation, size determination, quantification and characterization of molecular cargo of EVs lack greater rigor, standardization, and adequate quality controls to certify the enrichment or purity of the ensuing bioproducts. We are now initiating major guidelines based on the evolution of collective knowledge in recent years. The main points covered in this position paper are methods for the isolation and molecular characterization of EVs obtained from parasite-infected cell cultures, experimental animals, and patients. The guideline also includes a discussion of suggested protocols and functional assays in host cells.
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Affiliation(s)
- Carmen Fernandez‐Becerra
- ISGlobal, Barcelona Institute for Global HealthHospital Clínic‐Universitatde BarcelonaBarcelonaSpain
- IGTP Institut d'Investigació Germans Trias i PujolBadalona (Barcelona)Spain
- CIBERINFECISCIII‐CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIIMadridSpain
| | - Patrícia Xander
- Departamento de Ciências FarmacêuticasLaboratório de Imunologia Celular e Bioquímica de Fungos e ProtozoáriosDepartamento de Ciências FarmacêuticasInstituto de Ciências AmbientaisQuímicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP)São PauloBrazil
| | - Daniel Alfandari
- Department of Biomolecular SciencesWeizmann Institute of Science (WIS)RehovotIsrael
| | - George Dong
- The Research Institute of the McGill University Health CentreMcGill UniversityMontréalQuébecCanada
| | - Iris Aparici‐Herraiz
- ISGlobal, Barcelona Institute for Global HealthHospital Clínic‐Universitatde BarcelonaBarcelonaSpain
| | | | - Mehrdad Shokouhy
- Department of Immunotherapy and Leishmania Vaccine ResearchPasteur Institute of IranTehranIran
| | - Melisa Gualdron‐Lopez
- ISGlobal, Barcelona Institute for Global HealthHospital Clínic‐Universitatde BarcelonaBarcelonaSpain
| | - Nicholy Lozano
- Departamento de Ciências FarmacêuticasLaboratório de Imunologia Celular e Bioquímica de Fungos e ProtozoáriosDepartamento de Ciências FarmacêuticasInstituto de Ciências AmbientaisQuímicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP)São PauloBrazil
| | - Nuria Cortes‐Serra
- ISGlobal, Barcelona Institute for Global HealthHospital Clínic‐Universitatde BarcelonaBarcelonaSpain
| | - Paula Abou Karam
- Department of Biomolecular SciencesWeizmann Institute of Science (WIS)RehovotIsrael
| | - Paula Meneghetti
- Departamento de Ciências FarmacêuticasLaboratório de Imunologia Celular e Bioquímica de Fungos e ProtozoáriosDepartamento de Ciências FarmacêuticasInstituto de Ciências AmbientaisQuímicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP)São PauloBrazil
| | - Rafael Pedro Madeira
- Departamento de Ciências FarmacêuticasLaboratório de Imunologia Celular e Bioquímica de Fungos e ProtozoáriosDepartamento de Ciências FarmacêuticasInstituto de Ciências AmbientaisQuímicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP)São PauloBrazil
| | - Ziv Porat
- Flow Cytometry UnitLife Sciences Core Facilities, WISRehovotIsrael
| | | | - Adriana Oliveira Costa
- Departamento de Análises Clínicas e ToxicológicasFaculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG)Belo HorizonteMinas GeraisBrasil
| | - Sima Rafati
- Department of Immunotherapy and Leishmania Vaccine ResearchPasteur Institute of IranTehranIran
| | - Anabela‐Cordeiro da Silva
- Host‐Parasite Interactions GroupInstitute of Research and Innovation in HealthUniversity of PortoPortoPortugal
- Department of Biological SciencesFaculty of PharmacyUniversity of PortoPortoPortugal
| | - Nuno Santarém
- Host‐Parasite Interactions GroupInstitute of Research and Innovation in HealthUniversity of PortoPortoPortugal
- Department of Biological SciencesFaculty of PharmacyUniversity of PortoPortoPortugal
| | | | - Marcel I. Ramirez
- EVAHPI ‐ Extracellular Vesicles and Host‐Parasite Interactions Research Group Laboratório de Biologia Molecular e Sistemática de TripanossomatideosInstituto Carlos Chagas‐FiocruzCuritibaParanáBrasil
| | - Dolores Bernal
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències BiològiquesUniversitat de ValènciaBurjassotValenciaSpain
| | - Antonio Marcilla
- Àrea de Parasitologia, Departament de Farmàcia i Tecnologia Farmacèutica i ParasitologiaUniversitat de ValènciaBurjassotValenciaSpain
| | - Vera Lucia Pereira‐Chioccola
- Laboratório de Biologia Molecular de Parasitas e Fungos, Centro de Parasitologia e MicologiaInstituto Adolfo Lutz (IAL)São PauloBrasil
| | - Lysangela Ronalte Alves
- Laboratório de Regulação da Expressão GênicaInstituto Carlos ChagasFiocruz ParanáCuritibaBrazil
- Research Center in Infectious DiseasesDivision of Infectious Disease and Immunity CHU de Quebec Research CenterDepartment of MicrobiologyInfectious Disease and ImmunologyFaculty of MedicineUniversity LavalQuebec CityQuebecCanada
| | - Hernando Del Portillo
- ISGlobal, Barcelona Institute for Global HealthHospital Clínic‐Universitatde BarcelonaBarcelonaSpain
- IGTP Institut d'Investigació Germans Trias i PujolBadalona (Barcelona)Spain
- ICREA Institució Catalana de Recerca i Estudis Avanc¸ats (ICREA)BarcelonaSpain
| | - Neta Regev‐Rudzki
- Department of Biomolecular SciencesWeizmann Institute of Science (WIS)RehovotIsrael
| | - Igor Correia de Almeida
- Department of Biological SciencesBorder Biomedical Research CenterThe University of Texas at El PasoEl PasoTexasUSA
| | - Sergio Schenkman
- Departamento de MicrobiologiaImunologia e Parasitologia, UNIFESPSão PauloBrazil
| | - Martin Olivier
- The Research Institute of the McGill University Health CentreMcGill UniversityMontréalQuébecCanada
| | - Ana Claudia Torrecilhas
- Departamento de Ciências FarmacêuticasLaboratório de Imunologia Celular e Bioquímica de Fungos e ProtozoáriosDepartamento de Ciências FarmacêuticasInstituto de Ciências AmbientaisQuímicas e FarmacêuticasUniversidade Federal de São Paulo (UNIFESP)São PauloBrazil
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2
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Genetic manipulations in helminth parasites. J Parasit Dis 2023; 47:203-214. [PMID: 36712591 PMCID: PMC9869838 DOI: 10.1007/s12639-023-01567-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/12/2023] [Indexed: 01/24/2023] Open
Abstract
Screening of vaccine or drug target in parasitic helminth is hindered by lack of robust tool for functional studies of parasite protein which account for the availability of only a few anti-helminthic vaccines, diagnostic assay and slower pace of development of an anthelmintic drug. With the piling up of parasite transcriptomic and genomic data, in silico screening for possible vaccine/drug target could be validated by functional characterization of proteins by RNA interference or CRISPR/Cas9. These reverse genetic engineering tools have opened up a better avenue and opportunity for screening parasitic proteins in vitro as well as in vivo. RNA interference provides a technique for silencing targeted mRNA transcript for understanding a gene function in helminth as evidence by work in Caenorhabditis elegans. Recent genetic engineering tool, CRISPR/Cas9 allows knock-out/deletion of the desired gene in parasitic helminths and the other provision it provides in terms of gene knock-in/insertion in parasite genome is still to be explored in future. This manuscript discussed the work that has been carried out on RNAi and CRISPR/Cas9 for functional studies of helminth parasitic proteins.
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Zagoskin MV, Wang J, Neff AT, Veronezi GMB, Davis RE. Small RNA pathways in the nematode Ascaris in the absence of piRNAs. Nat Commun 2022; 13:837. [PMID: 35149688 PMCID: PMC8837657 DOI: 10.1038/s41467-022-28482-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/13/2022] [Indexed: 02/07/2023] Open
Abstract
Small RNA pathways play key and diverse regulatory roles in C. elegans, but our understanding of their conservation and contributions in other nematodes is limited. We analyzed small RNA pathways in the divergent parasitic nematode Ascaris. Ascaris has ten Argonautes with five worm-specific Argonautes (WAGOs) that associate with secondary 5’-triphosphate 22-24G-RNAs. These small RNAs target repetitive sequences or mature mRNAs and are similar to the C. elegans mutator, nuclear, and CSR-1 small RNA pathways. Even in the absence of a piRNA pathway, Ascaris CSR-1 may still function to “license” as well as fine-tune or repress gene expression. Ascaris ALG-4 and its associated 26G-RNAs target and likely repress specific mRNAs during testis meiosis. Ascaris WAGO small RNAs demonstrate target plasticity changing their targets between repeats and mRNAs during development. We provide a unique and comprehensive view of mRNA and small RNA expression throughout spermatogenesis. Overall, our study illustrates the conservation, divergence, dynamics, and flexibility of small RNA pathways in nematodes. The parasitic nematode Ascaris lacks piRNAs. Here the authors compare Argonaute proteins and small RNAs from C. elegans and Ascaris, expanding our understanding of the conservation, divergence, and flexibility of Argonautes and small RNA pathways in nematodes.
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Affiliation(s)
- Maxim V Zagoskin
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Jianbin Wang
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA. .,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA. .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA. .,UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA.
| | - Ashley T Neff
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Giovana M B Veronezi
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA. .,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA.
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Zawawi A, Else KJ. Soil-Transmitted Helminth Vaccines: Are We Getting Closer? Front Immunol 2020; 11:576748. [PMID: 33133094 PMCID: PMC7565266 DOI: 10.3389/fimmu.2020.576748] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/02/2020] [Indexed: 01/07/2023] Open
Abstract
Parasitic helminths infect over one-fourth of the human population resulting in significant morbidity, and in some cases, death in endemic countries. Despite mass drug administration (MDA) to school-aged children and other control measures, helminth infections are spreading into new areas. Thus, there is a strong rationale for developing anthelminthic vaccines as cost-effective, long-term immunological control strategies, which, unlike MDA, are not haunted by the threat of emerging drug-resistant helminths nor limited by reinfection risk. Advances in vaccinology, immunology, and immunomics include the development of new tools that improve the safety, immunogenicity, and efficacy of vaccines; and some of these tools have been used in the development of helminth vaccines. The development of anthelminthic vaccines is fraught with difficulty. Multiple lifecycle stages exist each presenting stage-specific antigens. Further, helminth parasites are notorious for their ability to dampen down and regulate host immunity. One of the first significant challenges in developing any vaccine is identifying suitable candidate protective antigens. This review explores our current knowledge in lead antigen identification and reports on recent pre-clinical and clinical trials in the context of the soil-transmitted helminths Trichuris, the hookworms and Ascaris. Ultimately, a multivalent anthelminthic vaccine could become an essential tool for achieving the medium-to long-term goal of controlling, or even eliminating helminth infections.
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Affiliation(s)
- Ayat Zawawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia,*Correspondence: Ayat Zawawi
| | - Kathryn J. Else
- Manchester Academic Health Science Centre, Faculty of Biology, Medicine, and Health, School of Biological Sciences, Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom,Kathryn J. Else
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Gasser RB, Korhonen PK, Zhu XQ, Young ND. Harnessing the Toxocara Genome to Underpin Toxocariasis Research and New Interventions. ADVANCES IN PARASITOLOGY 2016; 91:87-110. [PMID: 27015948 DOI: 10.1016/bs.apar.2015.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Parasitic worms, such as flatworms (platyhelminths) and roundworms (nematodes), cause substantial morbidity and mortality in animals and people globally. The ascaridoid nematode Toxocara canis is a zoonotic parasite of socioeconomic significance worldwide. In humans, this worm causes toxocariasis (disease) mainly in underprivileged communities in both the developed and developing worlds. While reasonably well studied from clinical and epidemiological perspectives, little is understood about the molecular biology of T. canis, its relationship with its hosts and the disease that it causes. However, a recent report of the draft genome and transcriptomes of T. canis should underpin many fundamental and applied research areas in the future. The present article gives a background on Toxocara and toxocariasis, a brief account of diagnostic approaches for specific identification and genetic analysis, and gives a perspective on the impact that the genome of T. canis and advanced molecular technologies could have on our understanding of the parasite and the diseases that it causes as well as the design of new and improved approaches for the diagnosis, treatment and control of toxocariasis.
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McCoy CJ, Warnock ND, Atkinson LE, Atcheson E, Martin RJ, Robertson AP, Maule AG, Marks NJ, Mousley A. RNA interference in adult Ascaris suum--an opportunity for the development of a functional genomics platform that supports organism-, tissue- and cell-based biology in a nematode parasite. Int J Parasitol 2015; 45:673-8. [PMID: 26149642 PMCID: PMC4563943 DOI: 10.1016/j.ijpara.2015.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 05/19/2015] [Accepted: 05/22/2015] [Indexed: 11/03/2022]
Abstract
The sustainable control of animal parasitic nematodes requires the development of efficient functional genomics platforms to facilitate target validation and enhance anthelmintic discovery. Unfortunately, the utility of RNA interference (RNAi) for the validation of novel drug targets in nematode parasites remains problematic. Ascaris suum is an important veterinary parasite and a zoonotic pathogen. Here we show that adult A. suum is RNAi competent, and highlight the induction, spread and consistency of RNAi across multiple tissue types. This platform provides a new opportunity to undertake whole organism-, tissue- and cell-level gene function studies to enhance target validation processes for nematode parasites of veterinary/medical significance.
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Affiliation(s)
- Ciaran J McCoy
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Neil D Warnock
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Louise E Atkinson
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Erwan Atcheson
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Richard J Martin
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Alan P Robertson
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, USA
| | - Aaron G Maule
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Nikki J Marks
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Angela Mousley
- Parasitology, Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK.
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Zhu XQ, Korhonen PK, Cai H, Young ND, Nejsum P, von Samson-Himmelstjerna G, Boag PR, Tan P, Li Q, Min J, Yang Y, Wang X, Fang X, Hall RS, Hofmann A, Sternberg PW, Jex AR, Gasser RB. Genetic blueprint of the zoonotic pathogen Toxocara canis. Nat Commun 2015; 6:6145. [PMID: 25649139 PMCID: PMC4327413 DOI: 10.1038/ncomms7145] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 12/11/2014] [Indexed: 11/09/2022] Open
Abstract
Toxocara canis is a zoonotic parasite of major socioeconomic importance worldwide. In humans, this nematode causes disease (toxocariasis) mainly in the under-privileged communities in developed and developing countries. Although relatively well studied from clinical and epidemiological perspectives, to date, there has been no global investigation of the molecular biology of this parasite. Here we use next-generation sequencing to produce a draft genome and transcriptome of T. canis to support future biological and biotechnological investigations. This genome is 317 Mb in size, has a repeat content of 13.5% and encodes at least 18,596 protein-coding genes. We study transcription in a larval, as well as adult female and male stages, characterize the parasite’s gene-silencing machinery, explore molecules involved in development or host–parasite interactions and predict intervention targets. The draft genome of T. canis should provide a useful resource for future molecular studies of this and other, related parasites. Toxocara canis is a zoonotic parasite of major worldwide socioeconomic importance. Here, the authors sequence the genome and transcriptome of T. canis, and highlight potential mechanisms involved in development and host–parasite interactions that could support the pursuit of new drug interventions.
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Affiliation(s)
- Xing-Quan Zhu
- 1] 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 Province, China [2] Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Pasi K Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | | | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Peter Nejsum
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | | | - Peter R Boag
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Patrick Tan
- 1] Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore 138672, Republic of Singapore [2] Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Republic of Singapore
| | | | | | | | | | | | - Ross S Hall
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Andreas Hofmann
- Structural Chemistry Program, Eskitis Institute, Griffith University, Brisbane 4111, Queensland, Australia
| | - Paul W Sternberg
- HHMI, Division of Biology, California Institute of Technology, Pasadena 91125, California, USA
| | - Aaron R Jex
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
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A perfect time to harness advanced molecular technologies to explore the fundamental biology of Toxocara species. Vet Parasitol 2013; 193:353-64. [DOI: 10.1016/j.vetpar.2012.12.031] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Current drug targets for helminthic diseases. Parasitol Res 2013; 112:1819-31. [PMID: 23529336 DOI: 10.1007/s00436-013-3383-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/05/2013] [Indexed: 01/08/2023]
Abstract
More than 2 billion people are infected with helminth parasites across the globe. The burgeoning drug resistance against current anthelmintics in parasitic worms of humans and livestock requires urgent attention to tackle these recalcitrant worms. This review focuses on the advancements made in the area of helminth drug target discovery especially from the last few couple of decades. It highlights various approaches made in this field and enlists the potential drug targets currently being pursued to target economically important helminth species both from human as well as livestock to combat disease pathology of schistosomiasis, onchocerciasis, lymphatic filariasis, and other important macroparasitic diseases. Research in the helminths study is trending to identify potential and druggable targets through genomic, proteomic, biochemical, biophysical, in vitro experiments, and in vivo experiments in animal models. The availability of major helminths genome sequences and the subsequent availability of genome-scale functional datasets through in silico search and prioritization are expected to guide the experimental work necessary for target-based drug discovery. Organized and documented list of drug targets from various helminths of economic importance have been systematically covered in this review for further exploring their use and applications, which can give physicians and veterinarians effective drugs in hand to enable them control worm infections.
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Hagen J, Lee EF, Fairlie WD, Kalinna BH. Functional genomics approaches in parasitic helminths. Parasite Immunol 2012; 34:163-82. [PMID: 21711361 DOI: 10.1111/j.1365-3024.2011.01306.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As research on parasitic helminths is moving into the post-genomic era, an enormous effort is directed towards deciphering gene function and to achieve gene annotation. The sequences that are available in public databases undoubtedly hold information that can be utilized for new interventions and control but the exploitation of these resources has until recently remained difficult. Only now, with the emergence of methods to genetically manipulate and transform parasitic worms will it be possible to gain a comprehensive understanding of the molecular mechanisms involved in nutrition, metabolism, developmental switches/maturation and interaction with the host immune system. This review focuses on functional genomics approaches in parasitic helminths that are currently used, to highlight potential applications of these technologies in the areas of cell biology, systems biology and immunobiology of parasitic helminths.
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Affiliation(s)
- J Hagen
- Department of Veterinary Science, Centre for Animal Biotechnology, The University of Melbourne, Vic., Australia
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11
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Chen E, Khan L, Zhang L, Nguyen J, Cramarossa G, Tsao M, Danjoux C, Barnes E, Sahgal A, Holden L, Jon F, Dennis K, Culleton S, Chow E. Symptom clusters in patients with bone metastases—a reanalysis comparing different statistical methods. Support Care Cancer 2012; 20:2811-20. [DOI: 10.1007/s00520-012-1403-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 02/03/2012] [Indexed: 12/14/2022]
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12
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Khan L, Cramarossa G, Chen E, Nguyen J, Zhang L, Tsao M, Danjoux C, Barnes E, Sahgal A, Holden L, Jon F, Culleton S, Chow E. Symptom Clusters Using the Edmonton Symptom Assessment System in Patients With Bone Metastases: A Reanalysis Comparing Different Statistical Methods. World J Oncol 2012; 3:23-32. [PMID: 29147274 PMCID: PMC5649832 DOI: 10.4021/wjon403w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2011] [Indexed: 12/04/2022] Open
Abstract
Background To determine whether symptom clusters in patients with bone metastases vary when extracted using three different statistical methods. To compare the temporal composition of symptom clusters in responders versus non-responders to palliative radiation treatment. Methods A previous dataset of 518 bone metastases patients who completed the Edmonton Symptom Assessment System (ESAS) was used in this study. Clusters derived using Principal Component Analysis (PCA) in our previous study were compared to symptom clusters extracted using Hierarchical Cluster Analysis (HCA) and Exploratory Factor Analysis (EFA). Clusters were derived at baseline, and 1, 2, 4, 8 and 12 weeks after radiation treatment. The patient sample was further divided into responders versus non-responders to radiotherapy. The three statistical methods were performed to identify clusters in the subgroups at each time point. Results A complete consensus between HCA, EFA and PCA for the number and composition of symptom clusters was not reached at any time point. Furthermore, little correlation in clusters was found between the three statistical methods despite the use of an identical data set. As expected, different symptom clusters were observed in the responders and non-responders with all three statistical methods. In addition, clusters varied at each time point within each subgroup. Depression and anxiety were consistently found in the same cluster. Conclusion The quantity, composition, and occurrence of symptom clusters varied based on which statistical method was employed. The use of a common analytical method is necessary for consistency and comparison purposes in future symptom cluster research.
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Affiliation(s)
- Luluel Khan
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - Gemma Cramarossa
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - Emily Chen
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - Janet Nguyen
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - Liying Zhang
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - May Tsao
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - Cyril Danjoux
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - Elizabeth Barnes
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - Arjun Sahgal
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - Lori Holden
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - Flo Jon
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - Shaelyn Culleton
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
| | - Edward Chow
- Rapid Response Radiotherapy Program, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Canada
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Abstract
Parasitic diseases cause important losses in public and veterinary health worldwide. Novel drugs, more reliable diagnostic techniques and vaccine candidates are urgently needed. Due to the complexity of parasites and the intricate relationship with their hosts, development of successful tools to fight parasites has been very limited to date. The growing information on individual parasite genomes is now allowing the use of a broader range of potential strategies to gain deeper insights into the host-parasite relationship and has increased the possibilities to develop molecular-based tools in the field of parasitology. Nevertheless, functional studies of respective genes are still scarce. The RNA interference phenomenon resulting in the regulation of protein expression through the specific degradation of defined mRNAs, and more specifically the possibility of artificially induce it, has shown to be a powerful tool for the investigation of proteins function in many organisms. Recent advances in the design and delivery of targeting molecules allow efficient and highly specific gene silencing in different types of parasites, pointing out this technology as a powerful tool for the identification of novel vaccine candidates or drug targets at the high-throughput level in the near future, and could enable researchers to functionally annotate parasite genomes. The aim of this review is to provide a comprehensive overview on the current advances and pitfalls in gene silencing mechanisms, techniques, applications and prospects in animal parasites.
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Comparative transcriptome sequencing of germline and somatic tissues of the Ascaris suum gonad. BMC Genomics 2011; 12:481. [PMID: 21962222 PMCID: PMC3203103 DOI: 10.1186/1471-2164-12-481] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 10/01/2011] [Indexed: 11/16/2022] Open
Abstract
Background Ascaris suum (large roundworm of pigs) is a parasitic nematode that causes substantial losses to the meat industry. This nematode is suitable for biochemical studies because, unlike C. elegans, homogeneous tissue samples can be obtained by dissection. It has large sperm, produced in great numbers that permit biochemical studies of sperm motility. Widespread study of A. suum would be facilitated by more comprehensive genome resources and, to this end, we have produced a gonad transcriptome of A. suum. Results Two 454 pyrosequencing runs generated 572,982 and 588,651 reads for germline (TES) and somatic (VAS) tissues of the A. suum gonad, respectively. 86% of the high-quality (HQ) reads were assembled into 9,955 contigs and 69,791 HQ reads remained as singletons. 2.4 million bp of unique sequences were obtained with a coverage that reached 16.1-fold. 4,877 contigs and 14,339 singletons were annotated according to the C. elegans protein and the Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases. Comparison of TES and VAS transcriptomes demonstrated that genes participating in DNA replication, RNA transcription and ubiquitin-proteasome pathways are expressed at significantly higher levels in TES tissues than in VAS tissues. Comparison of the A. suum TES transcriptome with the C. elegans microarray dataset identified 165 A. suum germline-enriched genes (83% are spermatogenesis-enriched). Many of these genes encode serine/threonine kinases and phosphatases (KPs) as well as tyrosine KPs. Immunoblot analysis further suggested a critical role of phosphorylation in both testis development and spermatogenesis. A total of 2,681 A. suum genes were identified to have associated RNAi phenotypes in C. elegans, the majority of which display embryonic lethality, slow growth, larval arrest or sterility. Conclusions Using deep sequencing technology, this study has produced a gonad transcriptome of A. suum. By comparison with C. elegans datasets, we identified sets of genes associated with spermatogenesis and gonad development in A. suum. The newly identified genes encoding KPs may help determine signaling pathways that operate during spermatogenesis. A large portion of A. suum gonadal genes have related RNAi phenotypes in C. elegans and, thus, might be RNAi targets for parasite control.
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Maule AG, McVeigh P, Dalzell JJ, Atkinson L, Mousley A, Marks NJ. An eye on RNAi in nematode parasites. Trends Parasitol 2011; 27:505-13. [PMID: 21885343 DOI: 10.1016/j.pt.2011.07.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/27/2011] [Accepted: 07/29/2011] [Indexed: 11/19/2022]
Abstract
RNA interference (RNAi) has revolutionised approaches to gene function determination. From a parasitology perspective, gene function studies have the added dimension of providing validation data, increasingly deemed essential to the initial phases of drug target selection, pre-screen development. Notionally advantageous to those working on nematode parasites is the fact that Caenorhabditis elegans research spawned RNAi discovery and continues to seed our understanding of its fundamentals. Unfortunately, RNAi data for nematode parasites illustrate variable and inconsistent susceptibilities which undermine confidence and exploitation. Now well-ensconced in an era of nematode parasite genomics, we can begin to unscramble this variation.
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Affiliation(s)
- Aaron G Maule
- Molecular Bioscience-Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK.
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