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Rozario T, Collins JJ, Newmark PA. The good, the bad, and the ugly: From planarians to parasites. Curr Top Dev Biol 2022; 147:345-373. [PMID: 35337455 DOI: 10.1016/bs.ctdb.2021.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Platyhelminthes can perhaps rightly be described as a phylum of the good, the bad, and the ugly: remarkable free-living worms that colonize land, river, and sea, which are often rife with color and can display extraordinary regenerative ability; parasitic worms like schistosomes that cause devastating disease and suffering; and monstrous tapeworms that are the stuff of nightmares. In this chapter, we will explore how our research expanded beyond free-living planarians to their gruesome parasitic cousins. We start with Schistosoma mansoni, which is not a new model; however, approaching these parasites from a developmental perspective required a reinvention that may hold generalizable lessons to basic biologists interested in pivoting to disease models. We then turn to our (re)establishment of the rat tapeworm Hymenolepis diminuta, a once-favorite model that had been largely forgotten by the molecular biology revolution. Here we tell our stories in three, first-person narratives in order to convey personal views of our experiences. Welcome to the dark side.
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Affiliation(s)
- Tania Rozario
- Center for Tropical and Emerging Global Diseases and Department of Genetics, University of Georgia, Athens, GA, United States.
| | - James J Collins
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, United States.
| | - Phillip A Newmark
- Howard Hughes Medical Institute, Morgridge Institute for Research, Department of Integrative Biology, University of Wisconsin, Madison, WI, United States.
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2
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Gondal MN, Chaudhary SU. Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. Front Oncol 2021; 11:712505. [PMID: 34900668 PMCID: PMC8652070 DOI: 10.3389/fonc.2021.712505] [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: 05/20/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022] Open
Abstract
Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of scale-specific biomolecular data on cancer that now populates several online databases and resources. Cancer systems biology models built using this data have the potential to provide specific insights into complex multifactorial aberrations underpinning tumor initiation, development, and metastasis. Furthermore, the annotation of these single- and multi-scale models with patient data can additionally assist in designing personalized therapeutic interventions as well as aid in clinical decision-making. Here, we have systematically reviewed the emergence and evolution of (i) repositories with scale-specific and multi-scale biomolecular cancer data, (ii) systems biology models developed using this data, (iii) associated simulation software for the development of personalized cancer therapeutics, and (iv) translational attempts to pipeline multi-scale panomics data for data-driven in silico clinical oncology. The review concludes that the absence of a generic, zero-code, panomics-based multi-scale modeling pipeline and associated software framework, impedes the development and seamless deployment of personalized in silico multi-scale models in clinical settings.
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Affiliation(s)
- Mahnoor Naseer Gondal
- Biomedical Informatics Research Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
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Luo F, Yin M, Mo X, Sun C, Wu Q, Zhu B, Xiang M, Wang J, Wang Y, Li J, Zhang T, Xu B, Zheng H, Feng Z, Hu W. An improved genome assembly of the fluke Schistosoma japonicum. PLoS Negl Trop Dis 2019; 13:e0007612. [PMID: 31390359 PMCID: PMC6685614 DOI: 10.1371/journal.pntd.0007612] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 07/08/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery. FINDINGS In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation. CONCLUSIONS Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future.
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Affiliation(s)
- Fang Luo
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Mingbo Yin
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
| | - Xiaojin Mo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
| | - Chengsong Sun
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Qunfeng Wu
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Bingkuan Zhu
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Manyu Xiang
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jipeng Wang
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi Wang
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jian Li
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Zheng Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
| | - Wei Hu
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
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Sotillo J, Pearson MS, Loukas A. Trematode Genomics and Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1154:411-436. [PMID: 31297769 DOI: 10.1007/978-3-030-18616-6_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Trematode infections are among the most neglected tropical diseases despite their worldwide distribution and extraordinary ability to parasitise many different host species and host tissues. Furthermore, these parasites are of great socioeconomic, medical, veterinary and agricultural importance. During the last 10 years, there have been increasing efforts to overcome the lack of information on different "omic" resources such as proteomics and genomics. Herein, we focus on the recent advances in genomics and proteomics from trematodes of human importance, including liver, blood, intestinal and lung flukes. We also provide information on the latest technologies applied to study the biology of trematodes as well as on the resources available for the study of the molecular aspects of this group of helminths.
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Affiliation(s)
- Javier Sotillo
- Centre for Molecular Therapeutics, Australian Institute for Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.
| | - Mark S Pearson
- Centre for Molecular Therapeutics, Australian Institute for Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute for Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
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Host- and Helminth-Derived Endocannabinoids That Have Effects on Host Immunity Are Generated during Infection. Infect Immun 2018; 86:IAI.00441-18. [PMID: 30104215 DOI: 10.1128/iai.00441-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/07/2018] [Indexed: 02/07/2023] Open
Abstract
Helminths have coevolved with their hosts, resulting in the development of specialized host immune mechanisms and parasite-specific regulatory products. Identification of new pathways that regulate helminth infection could provide a better understanding of host-helminth interaction and may identify new therapeutic targets for helminth infection. Here we identify the endocannabinoid system as a new mechanism that influences host immunity to helminths. Endocannabinoids are lipid-derived signaling molecules that control important physiologic processes, such as feeding behavior and metabolism. Following murine infection with Nippostrongylus brasiliensis, an intestinal nematode with a life cycle similar to that of hookworms, we observed increased levels of endocannabinoids (2-arachidonoylglycerol [2-AG] or anandamide [AEA]) and the endocannabinoid-like molecule oleoylethanolamine (OEA) in infected lung and intestine. To investigate endocannabinoid function in helminth infection, we employed pharmacological inhibitors of cannabinoid subtype receptors 1 and 2 (CB1R and CB2R). Compared to findings for vehicle-treated mice, inhibition of CB1R but not CB2R resulted in increased N. brasiliensis worm burden and egg output, associated with significantly decreased expression of the T helper type 2 cytokine interleukin 5 (IL-5) in intestinal tissue and splenocyte cultures. Strikingly, bioinformatic analysis of genomic and transcriptome sequencing (RNA-seq) data sets identified putative genes encoding endocannabinoid biosynthetic and degradative enzymes in many parasitic nematodes. To test the novel hypothesis that helminth parasites produce their own endocannabinoids, we measured endocannabinoid levels in N. brasiliensis by mass spectrometry and quantitative PCR and found that N. brasiliensis parasites produced endocannabinoids, especially at the infectious larval stage. To our knowledge, this is the first report of helminth- and host-derived endocannabinoids that promote host immune responses and reduce parasite burden.
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Meshgi B, Jalousian F, Fathi S, Jahani Z. Design and synthesis of a new peptide derived from Fasciola gigantica cathepsin L1 with potential application in serodiagnosis of fascioliasis. Exp Parasitol 2018; 189:76-86. [PMID: 29679594 DOI: 10.1016/j.exppara.2018.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/06/2018] [Accepted: 04/13/2018] [Indexed: 01/18/2023]
Abstract
Fascioliasis is a global parasitic disease that affects domestic animals and causes considerable economic losses in the process of domestic animal breeding in endemic regions. The cause of the disease involves a liver trematode of the genus Fasciola, which secretes materials into a host's body (mainly proteins) in order to protect it from the host's immune system. These materials can be involved in the migration, growth, and nutrition of the parasite. Among the expressive proteins of Fasciola, proteases have been introduced as the appropriate targets for diagnosis, treatment, and vaccination against parasites. Cathepsin L (CL) is a member of cysteine proteases; it is widely expressed in the Fasciola species. The aim of this study was to evaluate two synthetic peptides from F. gigantica CL1 for improving serological diagnosis of the Fasciola infection. Therefore, the potential diagnostic value of the surface epitopes of CL1 was assessed using ELISA. In the current study, bioinformatics tools were applied to select two appropriate epitopes of Fasciola Cathepsin L1 as synthetic antigens. Their diagnostic values were evaluated by two methods of indirect ELISA and dot blot analysis. The findings revealed that the first peptide at a dilution ratio of 1:400 and the second peptide at a dilution ratio of 1:100 had the best results and the best concentration of antigens was introduced at 4 μg/ml. Moreover, 191 sera samples were analyzed by both peptides by using the ELISA method, including fascioliasis sera, other parasitic sera and negative sera. The sensitivity of the peptides 1-ELISA and peptide 2-ELISA for the diagnosis of the various cases was 100%. The specificity of the first peptide was 87.3% and its efficacy was determined to be 93.65%. The specificity and the efficacy of the second peptide were 79% and 89.5%, respectively. The positive predictive values of the first and second peptides were obtained to be 86.27% and 79.27% respectively, and the negative predictive values of both peptides was calculated as 100%. In conclusion, the results of this study indicated that the peptide 1 from CL1 may be used as an appropriate antigen for the diagnosis of fascioliasis if the findings are backed up by using other serodiagnostic methods for checking serological cross-reactivity linked to other parasites.
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Affiliation(s)
- Behnam Meshgi
- Department of Parasitology, Faculty of Veterinary Medicine, University of Tehran (Center of Excellent of Ecosystem and Ultrastructural Changes of Helminthes), Tehran, Iran.
| | - Fatemeh Jalousian
- Department of Parasitology, Faculty of Veterinary Medicine, University of Tehran (Center of Excellent of Ecosystem and Ultrastructural Changes of Helminthes), Tehran, Iran
| | - Saeid Fathi
- Department of Parasitology, Faculty of Veterinary Medicine, University of Tehran (Center of Excellent of Ecosystem and Ultrastructural Changes of Helminthes), Tehran, Iran
| | - Zahra Jahani
- Department of Parasitology, Faculty of Veterinary Medicine, University of Tehran (Center of Excellent of Ecosystem and Ultrastructural Changes of Helminthes), Tehran, Iran
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Eccles D, Chandler J, Camberis M, Henrissat B, Koren S, Le Gros G, Ewbank JJ. De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads. BMC Biol 2018; 16:6. [PMID: 29325570 PMCID: PMC5765664 DOI: 10.1186/s12915-017-0473-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/14/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Eukaryotic genome assembly remains a challenge in part due to the prevalence of complex DNA repeats. This is a particularly acute problem for holocentric nematodes because of the large number of satellite DNA sequences found throughout their genomes. These have been recalcitrant to most genome sequencing methods. At the same time, many nematodes are parasites and some represent a serious threat to human health. There is a pressing need for better molecular characterization of animal and plant parasitic nematodes. The advent of long-read DNA sequencing methods offers the promise of resolving complex genomes. RESULTS Using Nippostrongylus brasiliensis as a test case, applying improved base-calling algorithms and assembly methods, we demonstrate the feasibility of de novo genome assembly matching current community standards using only MinION long reads. In doing so, we uncovered an unexpected diversity of very long and complex DNA sequences repeated throughout the N. brasiliensis genome, including massive tandem repeats of tRNA genes. CONCLUSION Base-calling and assembly methods have improved sufficiently that de novo genome assembly of large complex genomes is possible using only long reads. The method has the added advantage of preserving haplotypic variants and so has the potential to be used in population analyses.
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Affiliation(s)
- David Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Jodie Chandler
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Mali Camberis
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- CNRS UMR 7257, Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Graham Le Gros
- Malaghan Institute of Medical Research, Wellington, New Zealand.
| | - Jonathan J Ewbank
- Malaghan Institute of Medical Research, Wellington, New Zealand
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, CNRS, INSERM, Marseille, France
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Limitations of the Echinococcus granulosus genome sequence assemblies for analysis of the gene family encoding the EG95 vaccine antigen. Parasitology 2017; 145:807-813. [DOI: 10.1017/s0031182017001767] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AbstractEchinococcus granulosus is an important zoonotic parasite that is distributed worldwide. The EG95 vaccine was developed to assist with control of E. granulosus transmission through the parasite's livestock intermediate hosts. The vaccine is based on a recombinant antigen encoded by a gene which is a member of a multi-gene family. With the recent availability of two E. granulosus draft genomes, we sought to map the eg95 gene family to the genomes. We were unable to map unequivocally any of the eg95 gene family members which had previously been characterized by cloning and sequencing both strands of genomic DNA fragments. Our inability to map EG95-related genes to the genomes has revealed limitations in the assembled sequence data when utilized for gene family analyses. This study contrasts with the expectations expressed in often high-profile publications describing draft genomes of parasitic organisms, highlighting deficiencies in currently available genomic resources for E. granulosus and provides a cautionary note for research which seeks to utilize these genome datasets.
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Chandler J, Camberis M, Bouchery T, Blaxter M, Le Gros G, Eccles DA. Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis. F1000Res 2017; 6:56. [PMID: 28491281 PMCID: PMC5399971 DOI: 10.12688/f1000research.10545.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/09/2017] [Indexed: 12/24/2022] Open
Abstract
Nippostrongylus brasiliensis, a nematode parasite of rodents, has a parasitic life cycle that is an extremely useful model for the study of human hookworm infection, particularly in regards to the induced immune response. The current reference genome for this parasite is highly fragmented with minimal annotation, but new advances in long-read sequencing suggest that a more complete and annotated assembly should be an achievable goal. We
de-novo assembled a single contig mitochondrial genome from
N. brasiliensis using MinION R9 nanopore data. The assembly was error-corrected using existing Illumina HiSeq reads, and annotated in full (i.e. gene boundary definitions without substantial gaps) by comparing with annotated genomes from similar parasite relatives. The mitochondrial genome has also been annotated with a preliminary electrical consensus sequence, using raw signal data generated from a Nanopore R9 flow cell.
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Affiliation(s)
- Jodie Chandler
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Mali Camberis
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Graham Le Gros
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - David A Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
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Duarte AM, Jenkins TP, Latrofa MS, Giannelli A, Papadopoulos E, de Carvalho LM, Nolan MJ, Otranto D, Cantacessi C. Helminth infections and gut microbiota - a feline perspective. Parasit Vectors 2016; 9:625. [PMID: 27912797 PMCID: PMC5135779 DOI: 10.1186/s13071-016-1908-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/22/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Investigations of the relationships between the gut microbiota and gastrointestinal parasitic nematodes are attracting growing interest by the scientific community, driven by the need to better understand the contribution of parasite-associated changes in the composition of the gut flora to both host malnutrition and immune modulation. These studies have however been carried out mainly in humans and experimental animals, while knowledge of the make-up of the gut commensal flora in presence or absence of infection by parasitic nematodes in domestic animals is limited. In this study, we investigate the qualitative and quantitative impact that infections by a widespread parasite of cats (i.e. Toxocara cati) exert on the gut microbiota of feline hosts. METHODS The faecal microbiota of cats with patent infection by T. cati (= Tc+), as well as that of negative controls (= Tc-) was examined via high-throughput sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene, followed by bioinformatics and biostatistical analyses of sequence data. RESULTS A total of 2,325,366 useable high-quality sequences were generated from the faecal samples analysed in this study and subjected to further bioinformatics analyses, which led to the identification of 128 OTUs and nine bacterial phyla, respectively. The phylum Firmicutes was predominant in all samples analysed (mean of 53.0%), followed by the phyla Proteobacteria (13.8%), Actinobacteria (13.7%) and Bacteroidetes (10.1%). Among others, bacteria of the order Lactobacillales, the family Enterococcaceae and genera Enterococcus and Dorea showed a trend towards increased abundance in Tc+ compared with Tc- samples, while no significant differences in OTU richness and diversity were recorded between Tc+ and Tc- samples (P = 0.485 and P = 0.581, respectively). However, Canonical Correlation and Redundancy Analyses were able to separate samples by infection status (P = 0.030 and P = 0.015, respectively), which suggests a correlation between the latter and the composition of the feline faecal microbiota. CONCLUSIONS In spite of the relatively small number of samples analysed, subtle differences in the composition of the gut microbiota of Tc+ vs Tc- cats could be identified, some of which in accordance with current data from humans and laboratory animal hosts. Nevertheless, the findings from this study contribute valuable knowledge to the yet little explored area of parasite-microbiota interactions in domestic animals.
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Affiliation(s)
- Ana M. Duarte
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- CIISA, Faculty of Veterinary Medicine, Universidade de Lisboa, Lisboa, Portugal
| | - Timothy P. Jenkins
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Maria S. Latrofa
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - Alessio Giannelli
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - Elias Papadopoulos
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Matthew J. Nolan
- Department of Pathology and Pathogen Biology, Royal Veterinary College, University of London, Hatfield, UK
| | - Domenico Otranto
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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The Role of Xenobiotic-Metabolizing Enzymes in Anthelmintic Deactivation and Resistance in Helminths. Trends Parasitol 2016; 32:481-491. [PMID: 26968642 DOI: 10.1016/j.pt.2016.02.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/03/2016] [Accepted: 02/10/2016] [Indexed: 12/24/2022]
Abstract
Xenobiotic-metabolizing enzymes (XMEs) modulate the biological activity and behavior of many drugs, including anthelmintics. The effects of anthelmintics can often be abolished by XMEs when the drugs are metabolized to an inefficient compound. XMEs therefore play a significant role in anthelmintic efficacy. Moreover, differences in XMEs between helminths are reflected by differences in anthelmintic metabolism between target species. Taking advantage of the newly sequenced genomes of many helminth species, progress in this field has been remarkable. The present review collects up to date information regarding the most important XMEs (phase I and phase II biotransformation enzymes; efflux transporters) in helminths. The participation of these XMEs in anthelmintic metabolism and their possible roles in drug resistance are evaluated.
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Human Trichuriasis: Whipworm Genetics, Phylogeny, Transmission and Future Research Directions. CURRENT TROPICAL MEDICINE REPORTS 2015. [DOI: 10.1007/s40475-015-0062-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Abstract
Alveolar and cystic echinococcosis, caused by the metacestode larval stages of the tapeworms Echinococcus multilocularis and Echinococcus granulosus, respectively, are life-threatening diseases and very difficult to treat. The introduction of benzimidazole-based chemotherapy, which targets parasite β-tubulin, has significantly improved the life-span and prognosis of echinococcosis patients. However, benzimidazoles show only parasitostatic activity, are associated with serious adverse side effects and have to be administered for very long time periods, underlining the need for new drugs. Very recently, the nuclear genomes of E. multilocularis and E. granulosus have been characterised, revealing a plethora of data for gaining a deeper understanding of host-parasite interaction, parasite development and parasite evolution. Combined with extensive transcriptome analyses of Echinococcus life cycle stages these investigations also yielded novel clues for targeted drug design. Recent years also witnessed significant advancements in the molecular and cellular characterisation of the Echinococcus 'germinative cell' population, which forms a unique stem cell system that differs from stem cells of other organisms in the expression of several genes associated with the maintenance of pluripotency. As the only parasite cell type capable of undergoing mitosis, the germinative cells are central to all developmental transitions of Echinococcus within the host and to parasite expansion via asexual proliferation. In the present article, we will briefly introduce and discuss recent advances in Echinococcus genomics and stem cell research in the context of drug design and development. Interestingly, it turns out that benzimidazoles seem to have very limited effects on Echinococcus germinative cells, which could explain the high recurrence rates observed after chemotherapeutic treatment of echinococcosis patients. This clearly indicates that future efforts into the development of parasitocidal drugs should also target the parasite's stem cell system.
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Affiliation(s)
- U Koziol
- University of Würzburg, Institute of Hygiene and Microbiology, Würzburg, Germany; Sección Bioquímica, Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay
| | - K Brehm
- University of Würzburg, Institute of Hygiene and Microbiology, Würzburg, Germany.
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14
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Sharma N, Singh V, Shyma KP. Role of parasitic vaccines in integrated control of parasitic diseases in livestock. Vet World 2015; 8:590-8. [PMID: 27047140 PMCID: PMC4774718 DOI: 10.14202/vetworld.2015.590-598] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/26/2015] [Accepted: 03/31/2015] [Indexed: 11/18/2022] Open
Abstract
Parasitic infections adversely affect animal’s health and threaten profitable animal production, thus affecting the economy of our country. These infections also play a major role in the spread of zoonotic diseases. Parasitic infections cause severe morbidity and mortality in animals especially those affecting the gastrointestinal system and thus affect the economy of livestock owner by decreasing the ability of the farmer to produce economically useful animal products. Due to all these reasons proper control of parasitic infection is critically important for sustained animal production. The most common and regularly used method to control parasitic infection is chemotherapy, which is very effective but has several disadvantages like drug resistance and drug residues. Integrated approaches to control parasitic infections should be formulated including grazing management, biological control, genetic resistance of hosts, and parasitic vaccines. India ranks first in cattle and buffalo population, but the majority of livestock owners have fewer herds, so other measures like grazing management, biological control, genetic resistance of hosts are not much practical to use. The most sustainable and economical approach to control parasitic infection in our country is to vaccinate animals, although vaccines increase the initial cost, but the immunity offered by the vaccine are long lived. Thus, vaccination of animals for various clinical, chronic, subclinical parasitic infections will be a cheaper and effective alternative to control parasitic infection for long time and improve animal production.
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Affiliation(s)
- Neelu Sharma
- Department of Veterinary Parasitology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar - 385 506, Gujarat, India
| | - Veer Singh
- Department of Veterinary Parasitology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar - 385 506, Gujarat, India
| | - K P Shyma
- Department of Veterinary Parasitology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar - 385 506, Gujarat, India
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15
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Cwiklinski K, Dalton JP, Dufresne PJ, La Course J, Williams DJ, Hodgkinson J, Paterson S. The Fasciola hepatica genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution. Genome Biol 2015; 16:71. [PMID: 25887684 PMCID: PMC4404566 DOI: 10.1186/s13059-015-0632-2] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/13/2015] [Indexed: 12/30/2022] Open
Abstract
Background The liver fluke Fasciola hepatica is a major pathogen of livestock worldwide, causing huge economic losses to agriculture, as well as 2.4 million human infections annually. Results Here we provide a draft genome for F. hepatica, which we find to be among the largest known pathogen genomes at 1.3 Gb. This size cannot be explained by genome duplication or expansion of a single repeat element, and remains a paradox given the burden it may impose on egg production necessary to transmit infection. Despite the potential for inbreeding by facultative self-fertilisation, substantial levels of polymorphism were found, which highlights the evolutionary potential for rapid adaptation to changes in host availability, climate change or to drug or vaccine interventions. Non-synonymous polymorphisms were elevated in genes shared with parasitic taxa, which may be particularly relevant for the ability of the parasite to adapt to a broad range of definitive mammalian and intermediate molluscan hosts. Large-scale transcriptional changes, particularly within expanded protease and tubulin families, were found as the parasite migrated from the gut, across the peritoneum and through the liver to mature in the bile ducts. We identify novel members of anti-oxidant and detoxification pathways and defined their differential expression through infection, which may explain the stage-specific efficacy of different anthelmintic drugs. Conclusions The genome analysis described here provides new insights into the evolution of this important pathogen, its adaptation to the host environment and external selection pressures. This analysis also provides a platform for research into novel drugs and vaccines. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0632-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Krystyna Cwiklinski
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. .,School of Biological Sciences, Medical Biology Centre, Queen's University of Belfast, Belfast, Northern Ireland, UK.
| | - John Pius Dalton
- School of Biological Sciences, Medical Biology Centre, Queen's University of Belfast, Belfast, Northern Ireland, UK. .,Institute of Parasitology, McGill University, Montreal, Quebec, Canada.
| | - Philippe J Dufresne
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada. .,Institut National de Santé Publique du Québec, Montreal, Quebec, Canada.
| | | | - Diana Jl Williams
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Jane Hodgkinson
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
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16
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Modelling the effects of mass drug administration on the molecular epidemiology of schistosomes. ADVANCES IN PARASITOLOGY 2015; 87:293-327. [PMID: 25765198 DOI: 10.1016/bs.apar.2014.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
As national governments scale up mass drug administration (MDA) programs aimed to combat neglected tropical diseases (NTDs), novel selection pressures on these parasites increase. To understand how parasite populations are affected by MDA and how to maximize the success of control programmes, it is imperative for epidemiological, molecular and mathematical modelling approaches to be combined. Modelling of parasite population genetic and genomic structure, particularly of the NTDs, has been limited through the availability of only a few molecular markers to date. The landscape of infectious disease research is being dramatically reshaped by next-generation sequencing technologies and our understanding of how repeated selective pressures are shaping parasite populations is radically altering. Genomics can provide high-resolution data on parasite population structure, and identify how loci may contribute to key phenotypes such as virulence and/or drug resistance. We discuss the incorporation of genetic and genomic data, focussing on the recently sequenced Schistosoma spp., into novel mathematical transmission models to inform our understanding of the impact of MDA and other control methods. We summarize what is known to date, the models that exist and how population genetics has given us an understanding of the effects of MDA on the parasites. We consider how genetic and genomic data have the potential to shape future research, highlighting key areas where data are lacking, and how future molecular epidemiology knowledge can aid understanding of transmission dynamics and the effects of MDA, ultimately informing public health policy makers of the best interventions for NTDs.
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17
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Pouchkina-Stantcheva NN, Cunningham LJ, Hrčkova G, Olson PD. RNA-mediated gene suppression and in vitro culture in Hymenolepis microstoma. Int J Parasitol 2013; 43:641-6. [PMID: 23639265 DOI: 10.1016/j.ijpara.2013.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 03/14/2013] [Accepted: 03/17/2013] [Indexed: 02/01/2023]
Abstract
Hymenolepis microstoma, the mouse bile-duct tapeworm, is a classical rodent-hosted model that provides easy laboratory access to all stages of the life cycle. Recent characterisation of its genome has greatly advanced its utility for molecular research, albeit contemporary techniques such as those for assaying gene function have yet to be developed in the system. Here we present research on the development of RNA-mediated gene suppression via RNA interference (RNAi), and on in vitro culture of the enteric, adult phase of the life cycle to support this work. We demonstrate up to 80% quantitative suppression of a Hox transcript via soaking activated juvenile worms with double-stranded RNAs. However, we were unable to achieve segmentation of the worms in culture despite extensive manipulations of the culture media and supplements, preventing functional interpretation. An alternative, in vivo approach to RNAi was also tested by exposing cysticercoids prior to inoculation in mice, but fluorescent labelling showed that the RNAs did not sufficiently penetrate the cyst body and no difference in expression was found between exposed and control groups grown in vivo. Genomic and transcriptomic data revealed that H. microstoma has two orthologs each of Dicer, Drosha and Ago-1-like genes and that expression of one of the Ago-1 genes appears exclusive to germline development, suggesting that two or more independent RNA-mediated pathways are in operation. These studies demonstrate the viability of RNAi in H. microstoma and extend the utility of the model for research in the genomic era.
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18
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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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19
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Chalmers IW, Hoffmann KF. Platyhelminth Venom Allergen-Like (VAL) proteins: revealing structural diversity, class-specific features and biological associations across the phylum. Parasitology 2012; 139:1231-45. [PMID: 22717097 PMCID: PMC3435950 DOI: 10.1017/s0031182012000704] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/23/2012] [Accepted: 03/23/2012] [Indexed: 12/31/2022]
Abstract
During platyhelminth infection, a cocktail of proteins is released by the parasite to aid invasion, initiate feeding, facilitate adaptation and mediate modulation of the host immune response. Included amongst these proteins is the Venom Allergen-Like (VAL) family, part of the larger sperm coating protein/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) superfamily. To explore the significance of this protein family during Platyhelminthes development and host interactions, we systematically summarize all published proteomic, genomic and immunological investigations of the VAL protein family to date. By conducting new genomic and transcriptomic interrogations to identify over 200 VAL proteins (228) from species in all 4 traditional taxonomic classes (Trematoda, Cestoda, Monogenea and Turbellaria), we further expand our knowledge related to platyhelminth VAL diversity across the phylum. Subsequent phylogenetic and tertiary structural analyses reveal several class-specific VAL features, which likely indicate a range of roles mediated by this protein family. Our comprehensive analysis of platyhelminth VALs represents a unifying synopsis for understanding diversity within this protein family and a firm context in which to initiate future functional characterization of these enigmatic members.
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Affiliation(s)
- Iain W Chalmers
- Institute of Biological, Environmental and Rural Sciences, Edward Llwyd Building, Penglais Campus, Aberystwyth University, Aberystwyth SY23 3DA, UK.
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Geyer KK, Hoffmann KF. Epigenetics: a key regulator of platyhelminth developmental biology? Int J Parasitol 2012; 42:221-4. [PMID: 22366548 DOI: 10.1016/j.ijpara.2012.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/07/2012] [Accepted: 02/09/2012] [Indexed: 11/18/2022]
Abstract
The Platyhelminthes (flukes/flatworms) are a large group of derived metazoans beautifully adapted for existence in diversely challenging ecosystems. As tractable examples of development and self-regeneration or as causative agents of aquacultural, veterinary and biomedically-relevant parasitic diseases, the platyhelminths are subject to intensive inter-disciplinary research. Given the complex lifestyles exhibited by individuals within this phylum, we postulate that epigenetic processes feature in many aspects of platyhelminth lifecycle diversity, development and environmentally-driven adaptations.
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Affiliation(s)
- Kathrin K Geyer
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth, UK
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BREHM K, CARLTON JM, HOFFMANN KF. Parasite genomics and post-genomic activities: 21st century resources for the parasite immunologist. Parasite Immunol 2012; 34:47-9. [DOI: 10.1111/j.1365-3024.2011.01346.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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