101
|
Platt RN, McDew-White M, Le Clec’h W, Chevalier FD, Allan F, Emery AM, Garba A, Hamidou AA, Ame SM, Webster JP, Rollinson D, Webster BL, Anderson TJC. Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites. Mol Biol Evol 2019; 36:2127-2142. [PMID: 31251352 PMCID: PMC6759076 DOI: 10.1093/molbev/msz154] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Introgression among parasite species has the potential to transfer traits of biomedical importance across species boundaries. The parasitic blood fluke Schistosoma haematobium causes urogenital schistosomiasis in humans across sub-Saharan Africa. Hybridization with other schistosome species is assumed to occur commonly, because genetic crosses between S. haematobium and livestock schistosomes, including S. bovis, can be staged in the laboratory, and sequencing of mtDNA and rDNA amplified from microscopic miracidia larvae frequently reveals markers from different species. However, the frequency, direction, age, and genomic consequences of hybridization are unknown. We hatched miracidia from eggs and sequenced the exomes from 96 individual S. haematobium miracidia from infected patients from Niger and the Zanzibar archipelago. These data revealed no evidence for contemporary hybridization between S. bovis and S. haematobium in our samples. However, all Nigerien S. haematobium genomes sampled show hybrid ancestry, with 3.3-8.2% of their nuclear genomes derived from S. bovis, providing evidence of an ancient introgression event that occurred at least 108-613 generations ago. Some S. bovis-derived alleles have spread to high frequency or reached fixation and show strong signatures of directional selection; the strongest signal spans a single gene in the invadolysin gene family (Chr. 4). Our results suggest that S. bovis/S. haematobium hybridization occurs rarely but demonstrate profound consequences of ancient introgression from a livestock parasite into the genome of S. haematobium, the most prevalent schistosome species infecting humans.
Collapse
Affiliation(s)
- Roy N Platt
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX
| | - Marina McDew-White
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX
| | - Winka Le Clec’h
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX
| | - Frédéric D Chevalier
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX
| | - Fiona Allan
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
- London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, St Mary’s Campus, London, United Kingdom
| | - Aidan M Emery
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
- London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, St Mary’s Campus, London, United Kingdom
| | - Amadou Garba
- Réseau International Schistosomoses, Environnement, Aménagement et Lutte (RISEAL-Niger), Niamey, Niger
| | - Amina A Hamidou
- Réseau International Schistosomoses, Environnement, Aménagement et Lutte (RISEAL-Niger), Niamey, Niger
| | - Shaali M Ame
- Public Health Laboratory - Ivo de Carneri, Pemba, United Republic of Tanzania
| | - Joanne P Webster
- London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, St Mary’s Campus, London, United Kingdom
- Centre for Emerging, Endemic and Exotic Diseases, Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, United Kingdom
| | - David Rollinson
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
- London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, St Mary’s Campus, London, United Kingdom
| | - Bonnie L Webster
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
- London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, St Mary’s Campus, London, United Kingdom
| | - Timothy J C Anderson
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX
| |
Collapse
|
102
|
Buddenborg SK, Kamel B, Hanelt B, Bu L, Zhang SM, Mkoji GM, Loker ES. The in vivo transcriptome of Schistosoma mansoni in the prominent vector species Biomphalaria pfeifferi with supporting observations from Biomphalaria glabrata. PLoS Negl Trop Dis 2019; 13:e0007013. [PMID: 31568484 PMCID: PMC6797213 DOI: 10.1371/journal.pntd.0007013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 10/17/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The full scope of the genes expressed by schistosomes during intramolluscan development has yet to be characterized. Understanding the gene products deployed by larval schistosomes in their snail hosts will provide insights into their establishment, maintenance, asexual reproduction, ability to castrate their hosts, and their prolific production of human-infective cercariae. Using the Illumina platform, the intramolluscan transcriptome of Schistosoma mansoni was investigated in field-derived specimens of the prominent vector species Biomphalaria pfeifferi at 1 and 3 days post infection (d) and from snails shedding cercariae. These S. mansoni samples were derived from the same snails used in our complementary B. pfeifferi transcriptomic study. We supplemented this view with microarray analyses of S. mansoni from B. glabrata at 2d, 4d, 8d, 16d, and 32d to highlight robust features of S. mansoni transcription, even when a different technique and vector species was used. PRINCIPAL FINDINGS Transcripts representing at least 7,740 (66%) of known S. mansoni genes were expressed during intramolluscan development, with the greatest number expressed in snails shedding cercariae. Many transcripts were constitutively expressed throughout development featuring membrane transporters, and metabolic enzymes involved in protein and nucleic acid synthesis and cell division. Several proteases and protease inhibitors were expressed at all stages, including some proteases usually associated with cercariae. Transcripts associated with G-protein coupled receptors, germ cell perpetuation, and stress responses and defense were well represented. We noted transcripts homologous to planarian anti-bacterial factors, several neural development or neuropeptide transcripts including neuropeptide Y, and receptors that may be associated with schistosome germinal cell maintenance that could also impact host reproduction. In at least one snail the presence of larvae of another digenean species (an amphistome) was associated with repressed S. mansoni transcriptional activity. CONCLUSIONS/SIGNIFICANCE This in vivo study, emphasizing field-derived snails and schistosomes, but supplemented with observations from a lab model, provides a distinct view from previous studies of development of cultured intramolluscan stages from lab-maintained organisms. We found many highly represented transcripts with suspected or unknown functions, with connection to intramolluscan development yet to be elucidated.
Collapse
Affiliation(s)
- Sarah K. Buddenborg
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States of America
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- * E-mail:
| | - Bishoy Kamel
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States of America
| | - Ben Hanelt
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States of America
| | - Lijing Bu
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States of America
| | - Si-Ming Zhang
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States of America
| | - Gerald M. Mkoji
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairob,i Kenya
| | - Eric S. Loker
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States of America
| |
Collapse
|
103
|
Promethazine exhibits antiparasitic properties in vitro and reduces worm burden, egg production, hepato-, and splenomegaly in a schistosomiasis animal model. Antimicrob Agents Chemother 2019:AAC.01208-19. [PMID: 31527034 DOI: 10.1128/aac.01208-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The treatment and control of schistosomiasis, a neglected disease that affects more than 200 million people worldwide, rely on the use of a single drug, praziquantel. A vaccine has yet to be developed and since new drug design and development is a lengthy and costly process, drug repurposing is a promising strategy. In this study, the efficacy of promethazine, a first-generation antihistamine, was evaluated against Schistosoma mansoni ex vivo and in a murine model of schistosomiasis. In vitro assays demonstrated that promethazine affected parasite motility, viability, and it induced severe tegumental damage in schistosomes. The LC50 of the drug was 5.84 μM. Similar to promethazine, schistosomes incubated with atropine, a classical anticholinergic drug, displayed reduced motor activity. In an animal model, promethazine treatment was introduced at an oral dose of 100 mg/kg for five successive days at different intervals from the time of infection, for the evaluation of the stage-specific susceptibility (pre-patent and patent infections). Various parasitological criteria indicated the in vivo antischistosomal effects of promethazine: there were significant reductions in worm burden, egg production, and hepato- and splenomegaly. The highest worm burden reduction was achieved with promethazine in patent infections (> 90%). Taken together, considering the importance of the repositioning of drugs in infectious diseases, especially those related to poverty, our data revealed the possibility of promethazine repositioning as an antischistosomal agent.
Collapse
|
104
|
Maciel LF, Morales-Vicente DA, Silveira GO, Ribeiro RO, Olberg GGO, Pires DS, Amaral MS, Verjovski-Almeida S. Weighted Gene Co-Expression Analyses Point to Long Non-Coding RNA Hub Genes at Different Schistosoma mansoni Life-Cycle Stages. Front Genet 2019; 10:823. [PMID: 31572441 PMCID: PMC6752179 DOI: 10.3389/fgene.2019.00823] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/09/2019] [Indexed: 01/21/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) (>200 nt) are expressed at levels lower than those of the protein-coding mRNAs, and in all eukaryotic model species where they have been characterized, they are transcribed from thousands of different genomic loci. In humans, some four dozen lncRNAs have been studied in detail, and they have been shown to play important roles in transcriptional regulation, acting in conjunction with transcription factors and epigenetic marks to modulate the tissue-type specific programs of transcriptional gene activation and repression. In Schistosoma mansoni, around 10,000 lncRNAs have been identified in previous works. However, the limited number of RNA-sequencing (RNA-seq) libraries that had been previously assessed, together with the use of old and incomplete versions of the S. mansoni genome and protein-coding transcriptome annotations, have hampered the identification of all lncRNAs expressed in the parasite. Here we have used 633 publicly available S. mansoni RNA-seq libraries from whole worms at different stages (n = 121), from isolated tissues (n = 24), from cell-populations (n = 81), and from single-cells (n = 407). We have assembled a set of 16,583 lncRNA transcripts originated from 10,024 genes, of which 11,022 are novel S. mansoni lncRNA transcripts, whereas the remaining 5,561 transcripts comprise 120 lncRNAs that are identical to and 5,441 lncRNAs that have gene overlap with S. mansoni lncRNAs already reported in previous works. Most importantly, our more stringent assembly and filtering pipeline has identified and removed a set of 4,293 lncRNA transcripts from previous publications that were in fact derived from partially processed mRNAs with intron retention. We have used weighted gene co-expression network analyses and identified 15 different gene co-expression modules. Each parasite life-cycle stage has at least one highly correlated gene co-expression module, and each module is comprised of hundreds to thousands lncRNAs and mRNAs having correlated co-expression patterns at different stages. Inspection of the top most highly connected genes within the modules’ networks has shown that different lncRNAs are hub genes at different life-cycle stages, being among the most promising candidate lncRNAs to be further explored for functional characterization.
Collapse
Affiliation(s)
- Lucas F Maciel
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil.,Programa Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
| | - David A Morales-Vicente
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Gilbert O Silveira
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Raphael O Ribeiro
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Giovanna G O Olberg
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - David S Pires
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Murilo S Amaral
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
105
|
Lu Z, Spänig S, Weth O, Grevelding CG. Males, the Wrongly Neglected Partners of the Biologically Unprecedented Male-Female Interaction of Schistosomes. Front Genet 2019; 10:796. [PMID: 31552097 PMCID: PMC6743411 DOI: 10.3389/fgene.2019.00796] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/30/2019] [Indexed: 01/18/2023] Open
Abstract
Schistosomes are the only platyhelminths that have evolved separate sexes, and they exhibit a unique reproductive biology because the female's sexual maturation depends on a constant pairing contact with the male. In the female, pairing leads to gonad differentiation, which is associated with substantial morphological changes, and controls among others the expression of gonad-associated genes. In the male, no morphological changes have been observed after pairing, although first data indicated an effect of pairing on gene transcription. Comprehensive transcriptomic approaches have revealed an unexpected high number of genes that are differentially transcribed in the male after pairing. Their identities suggest roles for the male that are not restricted to feeding and enhanced muscular power to transport paired female and, as assumed before, to induce its sexual maturation by one "magic" factor. Instead, a more complex picture emerges in which both partners live in a reciprocal sender-recipient relationship that not only affects the gonads of both genders but may also involve tactile stimuli, transforming growth factor β signaling, nutritional parts, and neuronal processes, including neuropeptides and G protein-coupled receptor signaling. This review provides a summary of transcriptomics including an overview of genes expressed in a pairing-dependent manner in schistosome males. This may stimulate further research in understanding the role of the male as the recipient of the female's signals upon pairing, the male's "capacitation," and its subsequent competence as a sender of information. The latter process finally transforms a sexually immature, autonomous female without completely developed gonads into a sexually mature, partially non-autonomous female with fully differentiated gonads and enormous egg production capacity.
Collapse
Affiliation(s)
- Zhigang Lu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Insitute for Parasitology, BFS, Justus Liebig University Giessen, Giessen, Germany
| | - Sebastian Spänig
- Department of Mathematics & Computer Science, University of Marburg, Marburg, Germany
| | - Oliver Weth
- Insitute for Parasitology, BFS, Justus Liebig University Giessen, Giessen, Germany
| | | |
Collapse
|
106
|
Lamolle G, Fontenla S, Rijo G, Tort JF, Smircich P. Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes. Front Genet 2019; 10:771. [PMID: 31543897 PMCID: PMC6739440 DOI: 10.3389/fgene.2019.00771] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/22/2019] [Indexed: 11/13/2022] Open
Abstract
In the present work, we performed a comparative genome-wide analysis of 22 species representative of the main clades and lifestyles of the phylum Platyhelminthes. We selected a set of 700 orthologous genes conserved in all species, measuring changes in GC content, codon, and amino acid usage in orthologous positions. Values of 3rd codon position GC spanned over a wide range, allowing to discriminate two distinctive clusters within freshwater turbellarians, Cestodes and Trematodes respectively. Furthermore, a hierarchical clustering of codon usage data differs remarkably from the phylogenetic tree. Additionally, we detected a synonymous codon usage bias that was more dramatic in extreme GC-poor or GC-rich genomes, i.e., GC-poor Schistosomes preferred to use AT-rich terminated synonymous codons, while GC-rich M. lignano showed the opposite behavior. Interestingly, these biases impacted the amino acidic usage, with preferred amino acids encoded by codons following the GC content trend. These are associated with non-synonymous substitutions at orthologous positions. The detailed analysis of the synonymous and non-synonymous changes provides evidence for a two-hit mechanism where both mutation and selection forces drive the diverse coding strategies of flatworms.
Collapse
Affiliation(s)
- Guillermo Lamolle
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Gastón Rijo
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Jose F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, IIBCE, MEC, Montevideo, Uruguay.,Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la Republica, UDELAR, Montevideo, Uruguay
| |
Collapse
|
107
|
Stroehlein AJ, Korhonen PK, Chong TM, Lim YL, Chan KG, Webster B, Rollinson D, Brindley PJ, Gasser RB, Young ND. High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing. Gigascience 2019; 8:giz108. [PMID: 31494670 PMCID: PMC6736295 DOI: 10.1093/gigascience/giz108] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/25/2019] [Accepted: 08/10/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease affecting >100 million people worldwide. Chronic infection with this parasitic trematode can lead to urogenital conditions including female genital schistosomiasis and bladder cancer. At the molecular level, little is known about this blood fluke and the pathogenesis of the disease that it causes. To support molecular studies of this carcinogenic worm, we reported a draft genome for S. haematobium in 2012. Although a useful resource, its utility has been somewhat limited by its fragmentation. FINDINGS Here, we systematically enhanced the draft genome of S. haematobium using a single-molecule and long-range DNA-sequencing approach. We achieved a major improvement in the accuracy and contiguity of the genome assembly, making it superior or comparable to assemblies for other schistosome species. We transferred curated gene models to this assembly and, using enhanced gene annotation pipelines, inferred a gene set with as many or more complete gene models as those of other well-studied schistosomes. Using conserved, single-copy orthologs, we assessed the phylogenetic position of S. haematobium in relation to other parasitic flatworms for which draft genomes were available. CONCLUSIONS We report a substantially enhanced genomic resource that represents a solid foundation for molecular research on S. haematobium and is poised to better underpin population and functional genomic investigations and to accelerate the search for new disease interventions.
Collapse
Affiliation(s)
- Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
| | - Teik Min Chong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Yan Lue Lim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Bonnie Webster
- Parasites and Vectors Division, The Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
| | - David Rollinson
- Parasites and Vectors Division, The Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
| | - Paul J Brindley
- School of Medicine & Health Sciences, Department of Microbiology, Immunology & Tropical Medicine, George Washington University, 2300 Eye Street, NW, Suite 502, Washington, DC 20037, USA
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
| |
Collapse
|
108
|
Discovery of novel Schistosoma mansoni PDE4A inhibitors as potential agents against schistosomiasis. Future Med Chem 2019; 11:1703-1720. [PMID: 31370708 DOI: 10.4155/fmc-2018-0592] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Aim: Due to the urgent need for effective drugs to treat schistosomiasis that act through a known molecular mechanism of action, we focused on a target-based approach with the aim to discover inhibitors of a cyclic nucleotide phosphodiesterase from Schistosoma mansoni (SmPDE4A). Materials & methods: To discover new inhibitors of SmPDE4A homology models of the enzyme structure were constructed based on known human and protozoan homologs. The best two models were selected for subsequent virtual screening of our in-house chemical library. Results & conclusion: A total of 25 library compounds were selected for experimental confirmation as SmPDE4A inhibitors and after dose-response experiments, three top hits were identified. The results presented validate the virtual screening approach to identify new inhibitors for clinically relevant phosphodiesterases.
Collapse
|
109
|
Caffrey CR, El‐Sakkary N, Mäder P, Krieg R, Becker K, Schlitzer M, Drewry DH, Vennerstrom JL, Grevelding CG. Drug Discovery and Development for Schistosomiasis. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/9783527808656.ch8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
110
|
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.
Collapse
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
| |
Collapse
|
111
|
Doenhoff MJ, Modha J, Walker AJ. Failure of in vitro-cultured schistosomes to produce eggs: how does the parasite meet its needs for host-derived cytokines such as TGF-β? Int J Parasitol 2019; 49:747-757. [PMID: 31348959 DOI: 10.1016/j.ijpara.2019.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/03/2019] [Accepted: 05/09/2019] [Indexed: 12/20/2022]
Abstract
When adult schistosome worm pairs are transferred from experimental hosts to in vitro culture they cease producing viable eggs within a few days. Female worms in unisexual infections fail to mature, and when mature adult females are separated from male partners they regress sexually. Worms cultured from the larval stage are also permanently reproductively defective. The cytokine transforming growth factor beta derived from the mammalian host is considered important in stimulating schistosome female worm maturation and maintenance of fecundity. The means by which schistosomes acquire TGF-β have not been elucidated, but direct uptake in vivo seems unlikely as the concentration of free, biologically active cytokine in host blood is very low. Here we review the complexities of schistosome development and male-female interactions, and we speculate about two possibilities on how worms obtain the TGF-β they are assumed to need: (i) worms may have mechanisms to free active cytokine from the latency-inducing complex of proteins in which it is associated, and/or (ii) they may obtain the cytokine from alpha 2-macroglobulin, a blood-borne protease inhibitor to which TGF-β can bind. These ideas are experimentally testable.
Collapse
Affiliation(s)
- Michael J Doenhoff
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Jay Modha
- Modha Biomedical Ltd, 9B St Cuthberts Avenue, Great Glen, Leicester LE8 9EJ, UK
| | - Anthony J Walker
- Molecular Parasitology Laboratory, School of Life Sciences Pharmacy and Chemistry, Kingston University, Kingston University, Penrhyn Road, Kingston upon Thames, Surrey KT1 2EE, UK
| |
Collapse
|
112
|
Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. Dosage Compensation throughout the Schistosoma mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome. Genome Biol Evol 2019; 11:1909-1922. [PMID: 31273378 PMCID: PMC6628874 DOI: 10.1093/gbe/evz133] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2019] [Indexed: 12/12/2022] Open
Abstract
Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3, and H4K20me1 histone marks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.
Collapse
Affiliation(s)
- Marion A L Picard
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - David Roquis
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Ingo Bulla
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Ronaldo C Augusto
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Nathalie Arancibia
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Christoph Grunau
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Jérôme Boissier
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| | - Céline Cosseau
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier, Perpignan, France
| |
Collapse
|
113
|
Haeberlein S, Angrisano A, Quack T, Lu Z, Kellershohn J, Blohm A, Grevelding CG, Hahnel SR. Identification of a new panel of reference genes to study pairing-dependent gene expression in Schistosoma mansoni. Int J Parasitol 2019; 49:615-624. [PMID: 31136746 DOI: 10.1016/j.ijpara.2019.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/09/2019] [Accepted: 01/15/2019] [Indexed: 12/18/2022]
Abstract
Facilitated by the Schistosoma mansoni genome project, multiple transcriptomic studies were performed over the last decade to elucidate gene expression patterns among different developmental stages of the complex schistosome life cycle. While these analyses enable the identification of candidate genes with key functions in schistosome biology, a diverse molecular tool set is needed that allows comprehensive functional characterization at the single gene level. This includes the availability of reliable reference genes to confirm changes in the transcription of genes of interest over different biological samples and experimental conditions. In particular, the investigation of one key aspect of schistosome biology, the pairing-dependent gene expression in females and males, requires knowledge on reference genes that are expressed independently of both pairing and of in vitro culture effects. Therefore, the present study focused on the identification of quantitative reverse transcription (qRT)-PCR reference genes suitable for the investigation of pairing-dependent gene expression in the S. mansoni male. The "pipeline" we present here is based on qRT-PCR analyses of high biological replication combined with three different statistical analysis tools, BestKeeper, geNorm, and NormFinder. Our approach resulted in a statistically robust ranking of 15 selected reference genes with respect to their transcription stability between pairing-unexperienced and -experienced males. We further tested the top seven candidate genes for their transcription stability during invitro culture of adult S. mansoni. Of these, the two most suitable reference genes were used to investigate the influence of the pairing contact on the transcription of genes of interest, comprising a tyrosine decarboxylase gene Smtdc1, an ebony ortholog Smebony, and the follistatin ortholog Smfst in S. mansoni males. Performing pairing, separation and re-pairing experiments with adult S. mansoni in vitro, our results indicate for the first time that pairing can act as a molecular on/off-switch of specific genes to strictly control their expression in schistosome males.
Collapse
Affiliation(s)
- Simone Haeberlein
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | | | - Thomas Quack
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | - Zhigang Lu
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Josina Kellershohn
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | - Ariane Blohm
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany
| | | | - Steffen R Hahnel
- Institute of Parasitology, BFS, Justus-Liebig-University, Giessen, Germany.
| |
Collapse
|
114
|
Guliaev AS, Semyenova SK. MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies. Mob DNA 2019; 10:21. [PMID: 31114637 PMCID: PMC6515669 DOI: 10.1186/s13100-019-0163-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/26/2019] [Indexed: 12/17/2022] Open
Abstract
Background Genomes of eukaryotes are inhabited by myriads of mobile genetic elements (MGEs) – transposons and retrotransposons - which play a great role in genome plasticity and evolution. A lot of computational tools were developed to annotate them either in genomic assemblies or raw reads using de novo or homology-based approaches. But there has been no pipeline enabling users to get coding and flanking sequences of MGEs suitable for a downstream analysis from genome assemblies. Results We developed a new pipeline, MGERT (Mobile Genetic Elements Retrieving Tool), that automates all the steps necessary to obtain protein-coding sequences of mobile genetic elements from genomic assemblies even if no previous knowledge on MGE content of a particular genome is available. Conclusions Using MGERT, researchers can easily find MGEs, their coding and flanking sequences in the genome of interest. Thus, this pipeline helps researchers to focus on the biological analysis of MGEs rather than excessive scripting and pipelining. Electronic supplementary material The online version of this article (10.1186/s13100-019-0163-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Andrei S Guliaev
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilov Str., 34/5, Moscow, 119334 Russia
| | - Seraphima K Semyenova
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilov Str., 34/5, Moscow, 119334 Russia
| |
Collapse
|
115
|
Ershov NI, Mordvinov VA, Prokhortchouk EB, Pakharukova MY, Gunbin KV, Ustyantsev K, Genaev MA, Blinov AG, Mazur A, Boulygina E, Tsygankova S, Khrameeva E, Chekanov N, Fan G, Xiao A, Zhang H, Xu X, Yang H, Solovyev V, Lee SMY, Liu X, Afonnikov DA, Skryabin KG. New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes. BMC Genomics 2019; 20:399. [PMID: 31117933 PMCID: PMC6530080 DOI: 10.1186/s12864-019-5752-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
Background The three epidemiologically important Opisthorchiidae liver flukes Opisthorchis felineus, O. viverrini, and Clonorchis sinensis, are believed to harbour similar potencies to provoke hepatobiliary diseases in their definitive hosts, although their populations have substantially different ecogeographical aspects including habitat, preferred hosts, population structure. Lack of O. felineus genomic data is an obstacle to the development of comparative molecular biological approaches necessary to obtain new knowledge about the biology of Opisthorchiidae trematodes, to identify essential pathways linked to parasite-host interaction, to predict genes that contribute to liver fluke pathogenesis and for the effective prevention and control of the disease. Results Here we present the first draft genome assembly of O. felineus and its gene repertoire accompanied by a comparative analysis with that of O. viverrini and Clonorchis sinensis. We observed both noticeably high heterozygosity of the sequenced individual and substantial genetic diversity in a pooled sample. This indicates that potency of O. felineus population for rapid adaptive response to control and preventive measures of opisthorchiasis is higher than in O. viverrini and C. sinensis. We also have found that all three species are characterized by more intensive involvement of trans-splicing in RNA processing compared to other trematodes. Conclusion All revealed peculiarities of structural organization of genomes are of extreme importance for a proper description of genes and their products in these parasitic species. This should be taken into account both in academic and applied research of epidemiologically important liver flukes. Further comparative genomics studies of liver flukes and non-carcinogenic flatworms allow for generation of well-grounded hypotheses on the mechanisms underlying development of cholangiocarcinoma associated with opisthorchiasis and clonorchiasis as well as species-specific mechanisms of these diseases. Electronic supplementary material The online version of this article (10.1186/s12864-019-5752-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nikita I Ershov
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia.
| | | | - Egor B Prokhortchouk
- Russian Federal Research Center for Biotechnology, 33/2 Leninsky prospect, Moscow, 119071, Russia. .,ZAO Genoanalytica, 1 Leninskie Gory street, Moscow, 119234, Russia.
| | - Mariya Y Pakharukova
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia.,Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
| | - Konstantin V Gunbin
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Kirill Ustyantsev
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Mikhail A Genaev
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Alexander G Blinov
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Alexander Mazur
- Russian Federal Research Center for Biotechnology, 33/2 Leninsky prospect, Moscow, 119071, Russia
| | | | | | | | - Nikolay Chekanov
- Russian Federal Research Center for Biotechnology, 33/2 Leninsky prospect, Moscow, 119071, Russia
| | - Guangyi Fan
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - An Xiao
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - He Zhang
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Huanming Yang
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Victor Solovyev
- Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY, 10549, USA
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Xin Liu
- BGI-Shenzhen, 11 Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Dmitry A Afonnikov
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave, Novosibirsk, 630090, Russia.,Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
| | - Konstantin G Skryabin
- Russian Federal Research Center for Biotechnology, 33/2 Leninsky prospect, Moscow, 119071, Russia.,Federal Research Center Kurchatov Institute, Moscow, Russia
| |
Collapse
|
116
|
Sotillo J, Pearson MS, Becker L, Mekonnen GG, Amoah AS, van Dam G, Corstjens PLAM, Murray J, Mduluza T, Mutapi F, Loukas A. In-depth proteomic characterization of Schistosoma haematobium: Towards the development of new tools for elimination. PLoS Negl Trop Dis 2019; 13:e0007362. [PMID: 31091291 PMCID: PMC6538189 DOI: 10.1371/journal.pntd.0007362] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/28/2019] [Accepted: 04/05/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Schistosomiasis is a neglected disease affecting hundreds of millions worldwide. Of the three main species affecting humans, Schistosoma haematobium is the most common, and is the leading cause of urogenital schistosomiasis. S. haematobium infection can cause different urogenital clinical complications, particularly in the bladder, and furthermore, this parasite has been strongly linked with squamous cell carcinoma. A comprehensive analysis of the molecular composition of its different proteomes will contribute to developing new tools against this devastating disease. METHODS AND FINDINGS By combining a comprehensive protein fractionation approach consisting of OFFGEL electrophoresis with high-throughput mass spectrometry, we have performed the first in-depth characterisation of the different discrete proteomes of S. haematobium that are predicted to interact with human host tissues, including the secreted and tegumental proteomes of adult flukes and secreted and soluble egg proteomes. A total of 662, 239, 210 and 138 proteins were found in the adult tegument, adult secreted, soluble egg and secreted egg proteomes, respectively. In addition, we probed these distinct proteomes with urine to assess urinary antibody responses from naturally infected human subjects with different infection intensities, and identified adult fluke secreted and tegument extracts as being the best predictors of infection. CONCLUSION We provide a comprehensive dataset of proteins from the adult and egg stages of S. haematobium and highlight their utility as diagnostic markers of infection intensity. Protein composition was markedly different between the different extracts, highlighting the distinct subsets of proteins that different development stages present in their different niches. Furthermore, we have identified adult fluke ES and tegument extracts as best predictors of infection using urine antibodies of naturally infected people. This study provides the first steps towards the development of novel tools to control this important neglected tropical disease.
Collapse
Affiliation(s)
- Javier Sotillo
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
- Laboratorio de Referencia en Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mark S. Pearson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Luke Becker
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Gebeyaw G. Mekonnen
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Abena S. Amoah
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Govert van Dam
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Paul L. A. M. Corstjens
- Department of Molecular Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Janice Murray
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, King's Buildings, Edinburgh, United Kingdom
| | - Takafira Mduluza
- Biochemistry Department, University of Zimbabwe, Mount Pleasant, Harare, Zimbabwe
- TIBA Partnership, NIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), University of Zimbabwe
| | - Francisca Mutapi
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, King's Buildings, Edinburgh, United Kingdom
- TIBA Partnership, NIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), University of Zimbabwe
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| |
Collapse
|
117
|
Lombardo FC, Pasche V, Panic G, Endriss Y, Keiser J. Life cycle maintenance and drug-sensitivity assays for early drug discovery in Schistosoma mansoni. Nat Protoc 2019; 14:461-481. [PMID: 30610241 DOI: 10.1038/s41596-018-0101-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Drug discovery for schistosomiasis is still limited to a handful of academic laboratories worldwide, with only a few novel antischistosomal lead compounds being actively researched. Despite recent international mobilization against the disease to stimulate and promote antischistosomal drug discovery, setting up a drug-screening flow with schistosome parasites remains challenging. Whereas numerous different protocols to obtain and cultivate schistosomes have been published, those describing the drug-screening process are scarce, and none gather together parasite cultivation and early drug discovery procedures. To help overcome this hurdle, we provide here a set of integrated methods either adapted from already-published protocols or based on our long-term experience in schistosomiasis research. Specifically, we detail the establishment and maintenance of the complex and several-week-long Schistosoma mansoni life cycle in a laboratory setting, as well as the means of retrieving and culturing the parasites at their relevant life stages. The in vitro and in vivo assays that are performed along the drug-screening cascade are also described. In these assays, which can be performed within 5 d, the effect of a drug is determined by phenotypic assessment of the parasites' viability and morphology, for which stage-specific scoring scales are proposed. Finally, the modalities for testing and evaluating a compound in vivo, constituting a procedure lasting up to 10 weeks, are presented in order to go from in vitro hit identification to the selection of early lead candidates.
Collapse
Affiliation(s)
- Flavio C Lombardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Valérian Pasche
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Gordana Panic
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Yvette Endriss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Jennifer Keiser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| |
Collapse
|
118
|
Vaca HR, Celentano AM, Macchiaroli N, Kamenetzky L, Camicia F, Rosenzvit MC. Histone deacetylase enzymes as potential drug targets of Neglected Tropical Diseases caused by cestodes. Int J Parasitol Drugs Drug Resist 2019; 9:120-132. [PMID: 30897528 PMCID: PMC6426703 DOI: 10.1016/j.ijpddr.2019.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 02/06/2023]
Abstract
Cestode parasites cause neglected diseases, such as echinococcosis and cysticercosis, which represent a significant problem in human and animal health. Benzimidazoles and praziquantel are the only available drugs for chemotherapy and it is therefore important to identify new alternative drugs against cestode parasites. Histone deacetylases (HDACs) are validated drug targets for the treatment of cancer and other diseases, including neglected diseases. However, knowledge of HDACs in cestodes is very scarce. In this work, we investigated cestode HDACs as potential drug targets to develop new therapies against neglected diseases caused by cestodes. Here we showed the full repertoire of HDAC coding genes in several members of the class Cestoda. Between 6 and 7 zinc-dependent HDAC coding genes were identified in the genomes of species from Echinococcus, Taenia, Mesocestoides and Hymenolepis genera. We classified them as Class I and II HDACs and analyzed their transcriptional expression levels throughout developmental stages of Echinococcus spp. We confirmed for the first time the complete HDAC8 nucleotide sequences from Echinococcus canadensis G7 and Mesocestoides corti. Homology models for these proteins showed particular structural features which differentiate them from HDAC8 from Homo sapiens. Furthermore, we showed that Trichostatin A (TSA), a pan-HDAC inhibitor, decreases the viability of M. corti, alters its tegument and morphology and produces an increment of the total amount of acetylated proteins, including acetylated histone H4. These results suggest that HDAC from cestodes are functional and might play important roles on survival and development. The particular structural features observed in cestode HDAC8 proteins suggest that these enzymes could be selectively targeted. This report provides the basis for further studies on cestode HDAC enzymes and for discovery of new HDAC inhibitors for the treatment of neglected diseases caused by cestode parasites.
Collapse
Affiliation(s)
- Hugo R Vaca
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Piso 13, Paraguay 2155, CP1121, Buenos Aires, Argentina
| | - Ana M Celentano
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Piso 13, Paraguay 2155, CP1121, Buenos Aires, Argentina; Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires (UBA), Piso 13, Paraguay 2155, CP1121, Buenos Aires, Argentina
| | - Natalia Macchiaroli
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Piso 13, Paraguay 2155, CP1121, Buenos Aires, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Piso 13, Paraguay 2155, CP1121, Buenos Aires, Argentina
| | - Federico Camicia
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Piso 13, Paraguay 2155, CP1121, Buenos Aires, Argentina.
| | - Mara C Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Piso 13, Paraguay 2155, CP1121, Buenos Aires, Argentina.
| |
Collapse
|
119
|
Haem Biology in Metazoan Parasites - 'The Bright Side of Haem'. Trends Parasitol 2019; 35:213-225. [PMID: 30686614 DOI: 10.1016/j.pt.2019.01.001] [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: 12/14/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/12/2022]
Abstract
Traditionally, host haem has been recognized as a cytotoxic molecule that parasites need to eliminate or detoxify in order to survive. However, recent evidence indicates that some lineages of parasites have lost genes that encode enzymes involved specifically in endogenous haem biosynthesis. Such lineages thus need to acquire and utilize haem originating from their host animal, making it an indispensable molecule for their survival and reproduction. In multicellular parasites, host haem needs to be systemically distributed throughout their bodies to meet the haem demands in all cell and tissue types. Host haem also gets deposited in parasite eggs, enabling embryogenesis and reproduction. Clearly, a better understanding of haem biology in multicellular parasites should elucidate organismal adaptations to obligatory blood-feeding.
Collapse
|
120
|
Avelar LDGA, Gava SG, Neves RH, Silva MCS, Araújo N, Tavares NC, Khal AE, Mattos ACA, Machado-Silva JR, Oliveira G, Mourão MDM. Smp38 MAP Kinase Regulation in Schistosoma mansoni: Roles in Survival, Oviposition, and Protection Against Oxidative Stress. Front Immunol 2019; 10:21. [PMID: 30733716 PMCID: PMC6353789 DOI: 10.3389/fimmu.2019.00021] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/07/2019] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic protein kinases (ePKs) are good medical targets for drug development in different biological systems. ePKs participate in many cellular processes, including the p38 MAPK regulation of homeostasis upon oxidative stress. We propose to assess the role of Smp38 MAPK signaling pathway in Schistosoma mansoni development and protection against oxidative stress, parasite survival, and also to elucidate which target genes have their expression regulated by Smp38 MAPK. After a significant reduction of up to 84% in the transcription level by Smp38 MAPK gene knockdown, no visible phenotypic changes were reported in schistosomula in culture. The development of adult worms was tested in vivo in mice infected with the Smp38 knocked-down schistosomula. It was observed that Smp38 MAPK has an essential role in the transformation and survival of the parasites as a low number of adult worms was recovered. Smp38 knockdown also resulted in decreased egg production, damaged adult worm tegument, and underdeveloped ovaries in females. Furthermore, only ~13% of the eggs produced developed into mature eggs. Our results suggest that inhibition of the Smp38 MAPK activity interfere in parasites protection against reactive oxygen species. Smp38 knockdown in adult worms resulted in 80% reduction in transcription levels on the 10th day, with consequent reduction of 94.4% in oviposition in vitro. In order to search for Smp38 MAPK pathway regulated genes, we used an RNASeq approach and identified 1,154 DEGs in Smp38 knockdown schistosomula. A substantial proportion of DEGs encode proteins with unknown function. The results indicate that Smp38 regulates essential signaling pathways for the establishment of parasite homeostasis, including genes related to antioxidant defense, structural composition of ribosomes, spliceosomes, cytoskeleton, as well as, purine and pyrimidine metabolism pathways. Our data show that the Smp38 MAPK signaling pathway is a critical route for parasite development and may present attractive therapeutic targets for the treatment and control of schistosomiasis.
Collapse
Affiliation(s)
- Lívia das Graças Amaral Avelar
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Brazil.,Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ, Belo Horizonte, Brazil
| | - Sandra Grossi Gava
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Brazil.,Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ, Belo Horizonte, Brazil
| | - Renata Heisler Neves
- Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Neusa Araújo
- Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ, Belo Horizonte, Brazil
| | | | - Assmaa El Khal
- Instituto René Rachou, Fundação Oswaldo Cruz-FIOCRUZ, Belo Horizonte, Brazil
| | | | | | | | | |
Collapse
|
121
|
Oey H, Zakrzewski M, Gravermann K, Young ND, Korhonen PK, Gobert GN, Nawaratna S, Hasan S, Martínez DM, You H, Lavin M, Jones MK, Ragan MA, Stoye J, Oleaga A, Emery AM, Webster BL, Rollinson D, Gasser RB, McManus DP, Krause L. Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium. PLoS Pathog 2019; 15:e1007513. [PMID: 30673782 PMCID: PMC6361461 DOI: 10.1371/journal.ppat.1007513] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 02/04/2019] [Accepted: 12/07/2018] [Indexed: 11/18/2022] Open
Abstract
Mesenteric infection by the parasitic blood fluke Schistosoma bovis is a common veterinary problem in Africa and the Middle East and occasionally in the Mediterranean Region. The species also has the ability to form interspecific hybrids with the human parasite S. haematobium with natural hybridisation observed in West Africa, presenting possible zoonotic transmission. Additionally, this exchange of alleles between species may dramatically influence disease dynamics and parasite evolution. We have generated a 374 Mb assembly of the S. bovis genome using Illumina and PacBio-based technologies. Despite infecting different hosts and organs, the genome sequences of S. bovis and S. haematobium appeared strikingly similar with 97% sequence identity. The two species share 98% of protein-coding genes, with an average sequence identity of 97.3% at the amino acid level. Genome comparison identified large continuous parts of the genome (up to several 100 kb) showing almost 100% sequence identity between S. bovis and S. haematobium. It is unlikely that this is a result of genome conservation and provides further evidence of natural interspecific hybridization between S. bovis and S. haematobium. Our results suggest that foreign DNA obtained by interspecific hybridization was maintained in the population through multiple meiosis cycles and that hybrids were sexually reproductive, producing viable offspring. The S. bovis genome assembly forms a highly valuable resource for studying schistosome evolution and exploring genetic regions that are associated with species-specific phenotypic traits. In this article we detail the assembly and functional annotation of the Schistosoma bovis genome. S. bovis is a parasitic flatworm that primarily infects bovines, with important economic consequences in affected countries. However, it is also a close relative of the human carcinogenic parasite Schistosoma haematobium which is a serious health issue in many endemic countries in Sub-Saharan Africa. The close relationship and overlapping geographical distribution of S. bovis and S. haematobium allows these to hybridise in the wild increasing their genetic diversity and presenting the risk of zoonotic transmission, i.e. the transmission from animals to humans. The hybridization between human and ruminant schistosomes is of particular interest as interspecific hybridization may have dramatic impacts on transmission rates, disease dynamics, control interventions and parasite evolution. By whole-genome sequencing and comparative genomics we present evidence that fertile hybrids are indeed present in the wild, presenting the potential risk of transmission from animal reservoirs to humans.
Collapse
Affiliation(s)
- Harald Oey
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Martha Zakrzewski
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kerstin Gravermann
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Geoffrey N. Gobert
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Sujeevi Nawaratna
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Shihab Hasan
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - David M. Martínez
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Hong You
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Martin Lavin
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Malcolm K. Jones
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Veterinary Science, University of Queensland, Gatton, QLD, Australia
| | - Mark A. Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Jens Stoye
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Ana Oleaga
- Institute of Natural Resources and Agrobiology (IRNASA, CSIC), Cordel de Merinas, Salamanca, Spain
| | - Aidan M. Emery
- Natural History Museum, Life Sciences Department, Parasites and Vectors Division, Cromwell Road, London, United Kingdom
| | - Bonnie L. Webster
- Natural History Museum, Life Sciences Department, Parasites and Vectors Division, Cromwell Road, London, United Kingdom
| | - David Rollinson
- Natural History Museum, Life Sciences Department, Parasites and Vectors Division, Cromwell Road, London, United Kingdom
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Donald P. McManus
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Lutz Krause
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- * E-mail:
| |
Collapse
|
122
|
Ittiprasert W, Mann VH, Karinshak SE, Coghlan A, Rinaldi G, Sankaranarayanan G, Chaidee A, Tanno T, Kumkhaek C, Prangtaworn P, Mentink-Kane MM, Cochran CJ, Driguez P, Holroyd N, Tracey A, Rodpai R, Everts B, Hokke CH, Hoffmann KF, Berriman M, Brindley PJ. Programmed genome editing of the omega-1 ribonuclease of the blood fluke, Schistosoma mansoni. eLife 2019; 8:41337. [PMID: 30644357 PMCID: PMC6355194 DOI: 10.7554/elife.41337] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/12/2018] [Indexed: 12/23/2022] Open
Abstract
CRISPR/Cas9-based genome editing has yet to be reported in species of the Platyhelminthes. We tested this approach by targeting omega-1 (ω1) of Schistosoma mansoni as proof of principle. This secreted ribonuclease is crucial for Th2 polarization and granuloma formation. Schistosome eggs were exposed to Cas9 complexed with guide RNA complementary to ω1 by electroporation or by transduction with lentiviral particles. Some eggs were also transfected with a single stranded donor template. Sequences of amplicons from gene-edited parasites exhibited Cas9-catalyzed mutations including homology directed repaired alleles, and other analyses revealed depletion of ω1 transcripts and the ribonuclease. Gene-edited eggs failed to polarize Th2 cytokine responses in macrophage/T-cell co-cultures, while the volume of pulmonary granulomas surrounding ω1-mutated eggs following tail-vein injection into mice was vastly reduced. Knock-out of ω1 and the diminished levels of these cytokines following exposure showcase the novel application of programmed gene editing for functional genomics in schistosomes. Schistosomiasis is a tropical disease that can cause serious health problems, including damage to the liver and kidneys, infertility and bladder cancer. Nearly a quarter billion people are currently infected, mostly in poor regions of sub-Saharan Africa, the Philippines and Brazil. A freshwater worm known as Schistosoma mansoni causes the disease. These parasites enter the human body by burrowing into the skin; once in the bloodstream, they move to various organs where they rapidly start to reproduce. Their eggs release several molecules, including a protein known as omega-1 ribonuclease, which can damage the surrounding tissues. A gene editing technique called CRISPR/Cas9 allows scientists to precisely target and then deactivate the genetic information a cell needs to produce a given protein. While the tool has been used in other species before, it was unknown if it could be applied to S. mansoni. Here, Ittiprasert et al. harnessed CRISPR/Cas9 to deactivate the gene that codes for omega-1 ribonuclease and create parasites that do not produce the protein, or only very little of it. The experiments showed that mice infected with the gene-edited worm eggs displayed far fewer symptoms of schistosomiasis compared to those that carry the non-edited parasites. Alongside this work, Arunsan et al. used CRISPR/Cas9 to inactivate a gene in another species of worm that can cause liver cancer in humans. Together, these findings demonstrate for the first time that the gene editing method can be adapted for use in parasitic flatworms, which are a major public health problem in tropical climates. This tool should help scientists understand how the parasites invade and damage our bodies, and provide new ideas for treatment and disease control.
Collapse
Affiliation(s)
- Wannaporn Ittiprasert
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States.,Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
| | - Victoria H Mann
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States.,Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
| | - Shannon E Karinshak
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
| | - Avril Coghlan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Gabriel Rinaldi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Apisit Chaidee
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States.,Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Toshihiko Tanno
- Department of Surgery, University of Maryland, Baltimore, United States.,Institute of Human Virology, University of Maryland, Baltimore, United States
| | - Chutima Kumkhaek
- Cellular and Molecular Therapeutics Laboratory, National Heart, Lungs and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Pannathee Prangtaworn
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States.,Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Christina J Cochran
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
| | - Patrick Driguez
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Rutchanee Rodpai
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Bart Everts
- Department of Parasitology, Leiden University Medical Center, Leiden, Netherlands
| | - Cornelis H Hokke
- Department of Parasitology, Leiden University Medical Center, Leiden, Netherlands
| | - Karl F Hoffmann
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Paul J Brindley
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
| |
Collapse
|
123
|
Gemma S, Federico S, Brogi S, Brindisi M, Butini S, Campiani G. Dealing with schistosomiasis: Current drug discovery strategies. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2019. [DOI: 10.1016/bs.armc.2019.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
124
|
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.
Collapse
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
| |
Collapse
|
125
|
Abstract
Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we report a broad comparative study of 81 genomes of parasitic and non-parasitic worms. We have identified gene family births and hundreds of expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed. We reveal extensive lineage-specific differences in core metabolism and protein families historically targeted for drug development. From an in silico screen, we have identified and prioritized new potential drug targets and compounds for testing. This comparative genomics resource provides a much-needed boost for the research community to understand and combat parasitic worms.
Collapse
|
126
|
Philippsen GS, DeMarco R. Impact of transposable elements in the architecture of genes of the human parasite Schistosoma mansoni. Mol Biochem Parasitol 2018; 228:27-31. [PMID: 30597185 DOI: 10.1016/j.molbiopara.2018.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 12/06/2018] [Accepted: 12/27/2018] [Indexed: 01/26/2023]
Abstract
The parasites belonging to the genus Schistosoma are agents of schistosomiasis, a disease estimated as affecting 235 million people in the world. To better understand the structure of Schistosoma mansoni genome, transposable elements (TEs) distribution and impact on gene structures were investigated. Our analyses indicated a differential distribution of TEs throughout the gene structure. Introns located at the 5' end of the genes are less prone to display TEs and introns lacking TEs tend to be shorter. Therefore, this could be one of the factors explaining previous data showing that S. mansoni displays shorter introns near the 5' end of the genes. Identification of six genes harboring TEs in their coding region suggests a positive contribution for the evolution of proteome repertory of S. mansoni. Taken together, our data suggest significant contributions of TEs to the architecture of genes from S. mansoni.
Collapse
Affiliation(s)
- Gisele S Philippsen
- Universidade Federal do Paraná, Jandaia do Sul, Dr. Maximiano street, n. 426, Paraná, Brazil.
| | - Ricardo DeMarco
- Departamento de Física e Ciência Interdisciplinar, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| |
Collapse
|
127
|
Stroehlein AJ, Gasser RB, Hall RS, Young ND. Interactive online application for the prediction, ranking and prioritisation of drug targets in Schistosoma haematobium. Parasit Vectors 2018; 11:605. [PMID: 30482220 PMCID: PMC6257948 DOI: 10.1186/s13071-018-3197-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/12/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Human schistosomiasis is a neglected tropical disease caused by parasitic worms of the genus Schistosoma that still affects some 200 million people. The mainstay of schistosomiasis control is a single drug, praziquantel. The reliance on this drug carries a risk of resistance emerging to this anthelmintic, such that research towards alternative anti-schistosomal drugs is warranted. In this context, a number of studies have employed computational approaches to prioritise proteins for investigation as drug targets, based on extensive genomic, transcriptomic and small-molecule data now available. METHODS Here, we established a customisable, online application for the prioritisation of drug targets and applied it, for the first time, to the entire inferred proteome of S. haematobium. This application enables selection of weighted and ranked proteins representing potential drug targets, and integrates transcriptional data, orthology and gene essentiality information as well as drug-drug target associations and chemical properties of predicted ligands. RESULTS Using this application, we defined 25 potential drug targets in S. haematobium that associated with approved drugs, and 3402 targets that (although they could not be linked to any compounds) are conserved among a range of socioeconomically important flatworm species and might represent targets for new trematocides. CONCLUSIONS The online application developed here represents an interactive, customisable, expandable and reproducible drug target ranking and prioritisation approach that should be useful for the prediction of drug targets in schistosomes and other species of parasitic worms in the future. We have demonstrated the utility of this online application by predicting potential drug targets in S. haematobium that can now be evaluated using functional genomics tools and/or small molecules, to establish whether they are indeed essential for parasite survival, and to assist in the discovery of novel anti-schistosomal compounds.
Collapse
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
| | - Robin B. Gasser
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010 Australia
| | - Ross S. Hall
- 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
| |
Collapse
|
128
|
Olson PD, Zarowiecki M, James K, Baillie A, Bartl G, Burchell P, Chellappoo A, Jarero F, Tan LY, Holroyd N, Berriman M. Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms. EvoDevo 2018; 9:21. [PMID: 30455861 PMCID: PMC6225667 DOI: 10.1186/s13227-018-0110-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 10/05/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tapeworms are agents of neglected tropical diseases responsible for significant health problems and economic loss. They also exhibit adaptations to a parasitic lifestyle that confound comparisons of their development with other animals. Identifying the genetic factors regulating their complex ontogeny is essential to understanding unique aspects of their biology and for advancing novel therapeutics. Here we use RNA sequencing to identify up-regulated signalling components, transcription factors and post-transcriptional/translational regulators (genes of interest, GOI) in the transcriptomes of Larvae and different regions of segmented worms in the tapeworm Hymenolepis microstoma and combine this with spatial gene expression analyses of a selection of genes. RESULTS RNA-seq reads collectively mapped to 90% of the > 12,000 gene models in the H. microstoma v.2 genome assembly, demonstrating that the transcriptome profiles captured a high percentage of predicted genes. Contrasts made between the transcriptomes of Larvae and whole, adult worms, and between the Scolex-Neck, mature strobila and gravid strobila, resulted in 4.5-30% of the genes determined to be differentially expressed. Among these, we identified 190 unique GOI up-regulated in one or more contrasts, including a large range of zinc finger, homeobox and other transcription factors, components of Wnt, Notch, Hedgehog and TGF-β/BMP signalling, and post-transcriptional regulators (e.g. Boule, Pumilio). Heatmap clusterings based on overall expression and on select groups of genes representing 'signals' and 'switches' showed that expression in the Scolex-Neck region is more similar to that of Larvae than to the mature or gravid regions of the adult worm, which was further reflected in large overlap of up-regulated GOI. CONCLUSIONS Spatial expression analyses in Larvae and adult worms corroborated inferences made from quantitative RNA-seq data and in most cases indicated consistency with canonical roles of the genes in other animals, including free-living flatworms. Recapitulation of developmental factors up-regulated during larval metamorphosis suggests that strobilar growth involves many of the same underlying gene regulatory networks despite the significant disparity in developmental outcomes. The majority of genes identified were investigated in tapeworms for the first time, setting the stage for advancing our understanding of developmental genetics in an important group of flatworm parasites.
Collapse
Affiliation(s)
- Peter D. Olson
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Magdalena Zarowiecki
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Katherine James
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Andrew Baillie
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Georgie Bartl
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Phil Burchell
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Azita Chellappoo
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Francesca Jarero
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Li Ying Tan
- Division of Parasites and Vectors, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Nancy Holroyd
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Matt Berriman
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| |
Collapse
|
129
|
Vasconcelos EJR, Mesel VC, daSilva LF, Pires DS, Lavezzo GM, Pereira ASA, Amaral MS, Verjovski-Almeida S. Atlas of Schistosoma mansoni long non-coding RNAs and their expression correlation to protein-coding genes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5051101. [PMID: 29992321 PMCID: PMC6041749 DOI: 10.1093/database/bay068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/11/2018] [Indexed: 11/23/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been widely discovered in several organisms with the help of high-throughput RNA sequencing. LncRNAs are over 200 nt-long transcripts that do not have protein-coding (PC) potential, having been reported in model organisms to act mainly on the overall control of PC gene expression. Little is known about the functionality of lncRNAs in evolutionarily ancient non-model metazoan organisms, like Schistosoma mansoni, the parasite that causes schistosomiasis, one of the most prevalent infectious-parasitic diseases worldwide. In a recent transcriptomics effort, we identified thousands of S. mansoni lncRNAs predicted to be functional along the course of parasite development. Here, we present an online catalog of each of the S. mansoni lncRNAs whose expression is correlated to PC genes along the parasite life-cycle, which can be conveniently browsed and downloaded through a new web resource http://verjolab.usp.br. We also provide access now to navigation on the co-expression networks disclosed in our previous publication, where we correlated mRNAs and lncRNAs transcriptional patterns across five life-cycle stages/forms, pinpointing biological processes where lncRNAs might act upon. Database URL: http://verjolab.usp.br
Collapse
Affiliation(s)
- Elton J R Vasconcelos
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, 05503-900 São Paulo, SP, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil.,College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766-1854, USA
| | - Vinícius C Mesel
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, 05503-900 São Paulo, SP, Brazil
| | - Lucas F daSilva
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, 05503-900 São Paulo, SP, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - David S Pires
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, 05503-900 São Paulo, SP, Brazil
| | - Guilherme M Lavezzo
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, 05503-900 São Paulo, SP, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Adriana S A Pereira
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, 05503-900 São Paulo, SP, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Murilo S Amaral
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, 05503-900 São Paulo, SP, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, 05503-900 São Paulo, SP, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| |
Collapse
|
130
|
Le Clec’h W, Chevalier FD, McDew-White M, Allan F, Webster BL, Gouvras AN, Kinunghi S, Tchuenté LAT, Garba A, Mohammed KA, Ame SM, Webster JP, Rollinson D, Emery AM, Anderson TJC. Whole genome amplification and exome sequencing of archived schistosome miracidia. Parasitology 2018; 145:1739-1747. [PMID: 29806576 PMCID: PMC6193844 DOI: 10.1017/s0031182018000811] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Adult schistosomes live in the blood vessels and cannot easily be sampled from humans, so archived miracidia larvae hatched from eggs expelled in feces or urine are commonly used for population genetic studies. Large collections of archived miracidia on FTA cards are now available through the Schistosomiasis Collection at the Natural History Museum (SCAN). Here we describe protocols for whole genome amplification of Schistosoma mansoni and Schistosome haematobium miracidia from these cards, as well as real time PCR quantification of amplified schistosome DNA. We used microgram quantities of DNA obtained for exome capture and sequencing of single miracidia, generating dense polymorphism data across the exome. These methods will facilitate the transition from population genetics, using limited numbers of markers to population genomics using genome-wide marker information, maximising the value of collections such as SCAN.
Collapse
Affiliation(s)
- Winka Le Clec’h
- Texas Biomedical Research Institute, Department of Genetics, PO Box 760549, San Antonio, TX 78245-0549, USA
| | - Frédéric D. Chevalier
- Texas Biomedical Research Institute, Department of Genetics, PO Box 760549, San Antonio, TX 78245-0549, USA
| | - Marina McDew-White
- Texas Biomedical Research Institute, Department of Genetics, PO Box 760549, San Antonio, TX 78245-0549, USA
| | - Fiona Allan
- The Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, United Kingdom
| | - Bonnie L. Webster
- The Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, United Kingdom
| | - Anouk N. Gouvras
- The Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, United Kingdom
| | - Safari Kinunghi
- National Institute for Medical Research, Mwanza Research Centre, Mwanza, United Republic of Tanzania
| | - Louis-Albert Tchuem Tchuenté
- Laboratoire de Parasitologie et Ecologie, Université de Yaoundé I, Yaoundé, Cameroon
- Center for Schistosomiasis & Parasitology, P.O. Box 7244, Yaoundé, Cameroon
| | - Amadou Garba
- Réseau International Schistosomoses, Environnement, Aménagement et Lutte (RISEAL-Niger), 333, Avenue des Zarmakoye, B.P. 13724, Niamey, Niger
| | - Khalfan A. Mohammed
- Helminth Control Laboratory Unguja, Ministry of Health, Zanzibar, United Republic of Tanzania
| | - Shaali M. Ame
- Public Health Laboratory - Ivo de Carneri, Pemba, United Republic of Tanzania
| | - Joanne P. Webster
- Centre for Emerging, Endemic and Exotic Diseases, Department of Patholobiology and Population Sciences, Royal Veterinary College, University of London, AL9 7TA, UK United Kingdom
| | - David Rollinson
- The Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, United Kingdom
| | - Aidan M. Emery
- The Natural History Museum, Department of Life Sciences, Cromwell Road, London SW7 5BD, United Kingdom
| | - Timothy J. C. Anderson
- Texas Biomedical Research Institute, Department of Genetics, PO Box 760549, San Antonio, TX 78245-0549, USA
| |
Collapse
|
131
|
Preza M, Montagne J, Costábile A, Iriarte A, Castillo E, Koziol U. Analysis of classical neurotransmitter markers in tapeworms: Evidence for extensive loss of neurotransmitter pathways. Int J Parasitol 2018; 48:979-992. [DOI: 10.1016/j.ijpara.2018.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/30/2018] [Accepted: 06/06/2018] [Indexed: 12/28/2022]
|
132
|
A metalloprotease produced by larval Schistosoma mansoni facilitates infection establishment and maintenance in the snail host by interfering with immune cell function. PLoS Pathog 2018; 14:e1007393. [PMID: 30372490 PMCID: PMC6224180 DOI: 10.1371/journal.ppat.1007393] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 11/08/2018] [Accepted: 10/08/2018] [Indexed: 11/18/2022] Open
Abstract
Metalloproteases (MPs) have demonstrated roles in immune modulation. In some cases, these enzymes are produced by parasites to influence host immune responses such that parasite infection is facilitated. One of the best examples of parasite-mediated immune modulation is the matrix metalloprotease (MMP) leishmanolysin (Gp63), which is produced by species of the genus Leishmania to evade killing by host macrophages. Leishmanolysin-like proteins appear to be quite common in many invertebrates, however our understanding of the functions of these non-leishmania enzymes is limited. Numerous proteomic and transcriptomic screens of schistosomes, at all life cycle stages of the parasite, have identified leishmanolysin-like MPs as being present in abundance; with the highest levels being found during the intramolluscan larval stages and being produced by cercaria. This study aims to functionally characterize a Schistosoma mansoni variant of leishmanolysin that most resembles the enzyme produced by Leishmania, termed SmLeish. We demonstrate that SmLeish is an important component of S. mansoni excretory/secretory (ES) products and is produced by the sporocyst during infection. The presence of SmLeish interferes with the migration of Biomphalaria glabrata haemocytes, and causes them to present a phenotype that is less capable of sporocyst encapsulation. Knockdown of SmLeish in S. mansoni miracidia prior to exposure to susceptible B. glabrata reduces miracidia penetration success, causes a delay in reaching patent infection, and lowers cercaria output from infected snails. Parasitic flatworms, or digenetic trematodes, cause a wide range of diseases of both medical and agricultural importance. Nearly all species of digenea require specific species of snail for their larval development and transmission. The factors underpinning snail host specificity and how they dictate infection establishment and maintenance are interesting areas of research, both from the perspective of evolutionary immunology and potential application in the design of tools that aim to prevent trematode transmission. Currently, our understanding of snail-trematode associations is one-sided, being predominantly derived from studies that have focused on the snail immune response, with almost nothing known about how the parasite facilitates infection. Metalloproteases, such as leishmanolysin, are proteolytic enzymes; some of which are produced by parasites to influence host immune responses and facilitate parasite success upon encountering the host defense response. Here, we have functionally characterized a leishmanolysin-like metalloprotease (SmLeish) from Schistosoma mansoni, a causative agent of human schistosomiasis, which afflicts over 260 million people globally. We demonstrate that SmLeish is associated with developing sporocysts and is also located in S. mansoni excretory/secretory products and interferes with snail haemocyte morphology and migration. Knockdown of SmLeish in S. mansoni miracidia prior to exposure to Biomphalaria glabrata snails reduces miracidia penetration success, delays attainment of patent infections, and lowers cercaria output from infected snails.
Collapse
|
133
|
Pereira ASA, Amaral MS, Vasconcelos EJR, Pires DS, Asif H, daSilva LF, Morales-Vicente DA, Carneiro VC, Angeli CB, Palmisano G, Fantappie MR, Pierce RJ, Setubal JC, Verjovski-Almeida S. Inhibition of histone methyltransferase EZH2 in Schistosoma mansoni in vitro by GSK343 reduces egg laying and decreases the expression of genes implicated in DNA replication and noncoding RNA metabolism. PLoS Negl Trop Dis 2018; 12:e0006873. [PMID: 30365505 PMCID: PMC6221359 DOI: 10.1371/journal.pntd.0006873] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/07/2018] [Accepted: 09/24/2018] [Indexed: 11/19/2022] Open
Abstract
Background The possibility of emergence of praziquantel-resistant Schistosoma parasites and the lack of other effective drugs demand the discovery of new schistosomicidal agents. In this context the study of compounds that target histone-modifying enzymes is extremely promising. Our aim was to investigate the effect of inhibition of EZH2, a histone methyltransferase that is involved in chromatin remodeling processes and gene expression control; we tested different developmental forms of Schistosoma mansoni using GKS343, a selective inhibitor of EZH2 in human cells. Methodology/Principal findings Adult male and female worms and schistosomula were treated with different concentrations of GSK343 for up to two days in vitro. Western blotting showed a decrease in the H3K27me3 histone mark in all three developmental forms. Motility, mortality, pairing and egg laying were employed as schistosomicidal parameters for adult worms. Schistosomula viability was evaluated with propidium iodide staining and ATP quantification. Adult worms showed decreased motility when exposed to GSK343. Also, an approximate 40% reduction of egg laying by GSK343-treated females was observed when compared with controls (0.1% DMSO). Scanning electron microscopy showed the formation of bulges and bubbles throughout the dorsal region of GSK343-treated adult worms. In schistosomula the body was extremely contracted with the presence of numerous folds, and growth was markedly slowed. RNA-seq was applied to identify the metabolic pathways affected by GSK343 sublethal doses. GSK343-treated adult worms showed significantly altered expression of genes related to transmembrane transport, cellular homeostasis and egg development. In females, genes related to DNA replication and noncoding RNA metabolism processes were downregulated. Schistosomula showed altered expression of genes related to cell adhesion and membrane synthesis pathways. Conclusions/Significance The results indicated that GSK343 presents in vitro activities against S. mansoni, and the characterization of EZH2 as a new potential molecular target establishes EZH2 inhibitors as part of a promising new group of compounds that could be used for the development of schistosomicidal agents. Schistosomiasis is a chronic and debilitating disease caused by a trematode of the genus Schistosoma. The current strategy for the control of the disease involves treatment with praziquantel, the only available drug. The development of new drugs is therefore a top priority. Drugs that inhibit histone modifying enzymes have been used in cancer, altering gene expression, replication, repair and DNA recombination. Schistosoma parasites have some characteristics similar to malignant tumors, such as intense cell division and high levels of metabolic activity. Here we evaluate in Schistosoma mansoni the effect of GSK343, an inhibitor of the histone methyltransferase EZH2 that had been shown to arrest or reduce the growth of human cancer cells. We show that GSK343 causes damage to the parasite tegument and reduces egg laying in vitro, concomitant with a decrease in levels of H3K27me3, the histone mark put in place by EZH2. RNA-seq and proteomic analyses of treated parasites showed changes in the expression of hundreds of genes involved in important metabolic processes. In females, a marked decrease was observed in the expression of genes related to processes such as DNA replication and noncoding RNA metabolism. In conclusion, the histone methyltransferase EZH2 seems to be a promising novel drug target against schistosomiasis.
Collapse
Affiliation(s)
- Adriana S. A. Pereira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, Brasil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Murilo S. Amaral
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, Brasil
| | - Elton J. R. Vasconcelos
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, Brasil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - David S. Pires
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, Brasil
| | - Huma Asif
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, Brasil
| | - Lucas F. daSilva
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, Brasil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - David A. Morales-Vicente
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, Brasil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Vitor C. Carneiro
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Claudia B. Angeli
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Laboratório de Glicoproteômica, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Giuseppe Palmisano
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Laboratório de Glicoproteômica, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Marcelo R. Fantappie
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Raymond J. Pierce
- Centre d'Infection et d'Immunité de Lille, CNRS UMR 8204, Inserm U1019, CHU Lille, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - João C. Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, SP, Brasil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
- * E-mail:
| |
Collapse
|
134
|
Biswal DK, Roychowdhury T, Pandey P, Tandon V. De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski. PLoS One 2018; 13:e0205570. [PMID: 30325945 PMCID: PMC6191129 DOI: 10.1371/journal.pone.0205570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/27/2018] [Indexed: 11/19/2022] Open
Abstract
Many trematode parasites cause infection in humans and are thought to be a major public health problem. Their ecological diversity in different regions provides challenging questions on evolution of these organisms. In this report, we perform transcriptome analysis of the giant intestinal fluke, Fasciolopsis buski, using next generation sequencing technology. Short read sequences derived from polyA containing RNA of this organism were assembled into 30,677 unigenes that led to the annotation of 12,380 genes. Annotation of the assembled transcripts enabled insight into processes and pathways in the intestinal fluke, such as RNAi pathway and energy metabolism. The expressed kinome of the organism was characterized by identifying all protein kinases. A rough draft genome assembly for Fasciolopsis buski is also reported herewith with SRA accessions for crosschecking the findings in the analyzed transcriptome data. Transcriptome data also helped us to identify some of the expressed transposable elements. Though many Long Interspersed elements (LINEs) were identified, only two Short Interspersed Elements (SINEs) were visible. Overall transcriptome and draft genome analysis of F. buski helped us to characterize some of its important biological characteristics and provided enormous resources for development of a suitable diagnostic system and anti-parasitic therapeutic molecules.
Collapse
Affiliation(s)
| | - Tanmoy Roychowdhury
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Priyatama Pandey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Veena Tandon
- Department of Zoology, North-Eastern Hill University, Shillong, Meghalaya, India
| |
Collapse
|
135
|
Kincaid-Smith J, Picard MAL, Cosseau C, Boissier J, Severac D, Grunau C, Toulza E. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biol Evol 2018; 10:840-856. [PMID: 29447366 PMCID: PMC5861417 DOI: 10.1093/gbe/evy037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2018] [Indexed: 12/16/2022] Open
Abstract
Schistosomes are the causative agents of schistosomiasis, a neglected tropical disease affecting over 230 million people worldwide. Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatworms are unique among the common hermaphroditic trematodes as they have separate sexes. This so-called “evolutionary scandal” displays a female heterogametic genetic sex-determination system (ZZ males and ZW females), as well as a pronounced adult sexual dimorphism. These phenotypic differences are determined by a shared set of genes in both sexes, potentially leading to intralocus sexual conflicts. To resolve these conflicts in sexually selected traits, molecular mechanisms such as sex-biased gene expression could occur, but parent-of-origin gene expression also provides an alternative. In this work we investigated the latter mechanism, that is, genes expressed preferentially from either the maternal or the paternal allele, in Schistosoma mansoni species. To this end, transcriptomes from male and female hybrid adults obtained by strain crosses were sequenced. Strain-specific single nucleotide polymorphism (SNP) markers allowed us to discriminate the parental origin, while reciprocal crosses helped to differentiate parental expression from strain-specific expression. We identified genes containing SNPs expressed in a parent-of-origin manner consistent with paternal and maternal imprints. Although the majority of the SNPs was identified in mitochondrial and Z-specific loci, the remaining SNPs found in male and female transcriptomes were situated in genes that have the potential to explain sexual differences in schistosome parasites. Furthermore, we identified and validated four new Z-specific scaffolds.
Collapse
Affiliation(s)
- Julien Kincaid-Smith
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Perpignan, France
| | - Marion A L Picard
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Céline Cosseau
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Perpignan, France
| | - Jérôme Boissier
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Perpignan, France
| | - Dany Severac
- MGX, BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, France
| | - Christoph Grunau
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Perpignan, France
| | - Eve Toulza
- IHPE, University of Montpellier, CNRS, IFREMER, University of Perpignan Via Domitia, Perpignan, France
| |
Collapse
|
136
|
Phuphisut O, Ajawatanawong P, Limpanont Y, Reamtong O, Nuamtanong S, Ampawong S, Chaimon S, Dekumyoy P, Watthanakulpanich D, Swierczewski BE, Adisakwattana P. Transcriptomic analysis of male and female Schistosoma mekongi adult worms. Parasit Vectors 2018; 11:504. [PMID: 30201055 PMCID: PMC6131826 DOI: 10.1186/s13071-018-3086-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/29/2018] [Indexed: 12/23/2022] Open
Abstract
Background Schistosoma mekongi is one of five major causative agents of human schistosomiasis and is endemic to communities along the Mekong River in southern Lao People’s Democratic Republic (Laos) and northern Cambodia. Sporadic cases of schistosomiasis have been reported in travelers and immigrants who have visited endemic areas. Schistosoma mekongi biology and molecular biology is poorly understood, and few S. mekongi gene and transcript sequences are available in public databases. Results Transcriptome sequencing (RNA-Seq) of male and female S. mekongi adult worms (a total of three biological replicates for each sex) were analyzed and the results demonstrated that approximately 304.9 and 363.3 million high-quality clean reads with quality Q30 (> 90%) were obtained from male and female adult worms, respectively. A total of 119,604 contigs were assembled with an average length of 1273 nt and an N50 of 2017 nt. From the contigs, 20,798 annotated protein sequences and 48,256 annotated transcript sequences were obtained using BLASTP and BLASTX searches against the UniProt Trematoda database. A total of 4658 and 3509 transcripts were predominantly expressed in male and female worms, respectively. Male-biased transcripts were mostly involved in structural organization while female-biased transcripts were typically involved in cell differentiation and egg production. Interestingly, pathway enrichment analysis suggested that genes involved in the phosphatidylinositol signaling pathway may play important roles in the cellular processes and reproductive systems of S. mekongi worms. Conclusions We present comparative transcriptomic analyses of male and female S. mekongi adult worms, which provide a global view of the S. mekongi transcriptome as well as insights into differentially-expressed genes associated with each sex. This work provides valuable information and sequence resources for future studies of gene function and for ongoing whole genome sequencing efforts in S. mekongi. Electronic supplementary material The online version of this article (10.1186/s13071-018-3086-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Orawan Phuphisut
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pravech Ajawatanawong
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Yanin Limpanont
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Supaporn Nuamtanong
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sumate Ampawong
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Salisa Chaimon
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Paron Dekumyoy
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Dorn Watthanakulpanich
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Brett E Swierczewski
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| |
Collapse
|
137
|
Torini JR, Romanello L, Batista FAH, Serrão VHB, Faheem M, Zeraik AE, Bird L, Nettleship J, Reddivari Y, Owens R, DeMarco R, Borges JC, Brandão-Neto J, Pereira HD. The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleoside selectivity of PNPs. PLoS One 2018; 13:e0203532. [PMID: 30192840 PMCID: PMC6128611 DOI: 10.1371/journal.pone.0203532] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/22/2018] [Indexed: 12/16/2022] Open
Abstract
Purine nucleoside phosphorylases (PNPs) play an important role in the blood fluke parasite Schistosoma mansoni as a key enzyme of the purine salvage pathway. Here we present the structural and kinetic characterization of a new PNP isoform from S. mansoni, SmPNP2. Thermofluorescence screening of different ligands suggested cytidine and cytosine are potential ligands. The binding of cytosine and cytidine were confirmed by isothermal titration calorimetry, with a KD of 27 μM for cytosine, and a KM of 76.3 μM for cytidine. SmPNP2 also displays catalytic activity against inosine and adenosine, making it the first described PNP with robust catalytic activity towards both pyrimidines and purines. Crystal structures of SmPNP2 with different ligands were obtained and comparison of these structures with the previously described S. mansoni PNP (SmPNP1) provided clues for the unique capacity of SmPNP2 to bind pyrimidines. When compared with the structure of SmPNP1, substitutions in the vicinity of SmPNP2 active site alter the architecture of the nucleoside base binding site thus permitting an alternative binding mode for nucleosides, with a 180° rotation from the canonical binding mode. The remarkable plasticity of this binding site enhances our understanding of the correlation between structure and nucleotide selectivity, thus suggesting new ways to analyse PNP activity.
Collapse
Affiliation(s)
- Juliana Roberta Torini
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Larissa Romanello
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Fernanda Aparecida Heleno Batista
- Instituto de Química de São Carlos, Universidade de São Paulo - USP, São Carlos, São Paulo, Brazil
- Centro Nacional de Pesquisa em Energia e Materiais, Laboratório Nacional de Biociências, Campinas, São Paulo, Brazil
| | - Vitor Hugo Balasco Serrão
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Muhammad Faheem
- Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Federal District, Brazil
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Federal District, Brazil
| | - Ana Eliza Zeraik
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Louise Bird
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, United Kingdom
| | - Joanne Nettleship
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, United Kingdom
| | - Yamini Reddivari
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, United Kingdom
| | - Ray Owens
- OPPF-UK, Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, United Kingdom
| | - Ricardo DeMarco
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Júlio César Borges
- Instituto de Química de São Carlos, Universidade de São Paulo - USP, São Carlos, São Paulo, Brazil
| | - José Brandão-Neto
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Humberto D’Muniz Pereira
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
- * E-mail:
| |
Collapse
|
138
|
Anderson TJC, LoVerde PT, Le Clec'h W, Chevalier FD. Genetic Crosses and Linkage Mapping in Schistosome Parasites. Trends Parasitol 2018; 34:982-996. [PMID: 30150002 DOI: 10.1016/j.pt.2018.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/27/2018] [Accepted: 08/02/2018] [Indexed: 12/14/2022]
Abstract
Linkage mapping - utilizing experimental genetic crosses to examine cosegregation of phenotypic traits with genetic markers - is now 100 years old. Schistosome parasites are exquisitely well suited to linkage mapping approaches because genetic crosses can be conducted in the laboratory, thousands of progeny are produced, and elegant experimental work over the last 75 years has revealed heritable genetic variation in multiple biomedically important traits such as drug resistance, host specificity, and virulence. Application of this approach is timely because the improved genome assembly for Schistosoma mansoni and developing molecular toolkit for schistosomes increase our ability to link phenotype with genotype. We describe current progress and potential future directions of linkage mapping in schistosomes.
Collapse
Affiliation(s)
| | | | - Winka Le Clec'h
- Texas Biomedical Research Institute, San Antonio, Texas 78227, USA
| | | |
Collapse
|
139
|
Homan EJ, Bremel RD. A Role for Epitope Networking in Immunomodulation by Helminths. Front Immunol 2018; 9:1763. [PMID: 30108588 PMCID: PMC6079203 DOI: 10.3389/fimmu.2018.01763] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022] Open
Abstract
Helminth infections, by nematodes, trematodes, or cestodes, can lead to the modulation of host immune responses. This allows long-duration parasite infections and also impacts responses to co-infections. Surface, secreted, excreted, and shed proteins are thought to play a major role in modulation. A commonly reported feature of such immune modulation is the role of T regulatory (Treg) cells and IL-10. Efforts to identify helminth proteins, which cause immunomodulation, have identified candidates but not provided clarity as to a uniform mechanism driving modulation. In this study, we applied a bioinformatics systems approach, allowing us to analyze predicted T-cell epitopes of 17 helminth species and the responses to their surface proteins. In addition to major histocompatibility complex (MHC) binding, we analyzed amino acid motifs that would be recognized by T-cell receptors [T-cell-exposed motifs (TCEMs)]. All the helminth species examined have, within their surface proteins, peptides, which combine very common TCEMs with predicted high affinity binding to many human MHC alleles. This combination of features would result in large cognate T cell and a high probability of eliciting Treg responses. The TCEMs, which determine recognition by responding T-cell clones, are shared to a high degree between helminth species and with Plasmodium falciparum and Mycobacterium tuberculosis, both common co-infecting organisms. The implication of our observations is not only that Treg cells play a significant role in helminth-induced immune modulation but also that the epitope specificities of Treg responses are shared across species and genera of helminth. Hence, the immune response to a given helminth cannot be considered in isolation but rather forms part of an epitope ecosystem, or microenvironment, in which potentially immunosuppressive peptides in the helminth network via their common T-cell receptor recognition signals with T-cell epitopes in self proteins, microbiome, other helminths, and taxonomically unrelated pathogens. Such a systems approach provides a high-level view of the antigen-immune system signaling dynamics that may bias a host's immune response to helminth infections toward immune modulation. It may indicate how helminths have evolved to select for peptides that favor long-term parasite host coexistence.
Collapse
|
140
|
El-Sakkary N, Chen S, Arkin MR, Caffrey CR, Ribeiro P. Octopamine signaling in the metazoan pathogen Schistosoma mansoni: localization, small-molecule screening and opportunities for drug development. Dis Model Mech 2018; 11:dmm033563. [PMID: 29925529 PMCID: PMC6078403 DOI: 10.1242/dmm.033563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/12/2018] [Indexed: 11/20/2022] Open
Abstract
Schistosomiasis is a tropical disease caused by a flatworm trematode parasite that infects over 200 million people worldwide. Treatment and control of the disease rely on just one drug, praziquantel. The possibility of drug resistance coupled with praziquantel's variable efficacy encourages the identification of new drugs and drug targets. Disruption of neuromuscular homeostasis in parasitic worms is a validated strategy for drug development. In schistosomes, however, much remains to be understood about the organization of the nervous system, its component neurotransmitters and potential for drug discovery. Using synapsin as a neuronal marker, we map the central and peripheral nervous systems in the Schistosoma mansoni adult and schistosomulum (post-infective larva). We discover the widespread presence of octopamine (OA), a tyrosine-derived and invertebrate-specific neurotransmitter involved in neuromuscular coordination. OA labeling facilitated the discovery of two pairs of ganglia in the brain of the adult schistosome, rather than the one pair thus far reported for this and other trematodes. In quantitative phenotypic assays, OA and the structurally related tyrosine-derived phenolamine and catecholamine neurotransmitters differentially modulated schistosomulum motility and length. Similarly, from a screen of 28 drug agonists and antagonists of tyrosine-derivative signaling, certain drugs that act on OA and dopamine receptors induced robust and sometimes complex concentration-dependent effects on schistosome motility and length; in some cases, these effects occurred at concentrations achievable in vivo The present data advance our knowledge of the organization of the nervous system in this globally important pathogen and identify a number of drugs that interfere with tyrosine-derivative signaling, one or more of which might provide the basis for a new chemotherapeutic approach to treat schistosomiasis.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Nelly El-Sakkary
- Institute of Parasitology, McGill University, Macdonald Campus, 21, 111 Lakeshore Road, Ste Anne de Bellevue, Quebec, Canada H9X-3V9
| | - Steven Chen
- Small Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Department of Pathology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Paula Ribeiro
- Institute of Parasitology, McGill University, Macdonald Campus, 21, 111 Lakeshore Road, Ste Anne de Bellevue, Quebec, Canada H9X-3V9
| |
Collapse
|
141
|
Diemert DJ, Bottazzi ME, Plieskatt J, Hotez PJ, Bethony JM. Lessons along the Critical Path: Developing Vaccines against Human Helminths. Trends Parasitol 2018; 34:747-758. [PMID: 30064902 DOI: 10.1016/j.pt.2018.07.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/16/2022]
Abstract
Helminthic parasites are important targets for vaccine research as they infect an estimated 1 billion people worldwide. Despite significant progress in the discovery of defined antigens as candidates for vaccines, the potential of a helminth vaccine advancing to an investigational product to be tested in humans remains as challenging as it did 50 years ago. Candidate helminth vaccines must still advance along a 'critical path' of preclinical research, vaccine process development (which includes 'chemistry, manufacturing, and controls' or CMC), current good manufacturing practice (cGMP) production of the vaccine, and clinical trials. This path is highly targeted towards meeting the safety, immunogenicity, and efficacy criteria of regulatory bodies such as the US Food and Drug Administration (FDA). For nearly 20 years our product development partnership (PDP), the Texas Children's Hospital Center for Vaccine Development (TCH-CVD), has followed the critical paths of several novel subunit vaccines for the human hookworm Necator americanus and the intestinal trematode Schistosoma mansoni. Herein, we describe the critical lessons learned along this critical path.
Collapse
Affiliation(s)
- David J Diemert
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington DC, USA; Department of Medicine, The George Washington University, Washington DC, USA; Texas Children's Hospital Center for Vaccine Development - a Product Development Partnership, Houston, TX, USA
| | - Maria Elena Bottazzi
- Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA; Department of Biology, Baylor University, Waco, TX, USA; Texas Children's Hospital Center for Vaccine Development - a Product Development Partnership, Houston, TX, USA
| | - Jordan Plieskatt
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington DC, USA; Texas Children's Hospital Center for Vaccine Development - a Product Development Partnership, Houston, TX, USA
| | - Peter J Hotez
- Departments of Pediatrics and Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA; Department of Biology, Baylor University, Waco, TX, USA; Texas Children's Hospital Center for Vaccine Development - a Product Development Partnership, Houston, TX, USA
| | - Jeffrey M Bethony
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington DC, USA; Texas Children's Hospital Center for Vaccine Development - a Product Development Partnership, Houston, TX, USA.
| |
Collapse
|
142
|
Developmental Sensitivity in Schistosoma mansoni to Puromycin To Establish Drug Selection of Transgenic Schistosomes. Antimicrob Agents Chemother 2018; 62:AAC.02568-17. [PMID: 29760143 DOI: 10.1128/aac.02568-17] [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: 12/19/2017] [Accepted: 04/27/2018] [Indexed: 01/05/2023] Open
Abstract
Schistosomiasis is considered the most important disease caused by helminth parasites, in terms of morbidity and mortality. Tools to facilitate gain- and loss-of-function approaches can be expected to precipitate the discovery of novel interventions, and drug selection of transgenic schistosomes would facilitate the establishment of stable lines of engineered parasites. Sensitivity of developmental stages of schistosomes to the aminonucleoside antibiotic puromycin was investigated. For the schistosomulum and sporocyst stages, viability was quantified by fluorescence microscopy following dual staining with fluorescein diacetate and propidium iodine. By 6 days in culture, the 50% lethal concentration (LC50) for schistosomula was 19 μg/ml whereas the sporocysts were 45-fold more resilient. Puromycin potently inhibited the development of in vitro-laid eggs (LC50, 68 ng/ml) but was less effective against liver eggs (LC50, 387 μg/ml). Toxicity for adult stages was evaluated using the xCELLigence-based, real-time motility assay (xWORM), which revealed LC50s after 48 h of 4.9 and 17.3 μg/ml for male and female schistosomes, respectively. Also, schistosomula transduced with pseudotyped retrovirus encoding the puromycin resistance marker were partially rescued when cultured in the presence of the antibiotic. Together, these findings will facilitate selection on puromycin of transgenic schistosomes and the enrichment of cultures of transgenic eggs and sporocysts to facilitate the establishment of schistosome transgenic lines. Streamlining schistosome transgenesis with drug selection will open new avenues to understand parasite biology and hopefully lead to new interventions for this neglected tropical disease.
Collapse
|
143
|
Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding CG, Couté Y, Vicoso B. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife 2018; 7:e35684. [PMID: 30044216 PMCID: PMC6089595 DOI: 10.7554/elife.35684] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/16/2018] [Indexed: 12/05/2022] Open
Abstract
XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno's classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes.
Collapse
Affiliation(s)
| | - Celine Cosseau
- University of Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University MontpellierPerpignanFrance
| | - Sabrina Ferré
- Université Grenoble Alpes, CEA, Inserm, BIG-BGEGrenobleFrance
| | - Thomas Quack
- Institute for Parasitology, Biomedical Research Center SeltersbergJustus-Liebig-UniversityGiessenGermany
| | - Christoph G Grevelding
- Institute for Parasitology, Biomedical Research Center SeltersbergJustus-Liebig-UniversityGiessenGermany
| | - Yohann Couté
- Université Grenoble Alpes, CEA, Inserm, BIG-BGEGrenobleFrance
| | - Beatriz Vicoso
- Institute of Science and Technology AustriaKlosterneuburgAustria
| |
Collapse
|
144
|
Identification of 170 New Long Noncoding RNAs in Schistosoma mansoni. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1264697. [PMID: 30112357 PMCID: PMC6077669 DOI: 10.1155/2018/1264697] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/14/2018] [Accepted: 06/21/2018] [Indexed: 01/22/2023]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts generally longer than 200 nucleotides with no or poor protein coding potential, and most of their functions are also poorly characterized. Recently, an increasing number of studies have shown that lncRNAs can be involved in various critical biological processes such as organism development or cancer progression. Little, however, is known about their effects in helminths parasites, such as Schistosoma mansoni. Here, we present a computational pipeline to identify and characterize lncRNAs from RNA-seq data with high confidence from S. mansoni adult worms. Through the utilization of different criteria such as genome localization, exon number, gene length, and stability, we identified 170 new putative lncRNAs. All novel S. mansoni lncRNAs have no conserved synteny including human and mouse. These closest protein coding genes were enriched in 10 significant Gene Ontology terms related to metabolism, transport, and biosynthesis. Fifteen putative lncRNAs showed differential expression, and three displayed sex-specific differential expressions in praziquantel sensitive and resistant adult worm couples. Together, our method can predict a set of novel lncRNAs from the RNA-seq data. Some lncRNAs are shown to be differentially expressed suggesting that those novel lncRNAs can be given high priority in further functional studies focused on praziquantel resistance.
Collapse
|
145
|
Wang B, Lee J, Li P, Saberi A, Yang H, Liu C, Zhao M, Newmark PA. Stem cell heterogeneity drives the parasitic life cycle of Schistosoma mansoni. eLife 2018; 7:35449. [PMID: 29988015 PMCID: PMC6039179 DOI: 10.7554/elife.35449] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/08/2018] [Indexed: 12/14/2022] Open
Abstract
Schistosomes are parasitic flatworms infecting hundreds of millions of people. These parasites alternate between asexual reproduction in molluscan hosts and sexual reproduction in mammalian hosts; short-lived, water-borne stages infect each host. Thriving in such disparate environments requires remarkable developmental plasticity, manifested by five body plans deployed throughout the parasite’s life cycle. Stem cells in Schistosoma mansoni provide a potential source for such plasticity; however, the relationship between stem cells from different life-cycle stages remains unclear, as does the origin of the germline, required for sexual reproduction. Here, we show that subsets of larvally derived stem cells are likely sources of adult stem cells and the germline. We also identify a novel gene that serves as the earliest marker for the schistosome germline, which emerges inside the mammalian host and is ultimately responsible for disease pathology. This work reveals the stem cell heterogeneity driving the propagation of the schistosome life cycle. Parasitic flatworms called schistosomes infect around 250 million people, causing the disease schistosomiasis. Schistosomes live complex lives, spending part of their life cycle inside snails and part of it inside mammals; short-lived, water-borne stages infect each of these hosts. To thrive in such different environments, schistosomes go through several life-cycle stages. At each stage the flatworms transition to a new body plan adapted to its new environment. Understanding how these transitions occur could help researchers devise new strategies for eliminating these parasites. Previous research suggested that stem cells help schistosomes transition to new body plans. Stem cells have the ability to transform into many different cell types, and have been found in schistosome larvae and adults. However, the relationship between the larval and adult stem cells was not clear. Wang et al. used transcriptional profiling, a technique that measures the genes currently in use in different cells, to study the stem cells in the schistosome species Schistosoma mansoni. This uncovered four types of stem cell, each of which uses a slightly different combination of genes. Examining the behaviour of these cells at different schistosome life-cycle stages revealed that certain larval stem cells produce adult stem cells. Other larval stem cells seem to be the source of the ‘germline’ cells that make gametes (egg and sperm) and allow the parasites to reproduce sexually. Schistosomes only produce germline cells when they are inside mammals. Wang et al. found that as juvenile flatworms develop inside mouse blood vessels, a gene called eledh becomes active in some of their stem cells. Further investigation showed that this activity is the earliest indicator that germline cells are developing and is also required for proper development of the germline. This knowledge, along with future work to characterize the roles of the stem cell populations identified by Wang et al., could ultimately help researchers develop new ways to stop the spread of schistosomiasis.
Collapse
Affiliation(s)
- Bo Wang
- Department of Bioengineering, Stanford University, Stanford, United States.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States.,Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Jayhun Lee
- Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Pengyang Li
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Amir Saberi
- Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Huiying Yang
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Chang Liu
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Phillip A Newmark
- Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, United States
| |
Collapse
|
146
|
Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications. Biotechnol Adv 2018; 36:894-904. [DOI: 10.1016/j.biotechadv.2018.02.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/08/2018] [Accepted: 02/13/2018] [Indexed: 12/27/2022]
|
147
|
Hodgkinson JE, Cwiklinski K, Beesley N, Hartley C, Allen K, Williams DJL. Clonal amplification of Fasciola hepatica in Galba truncatula: within and between isolate variation of triclabendazole-susceptible and -resistant clones. Parasit Vectors 2018; 11:363. [PMID: 29941045 PMCID: PMC6020221 DOI: 10.1186/s13071-018-2952-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/13/2018] [Indexed: 11/10/2022] Open
Abstract
Background Fasciola hepatica is of worldwide significance, impacting on the health, welfare and productivity of livestock and regarded by WHO as a re-emerging zoonosis. Triclabendazole (TCBZ), the drug of choice for controlling acute fasciolosis in livestock, is also the drug used to treat human infections. However TCBZ-resistance is now considered a major threat to the effective control of F. hepatica. It has yet to be demonstrated whether F. hepatica undergoes a genetic clonal expansion in the snail intermediate host, Galba truncatula, and to what extent amplification of genotypes within the snail facilitates accumulation of drug resistant parasites. Little is known about genotypic and phenotypic variation within and between F. hepatica isolates. Results Six clonal isolates of F. hepatica (3× triclabendazole-resistant, TCBZ-R and 3× triclabendazole-susceptible, TCBZ-S) were generated. Snails infected with one miracidium started to shed cercariae 42–56 days post-infection and shed repeatedly up to a maximum of 11 times. A maximum of 884 cercariae were shed by one clonally-infected snail (FhLivS1) at a single time point, with > 3000 clonal metacercariae shed over its lifetime. Following experimental infection all 12 sheep were FEC positive at the time of TCBZ treatment. Sheep infected with one of three putative TCBZ-S clones and treated with TCBZ had no parasites in the liver at post-mortem, whilst sheep each infected with putative TCBZ-R isolates had 35–165 adult fluke at post-mortem, despite TCBZ treatment. All six untreated control animals had between 15–127 parasites. A single multi-locus genotype was reported for every fluke from each of the six clonal isolates. Adult F. hepatica showed considerable variation in weight, ranging from 20–280 mg, with variation in weight evident within and amongst clonal isolates. Conclusions A genetic clonal expansion occurs within G. truncatula, highlighting the potential for amplification of drug resistant genotypes of F. hepatica. Variation in the weight of parasites within and between clonal isolates and when comparing isolates that are either susceptible or resistant to TCBZ represent inherent variation in liver fluke and cannot be attributed to their resistance or susceptibility traits.
Collapse
Affiliation(s)
- Jane E Hodgkinson
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK.
| | - Krystyna Cwiklinski
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK.,School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Nicola Beesley
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK
| | - Catherine Hartley
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK
| | - Katherine Allen
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK
| | - Diana J L Williams
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK
| |
Collapse
|
148
|
Histone methylation changes are required for life cycle progression in the human parasite Schistosoma mansoni. PLoS Pathog 2018; 14:e1007066. [PMID: 29782530 PMCID: PMC5983875 DOI: 10.1371/journal.ppat.1007066] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/01/2018] [Accepted: 04/30/2018] [Indexed: 12/26/2022] Open
Abstract
Epigenetic mechanisms and chromatin structure play an important role in development. Their impact is therefore expected to be strong in parasites with complex life cycles and multiple, strikingly different, developmental stages, i.e. developmental plasticity. Some studies have already described how the chromatin structure, through histone modifications, varies from a developmental stage to another in a few unicellular parasites. While H3K4me3 profiles remain relatively constant, H3K27 trimethylation and bivalent methylation show strong variation. Inhibitors (A366 and GSK343) of H3K27 histone methyltransferase activity in S. mansoni efficiently blocked miracidium to sporocyst transition indicating that H3K27 trimethylation is required for life cycle progression. As S. mansoni is a multicellular parasite that significantly affects both the health and economy of endemic areas, a better understanding of fluke developmental processes within the definitive host will likely highlight novel disease control strategies. Towards this goal, we also studied H4K20me1 in female cercariae and adults. In particular, we found that bivalent trimethylation of H3K4 and H3K27 at the transcription start site of genes is a landmark of the cercarial stage. In cercariae, H3K27me3 presence and strong enrichment in H4K20me1 over long regions (10–100 kb) is associated with development related genes. Here, we provide a broad overview of the chromatin structure of a metazoan parasite throughout its most important lifecycle stages. The five developmental stages studied here present distinct chromatin structures, indicating that histone methylation plays an important role during development. Hence, components of the histone methylation (and demethylation) machinery may provide suitable Schistosomiasis control targets. Schistosoma mansoni is a parasitic flatworm and causative agent of intestinal schistosomiasis, a neglected tropical disease affecting 67 million people worldwide. The parasite has a complex life cycle involving two consecutive obligate hosts (a poikilotherm snail and a homeotherm mammal) and two transitions between these hosts as free-swimming larvae. Here, we show that the chromatin structure of five different developmental stages is characterized by specific changes in chemical modifications of histones, basic proteins that are closely associated with DNA (trimethylation of lysines 4 and 27 and histone H3, and monomethylation of lysine 20 on histone H4). These modifications occur around protein coding genes as well as within repetitive genomic elements. A functional role for histone methylation during schistosome development was elucidated by the use of epi-drugs targeting G9a/GLP and EZH2 histone methyltransferase orthologs in S. mansoni. Our results indicate that histone methylation plays an important role during schistosome development and suggest that the enzymes responsible for maintaining these chromatin modifications are suitable targets for anti-schistosomal drugs.
Collapse
|
149
|
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.
Collapse
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.
| |
Collapse
|
150
|
Dvorak J, Horn M. Serine proteases in schistosomes and other trematodes. Int J Parasitol 2018; 48:333-344. [PMID: 29477711 DOI: 10.1016/j.ijpara.2018.01.001] [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: 11/08/2017] [Revised: 01/19/2018] [Accepted: 01/25/2018] [Indexed: 02/04/2023]
Abstract
Trematodes, also known as flukes, are phylogenetically ancient parasitic organisms. Due to their importance as human and veterinary parasites, their proteins have been investigated extensively as drug and vaccine targets. Among those, proteases, as crucial enzymes for parasite survival, are considered candidate molecules for anti-parasitic interventions. Surprisingly however, trematode serine proteases, in comparison with other groups of proteases, are largely neglected. Genes encoding serine proteases have been identified in trematode genomes in significant abundance, but the biological roles and biochemical functions of these proteases are poorly understood. However, increasing volumes of genomic and proteomic studies, and accumulated experimental evidence, indicate that this class of proteases plays a substantial role in host-parasite interactions and parasite survival. Here, we discuss in detail serine proteases at genomic and protein levels, and their known or hypothetical functions.
Collapse
Affiliation(s)
- Jan Dvorak
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences in Prague, Kamycka 129, Prague CZ 165 21, Czech Republic.
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague CZ 166 10, Czech Republic.
| |
Collapse
|