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Tyagi R, Rosa BA, Swain A, Artyomov MN, Jasmer DP, Mitreva M. Intestinal cell diversity and treatment responses in a parasitic nematode at single cell resolution. BMC Genomics 2024; 25:341. [PMID: 38575858 PMCID: PMC10996262 DOI: 10.1186/s12864-024-10203-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Parasitic nematodes, significant pathogens for humans, animals, and plants, depend on diverse organ systems for intra-host survival. Understanding the cellular diversity and molecular variations underlying these functions holds promise for developing novel therapeutics, with specific emphasis on the neuromuscular system's functional diversity. The nematode intestine, crucial for anthelmintic therapies, exhibits diverse cellular phenotypes, and unraveling this diversity at the single-cell level is essential for advancing knowledge in anthelmintic research across various organ systems. RESULTS Here, using novel single-cell transcriptomics datasets, we delineate cellular diversity within the intestine of adult female Ascaris suum, a parasitic nematode species that infects animals and people. Gene transcripts expressed in individual nuclei of untreated intestinal cells resolved three phenotypic clusters, while lower stringency resolved additional subclusters and more potential diversity. Clusters 1 and 3 phenotypes displayed variable congruence with scRNA phenotypes of C. elegans intestinal cells, whereas the A. suum cluster 2 phenotype was markedly unique. Distinct functional pathway enrichment characterized each A. suum intestinal cell cluster. Cluster 2 was distinctly enriched for Clade III-associated genes, suggesting it evolved within clade III nematodes. Clusters also demonstrated differential transcriptional responsiveness to nematode intestinal toxic treatments, with Cluster 2 displaying the least responses to short-term intra-pseudocoelomic nematode intestinal toxin treatments. CONCLUSIONS This investigation presents advances in knowledge related to biological differences among major cell populations of adult A. suum intestinal cells. For the first time, diverse nematode intestinal cell populations were characterized, and associated biological markers of these cells were identified to support tracking of constituent cells under experimental conditions. These advances will promote better understanding of this and other parasitic nematodes of global importance, and will help to guide future anthelmintic treatments.
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Affiliation(s)
- Rahul Tyagi
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, 63110, St. Louis, MO, USA
| | - Bruce A Rosa
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, 63110, St. Louis, MO, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, 63110, Saint Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, 63110, Saint Louis, MO, USA
| | - Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, 99164, Pullman, WA, USA.
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, 63110, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, 63110, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, 63110, St Louis, MO, USA.
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2
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Dube F, Delhomme N, Martin F, Hinas A, Åbrink M, Svärd S, Tydén E. Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure. PLoS One 2024; 19:e0298039. [PMID: 38359071 PMCID: PMC10868809 DOI: 10.1371/journal.pone.0298039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
Anthelmintic resistance in equine parasite Parascaris univalens, compromises ivermectin (IVM) effectiveness and necessitates an in-depth understanding of its resistance mechanisms. Most research, primarily focused on holistic gene expression analyses, may overlook vital tissue-specific responses and often limit the scope of novel genes. This study leveraged gene co-expression network analysis to elucidate tissue-specific transcriptional responses and to identify core genes implicated in the IVM response in P. univalens. Adult worms (n = 28) were exposed to 10-11 M and 10-9 M IVM in vitro for 24 hours. RNA-sequencing examined transcriptional changes in the anterior end and intestine. Differential expression analysis revealed pronounced tissue differences, with the intestine exhibiting substantially more IVM-induced transcriptional activity. Gene co-expression network analysis identified seven modules significantly associated with the response to IVM. Within these, 219 core genes were detected, largely expressed in the intestinal tissue and spanning diverse biological processes with unspecific patterns. After 10-11 M IVM, intestinal tissue core genes showed transcriptional suppression, cell cycle inhibition, and ribosomal alterations. Interestingly, genes PgR028_g047 (sorb-1), PgB01_g200 (gmap-1) and PgR046_g017 (col-37 & col-102) switched from downregulation at 10-11 M to upregulation at 10-9 M IVM. The 10-9 M concentration induced expression of cuticle and membrane integrity core genes in the intestinal tissue. No clear core gene patterns were visible in the anterior end after 10-11 M IVM. However, after 10-9 M IVM, the anterior end mostly displayed downregulation, indicating disrupted transcriptional regulation. One interesting finding was the non-modular calcium-signaling gene, PgR047_g066 (gegf-1), which uniquely connected 71 genes across four modules. These genes were enriched for transmembrane signaling activity, suggesting that PgR047_g066 (gegf-1) could have a key signaling role. By unveiling tissue-specific expression patterns and highlighting biological processes through unbiased core gene detection, this study reveals intricate IVM responses in P. univalens. These findings suggest alternative drug uptake of IVM and can guide functional validations to further IVM resistance mechanism understanding.
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Affiliation(s)
- Faruk Dube
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Frida Martin
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Andrea Hinas
- Department of Cell and Molecular Biology, Uppsala University, Uppsala Sweden
| | - Magnus Åbrink
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Staffan Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala Sweden
| | - Eva Tydén
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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De R, Whiteley M, Azad RK. A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1. mSystems 2023; 8:e0047323. [PMID: 37921470 PMCID: PMC10734507 DOI: 10.1128/msystems.00473-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE We present here a new systems-level approach to decipher genetic factors and biological pathways associated with virulence and/or antibiotic treatment of bacterial pathogens. The power of this approach was demonstrated by application to a well-studied pathogen Pseudomonas aeruginosa PAO1. Our gene co-expression network-based approach unraveled known and unknown genes and their networks associated with pathogenicity in P. aeruginosa PAO1. The systems-level investigation of P. aeruginosa PAO1 helped identify putative pathogenicity and resistance-associated genetic factors that could not otherwise be detected by conventional approaches of differential gene expression analysis. The network-based analysis uncovered modules that harbor genes not previously reported by several original studies on P. aeruginosa virulence and resistance. These could potentially act as molecular determinants of P. aeruginosa PAO1 pathogenicity and responses to antibiotics.
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Affiliation(s)
- Ronika De
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
| | - Marvin Whiteley
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children’s Cystic Fibrosis Center, Atlanta, Georgia, USA
| | - Rajeev K. Azad
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
- Department of Mathematics, University of North Texas, Denton, Texas, USA
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4
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Phuphisut O, Poodeepiyasawat A, Yoonuan T, Watthanakulpanich D, Chotsiri P, Reamtong O, Mousley A, Gobert GN, Adisakwattana P. Transcriptome profiling of male and female Ascaris lumbricoides reproductive tissues. Parasit Vectors 2022; 15:477. [PMID: 36539906 PMCID: PMC9768952 DOI: 10.1186/s13071-022-05602-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Ascaris lumbricoides causes human ascariasis, the most prevalent helminth disease, infecting approximately 1 billion individuals globally. In 2019 the global disease burden was estimated to be 754,000 DALYs and resulted in 2090 deaths. In the absence of a vaccination strategy, treatment of ascariasis has relied on anthelminthic chemotherapy, but drug resistance is a concern. The propensity for reinfection is also a major challenge to disease control; female worms lay up to 200,000 eggs daily, which contaminate surrounding environments and remain viable for years, resulting in high transmission rates. Understanding the molecular mechanisms of reproductive processes, including control of egg production, spermatogenesis, oogenesis and embryogenesis, will drive the development of new drugs and/or vaccine targets for future ascariasis control. METHODS Transcriptome profiles of discrete reproductive and somatic tissue samples were generated from adult male and female worms using Illumina HiSeq with 2 × 150 bp paired-end sequencing. Male tissues included: testis germinal zone, testis part of vas deferens, seminal vesicle and somatic tissue. Female tissues included: ovary germinal zone, ovary part of the oviduct, uterus and somatic tissue. Differentially expressed genes (DEGs) were identified from the fragments per kilobases per million reads (FPKM) profiles. Hierarchical analysis was performed to identify tissue-specific genes. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were employed to identify significant terms and pathways for the DEGs. RESULTS DEGs involved in protein phosphorylation and adhesion molecules were indicated to play a crucial role in spermatogenesis and fertilization, respectively. Those genes associated with the G-protein-coupled receptor (GPCR) signaling pathway and small GTPase-mediated signal transduction pathway play an essential role in cytoskeleton organization during oogenesis. Additionally, DEGs associated with the SMA genes and TGF-β signaling pathway are crucial in adult female embryogenesis. Some genes associated with particular biological processes and pathways that were identified in this study have been linked to defects in germline development, embryogenesis and reproductive behavior. In the enriched KEGG pathway analysis, Hippo signaling, oxytocin signaling and tight junction pathways were identified to play a role in Ascaris male and female reproductive systems. CONCLUSIONS This study has provided comprehensive transcriptome profiles of discrete A. lumbricoides reproductive tissue samples, revealing the molecular basis of these functionally important tissues. The data generated from this study will provide fundamental knowledge on the reproductive biology of Ascaris and will inform future target identification for anti-ascariasis drugs and/or vaccines.
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Affiliation(s)
- Orawan Phuphisut
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Akkarin Poodeepiyasawat
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Tippayarat Yoonuan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Dorn Watthanakulpanich
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Palang Chotsiri
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, 10400, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Angela Mousley
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Geoffrey N Gobert
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
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Wang J. Genomics of the Parasitic Nematode Ascaris and Its Relatives. Genes (Basel) 2021; 12:493. [PMID: 33800545 PMCID: PMC8065839 DOI: 10.3390/genes12040493] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
Nematodes of the genus Ascaris are important parasites of humans and swine, and the phylogenetically related genera (Parascaris, Toxocara, and Baylisascaris) infect mammals of veterinary interest. Over the last decade, considerable genomic resources have been established for Ascaris, including complete germline and somatic genomes, comprehensive mRNA and small RNA transcriptomes, as well as genome-wide histone and chromatin data. These datasets provide a major resource for studies on the basic biology of these parasites and the host-parasite relationship. Ascaris and its relatives undergo programmed DNA elimination, a highly regulated process where chromosomes are fragmented and portions of the genome are lost in embryonic cells destined to adopt a somatic fate, whereas the genome remains intact in germ cells. Unlike many model organisms, Ascaris transcription drives early development beginning prior to pronuclear fusion. Studies on Ascaris demonstrated a complex small RNA network even in the absence of a piRNA pathway. Comparative genomics of these ascarids has provided perspectives on nematode sex chromosome evolution, programmed DNA elimination, and host-parasite coevolution. The genomic resources enable comparison of proteins across diverse species, revealing many new potential drug targets that could be used to control these parasitic nematodes.
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Affiliation(s)
- Jianbin Wang
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA;
- UT-Oak Ridge National Laboratory Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
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6
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Caraballo L, Zakzuk J, Acevedo N. Helminth-derived cystatins: the immunomodulatory properties of an Ascaris lumbricoides cystatin. Parasitology 2021; 148:1-13. [PMID: 33563346 DOI: 10.1017/s0031182021000214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Helminth infections such as ascariasis elicit a type 2 immune response resembling that involved in allergic inflammation, but differing to allergy, they are also accompanied with strong immunomodulation. This has stimulated an increasing number of investigations, not only to better understand the mechanisms of allergy and helminth immunity but to find parasite-derived anti-inflammatory products that could improve the current treatments of chronic non-communicable inflammatory diseases such as asthma. A great number of helminth-derived immunomodulators have been discovered and some of them extensively analysed, showing their potential use as anti-inflammatory drugs in clinical settings. Since Ascaris lumbricoides is one of the most successful parasites, several groups have focused on the immunomodulatory properties of this helminth. As a result, several excretory/secretory components and purified molecules have been analysed, revealing interesting anti-inflammatory activities potentially useful as therapeutic tools. One of these molecules is A. lumbricoides cystatin, whose genomic, cellular, molecular, and immunomodulatory properties are described in this review.
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Affiliation(s)
- Luis Caraballo
- Institute for Immunological Research, University of Cartagena, Cartagena de Indias, Colombia
| | - Josefina Zakzuk
- Institute for Immunological Research, University of Cartagena, Cartagena de Indias, Colombia
| | - Nathalie Acevedo
- Institute for Immunological Research, University of Cartagena, Cartagena de Indias, Colombia
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7
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Atkinson LE, McCoy CJ, Crooks BA, McKay FM, McVeigh P, McKenzie D, Irvine A, Harrington J, Rosa BA, Mitreva M, Marks NJ, Maule AG, Mousley A. Phylum-Spanning Neuropeptide GPCR Identification and Prioritization: Shaping Drug Target Discovery Pipelines for Nematode Parasite Control. Front Endocrinol (Lausanne) 2021; 12:718363. [PMID: 34659113 PMCID: PMC8515059 DOI: 10.3389/fendo.2021.718363] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/20/2021] [Indexed: 11/24/2022] Open
Abstract
Nematode parasites undermine human health and global food security. The frontline anthelmintic portfolio used to treat parasitic nematodes is threatened by the escalation of anthelmintic resistance, resulting in a demand for new drug targets for parasite control. Nematode neuropeptide signalling pathways represent an attractive source of novel drug targets which currently remain unexploited. The complexity of the nematode neuropeptidergic system challenges the discovery of new targets for parasite control, however recent advances in parasite 'omics' offers an opportunity for the in silico identification and prioritization of targets to seed anthelmintic discovery pipelines. In this study we employed Hidden Markov Model-based searches to identify ~1059 Caenorhabditis elegans neuropeptide G-protein coupled receptor (Ce-NP-GPCR) encoding gene homologs in the predicted protein datasets of 10 key parasitic nematodes that span several phylogenetic clades and lifestyles. We show that, whilst parasitic nematodes possess a reduced complement of Ce-NP-GPCRs, several receptors are broadly conserved across nematode species. To prioritize the most appealing parasitic nematode NP-GPCR anthelmintic targets, we developed a novel in silico nematode parasite drug target prioritization pipeline that incorporates pan-phylum NP-GPCR conservation, C. elegans-derived reverse genetics phenotype, and parasite life-stage specific expression datasets. Several NP-GPCRs emerge as the most attractive anthelmintic targets for broad spectrum nematode parasite control. Our analyses have also identified the most appropriate targets for species- and life stage- directed chemotherapies; in this context we have identified several NP-GPCRs with macrofilaricidal potential. These data focus functional validation efforts towards the most appealing NP-GPCR targets and, in addition, the prioritization strategy employed here provides a blueprint for parasitic nematode target selection beyond NP-GPCRs.
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Affiliation(s)
- Louise E. Atkinson
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Ciaran J. McCoy
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Bethany A. Crooks
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Fiona M. McKay
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Paul McVeigh
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Darrin McKenzie
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Allister Irvine
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - John Harrington
- Boehringer Ingelheim Animal Health, Athens, GA, United States
| | - Bruce A. Rosa
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Nikki J. Marks
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Aaron G. Maule
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Angela Mousley
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- *Correspondence: Angela Mousley,
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8
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Toward an understanding of the relation between gene regulation and 3D genome organization. QUANTITATIVE BIOLOGY 2020. [DOI: 10.1007/s40484-020-0221-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Eurmsirilerd E, Maduro MF. Evolution of Developmental GATA Factors in Nematodes. J Dev Biol 2020; 8:jdb8040027. [PMID: 33207804 PMCID: PMC7712238 DOI: 10.3390/jdb8040027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
GATA transcription factors are found in animals, plants, and fungi. In animals, they have important developmental roles in controlling specification of cell identities and executing tissue-specific differentiation. The Phylum Nematoda is a diverse group of vermiform animals that inhabit ecological niches all over the world. Both free-living and parasitic species are known, including those that cause human infectious disease. To date, GATA factors in nematodes have been studied almost exclusively in the model system C. elegans and its close relatives. In this study, we use newly available sequences to identify GATA factors across the nematode phylum. We find that most species have fewer than six GATA factors, but some species have 10 or more. Comparisons of gene and protein structure suggest that there were at most two GATA factors at the base of the phylum, which expanded by duplication and modification to result in a core set of four factors. The high degree of structural similarity with the corresponding orthologues in C. elegans suggests that the nematode GATA factors share similar functions in development.
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Affiliation(s)
- Ethan Eurmsirilerd
- Undergraduate Program in Biology, Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA;
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Morris F. Maduro
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, CA 92521, USA
- Correspondence:
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10
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Jasmer DP, Rosa BA, Tyagi R, Mitreva M. Rapid determination of nematode cell and organ susceptibility to toxic treatments. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2020; 14:167-182. [PMID: 33125935 PMCID: PMC7593349 DOI: 10.1016/j.ijpddr.2020.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/28/2022]
Abstract
In research focused on the intestine of parasitic nematodes, we recently identified small molecule inhibitors toxic to intestinal cells of larval Ascaris suum (nematode intestinal toxins/toxicants; “NITs”). Some NITs had anthelmintic activity across the phylogenetic diversity of the Nematoda. The whole-worm motility inhibition assay quantified anthelmintic activity, but worm responses to NITs in relation to pathology or affected molecular pathways was not acquired. In this study we extended this research to more comprehensively determine in whole larval A. suum the cells, organ systems, molecular targets, and potential cellular pathways involved in mechanisms of toxicity leading to cell death. The experimental system utilized fluorescent nuclear probes (bisbenzimide, propidium iodide), NITs, an A. suum larval parasite culture system and transcriptional responses (RNA-seq) to NITs. The approach provides for rapid resolution of NIT-induced cell death among organ systems (e.g. intestine, excretory, esophagus, hypodermis and seam cells, and nervous), discriminates among NITs based on cell death profiles, and identifies cells and organ systems with the greatest NIT sensitivity (e.g. intestine and apparent neuronal cells adjacent to the nerve ring). Application was extended to identify cells and organs sensitive to several existing anthelmintics. This approach also resolved intestinal cell death and irreparable damage induced in adult A. suum by two NITs, establishing a new model to elucidate relevant pathologic mechanisms in adult worms. RNA-seq analysis resolved A. suum genes responsive to treatments with three NITs, identifying dihydroorotate dehydrogenase (uridine synthesis) and RAB GTPase(s) (vesicle transport) as potential targets/pathways leading to cell death. A set of genes induced by all three NITs tested suggest common stress or survival responses activated by NITs. Beyond the presented specific lines of research, elements of the overall experimental system presented in this study have broad application toward systematic development of new anthelmintics. A unique rapid cell death assay was developed for parasitic nematodes. Multiple drug-like molecules cause widespread cell death in many organs of A. suum. Multiple cell and organ systems were validated as targets for anthelmintics. Potential drug targets/pathways were implicated in activating cell death processes.
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Affiliation(s)
- Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Bruce A Rosa
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rahul Tyagi
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, St. Louis, MO, 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, 63108, USA.
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11
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McHugh M, Williams P, Verma S, Powell-Coffman JA, Robertson AP, Martin RJ. Cholinergic receptors on intestine cells of Ascaris suum and activation of nAChRs by levamisole. Int J Parasitol Drugs Drug Resist 2020; 13:38-50. [PMID: 32470835 PMCID: PMC7256660 DOI: 10.1016/j.ijpddr.2020.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 11/19/2022]
Abstract
Cholinergic agonists, like levamisole, are a major class of anthelmintic drugs that are known to act selectively on nicotinic acetylcholine receptors (nAChRs) on the somatic muscle and nerves of nematode parasites to produce their contraction and spastic paralysis. Previous studies have suggested that in addition to the nAChRs found on muscle and nerves, there are nAChRs on non-excitable tissues of nematode parasites. We looked for evidence of nAChRs expression in the cells of the intestine of the large pig nematode, Ascaris suum, using RT-PCR and RNAscope in situ hybridization and detected mRNA of nAChR subunits in the cells. These subunits include components of the putative levamisole receptor in A. suum muscle: Asu-unc-38, Asu-unc-29, Asu-unc-63 and Asu-acr-8. Relative expression of these mRNAs in A. suum intestine was quantified by qPCR. We also looked for and found expression of G protein-linked acetylcholine receptors (Asu-gar-1). We used Fluo-3 AM to detect intracellular calcium changes in response to receptor activation by acetylcholine (as a non-selective agonist) and levamisole (as an L-type nAChR agonist) to look for evidence of functioning nAChRs in the intestine. We found that both acetylcholine and levamisole elicited increases in intracellular calcium but their signal profiles in isolated intestinal tissues were different, suggesting activation of different receptor sets. The levamisole responses were blocked by mecamylamine, a nicotinic receptor antagonist in A. suum, indicating the activation of intestinal nAChRs rather than G protein-linked acetylcholine receptors (GARs) by levamisole. The detection of nAChRs in cells of the intestine, in addition to those on muscles and nerves, reveals another site of action of the cholinergic anthelmintics and a site that may contribute to the synergistic interactions of cholinergic anthelmintics with other anthelmintics that affect the intestine (Cry5B).
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Affiliation(s)
- Mark McHugh
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Paul Williams
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Saurabh Verma
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jo Anne Powell-Coffman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Alan P Robertson
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Richard J Martin
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
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12
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Jasmer DP, Rosa BA, Tyagi R, Bulman CA, Beerntsen B, Urban JF, Sakanari J, Mitreva M. De novo identification of toxicants that cause irreparable damage to parasitic nematode intestinal cells. PLoS Negl Trop Dis 2020; 14:e0007942. [PMID: 32453724 PMCID: PMC7274465 DOI: 10.1371/journal.pntd.0007942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/05/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
Efforts to identify new drugs for therapeutic and preventive treatments against parasitic nematodes have gained increasing interest with expanding pathogen omics databases and drug databases from which new anthelmintic compounds might be identified. Here, a novel approach focused on integrating a pan-Nematoda multi-omics data targeted to a specific nematode organ system (the intestinal tract) with evidence-based filtering and chemogenomic screening was undertaken. Based on de novo computational target prioritization of the 3,564 conserved intestine genes in A. suum, exocytosis was identified as a high priority pathway, and predicted inhibitors of exocytosis were tested using the large roundworm (Ascaris suum larval stages), a filarial worm (Brugia pahangi adult and L3), a whipworm (Trichuris muris adult), and the non-parasitic nematode Caenorhabditis elegans. 10 of 13 inhibitors were found to cause rapid immotility in A. suum L3 larvae, and five inhibitors were effective against the three phylogenetically diverse parasitic nematode species, indicating potential for a broad spectrum anthelmintics. Several distinct pathologic phenotypes were resolved related to molting, motility, or intestinal cell and tissue damage using conventional and novel histologic methods. Pathologic profiles characteristic for each inhibitor will guide future research to uncover mechanisms of the anthelmintic effects and improve on drug designs. This progress firmly validates the focus on intestinal cell biology as a useful resource to develop novel anthelmintic strategies.
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Affiliation(s)
- Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Bruce A Rosa
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rahul Tyagi
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Christina A Bulman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Brenda Beerntsen
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, United States of America
| | - Joseph F Urban
- U.S. Department of Agriculture, Northeast Area, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasite Diseases Laboratory and Beltsville Human Nutrition Research Center, Diet Genomics and Immunology Laboratory, Beltsville, Maryland, United States of America
| | - Judy Sakanari
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
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13
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Jasmer DP, Rosa BA, Tyagi R, Mitreva M. Omics Driven Understanding of the Intestines of Parasitic Nematodes. Front Genet 2019; 10:652. [PMID: 31402928 PMCID: PMC6669237 DOI: 10.3389/fgene.2019.00652] [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: 04/06/2019] [Accepted: 06/19/2019] [Indexed: 01/25/2023] Open
Abstract
The biological and molecular complexity of nematodes has impeded research on development of new therapies for treatment and control. We have focused on the versatility of the nematode intestine as a target for new therapies. To that end, it is desirable to establish a broad and deep understanding of the molecular architecture underlying intestinal cell functions at the pan-Nematoda level. Multiomics data were generated to uncover the evolutionary principles underlying both conserved and adaptable features of the nematode intestine. Whole genomes were used to reveal the functional potential of the nematodes, tissue-specific transcriptomes provided a deep assessment of genes that are expressed in the adult nematode intestine, and comparison of selected core species was used to determine a first approximation of the pan-Nematoda intestinal transcriptome. Differentially expressed transcripts were also identified among intestinal regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. Profiling intestinal miRNAs targeting these genes identified the conserved intestinal miRNAs. Proteomics of intestinal cell compartments assigned proteins to several different intestinal cell compartments (intestinal tissue, the integral and peripheral intestinal membranes, and the intestinal lumen). Finally, advanced bioinformatic approaches were used to predict intestinal cell functional categories of seminal importance to parasite survival, which can now be experimentally tested and validated. The data provide the most comprehensive compilation of constitutively and differentially expressed genes, predicted gene regulators, and proteins of the nematode intestine. The information provides knowledge that is essential to understand molecular features of nematode intestinal cells and functions of fundamental importance to the intestine of many, if not all, parasitic nematodes.
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Affiliation(s)
- Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Bruce A Rosa
- McDonnell Genome Institute, Washington University, St. Louis, St. Louis, MI, United States
| | - Rahul Tyagi
- McDonnell Genome Institute, Washington University, St. Louis, St. Louis, MI, United States
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University, St. Louis, St. Louis, MI, United States.,Department of Internal Medicine, Washington University School of Medicine, St. Louis, MI, United States
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14
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The C. elegans intestine: organogenesis, digestion, and physiology. Cell Tissue Res 2019; 377:383-396. [DOI: 10.1007/s00441-019-03036-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/12/2019] [Indexed: 12/16/2022]
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15
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Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters. PLoS One 2019; 14:e0212678. [PMID: 30908494 PMCID: PMC6433290 DOI: 10.1371/journal.pone.0212678] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 02/07/2019] [Indexed: 12/03/2022] Open
Abstract
In higher eukaryotes, gene architecture and structural properties of promoters have emerged as significant factors influencing variation in number of transcripts (expression level) and specificity of gene expression in a tissue (expression breadth), which eventually shape the phenotype. In this study, transcriptome data of different tissue types at various developmental stages of A. thaliana, O. sativa, S. bicolor and Z. mays have been used to understand the relationship between properties of gene components and its expression. Our findings indicate that in plants, among all gene architecture and structural properties of promoters, compactness of genes in terms of intron content is significantly linked to gene expression level and breadth, whereas in human an exactly opposite scenario is seen. In plants, for the first time we have carried out a quantitative estimation of effect of a particular trait on expression level and breadth, by using multiple regression analysis and it confirms that intron content of primary transcript (as %) is a powerful determinant of expression breadth. Similarly, further regression analysis revealed that among structural properties of the promoters, stability is negatively linked to expression breadth, while DNase1 sensitivity strongly governs gene expression breadth in monocots and gene expression level in dicots. In addition, promoter regions of tissue specific genes are found to be enriched with TATA box and Y-patch motifs. Finally, multi copy orthologous genes in plants are found to be longer, highly regulated and tissue specific.
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16
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Leroux LP, Nasr M, Valanparambil R, Tam M, Rosa BA, Siciliani E, Hill DE, Zarlenga DS, Jaramillo M, Weinstock JV, Geary TG, Stevenson MM, Urban JF, Mitreva M, Jardim A. Analysis of the Trichuris suis excretory/secretory proteins as a function of life cycle stage and their immunomodulatory properties. Sci Rep 2018; 8:15921. [PMID: 30374177 PMCID: PMC6206011 DOI: 10.1038/s41598-018-34174-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/12/2018] [Indexed: 12/21/2022] Open
Abstract
Parasitic worms have a remarkable ability to modulate host immune responses through several mechanisms including excreted/secreted proteins (ESP), yet the exact nature of these proteins and their targets often remains elusive. Here, we performed mass spectrometry analyses of ESP (TsESP) from larval and adult stages of the pig whipworm Trichuris suis (Ts) and identified ~350 proteins. Transcriptomic analyses revealed large subsets of differentially expressed genes in the various life cycle stages of the parasite. Exposure of bone marrow-derived macrophages and dendritic cells to TsESP markedly diminished secretion of the pro-inflammatory cytokines TNFα and IL-12p70. Conversely, TsESP exposure strongly induced release of the anti-inflammatory cytokine IL-10, and also induced high levels of nitric oxide (NO) and upregulated arginase activity in macrophages. Interestingly, TsESP failed to directly induce CD4+ CD25+ FoxP3+ regulatory T cells (Treg cells), while OVA-pulsed TsESP-treated dendritic cells suppressed antigen-specific OT-II CD4+ T cell proliferation. Fractionation of TsESP identified a subset of proteins that promoted anti-inflammatory functions, an activity that was recapitulated using recombinant T. suis triosephosphate isomerase (TPI) and nucleoside diphosphate kinase (NDK). Our study helps illuminate the intricate balance that is characteristic of parasite-host interactions at the immunological interface, and further establishes the principle that specific parasite-derived proteins can modulate immune cell functions.
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Affiliation(s)
- Louis-Philippe Leroux
- Institute of Parasitology McGill University, Sainte-Anne-de-Bellevue, QC, Canada
- Centre for Host-Parasite Interaction (CHPI), Montreal, Canada
- Institut National de la Recherche Scientifique (INRS)-Institut Armand-Frappier (IAF), Laval, QC, Canada
| | - Mohamad Nasr
- Institute of Parasitology McGill University, Sainte-Anne-de-Bellevue, QC, Canada
- Centre for Host-Parasite Interaction (CHPI), Montreal, Canada
| | - Rajesh Valanparambil
- Centre for Host-Parasite Interaction (CHPI), Montreal, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC, Canada
| | - Mifong Tam
- Centre for Host-Parasite Interaction (CHPI), Montreal, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Bruce A Rosa
- McDonnell Genome Institute, Washington University in, St. Louis, MO, USA
| | - Elizabeth Siciliani
- Institute of Parasitology McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Dolores E Hill
- United States Department of Agriculture, Beltsville, MD, USA
| | | | - Maritza Jaramillo
- Centre for Host-Parasite Interaction (CHPI), Montreal, Canada
- Institut National de la Recherche Scientifique (INRS)-Institut Armand-Frappier (IAF), Laval, QC, Canada
| | - Joel V Weinstock
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, Tufts Medical Center, Boston, MA, USA
| | - Timothy G Geary
- Institute of Parasitology McGill University, Sainte-Anne-de-Bellevue, QC, Canada
- Centre for Host-Parasite Interaction (CHPI), Montreal, Canada
| | - Mary M Stevenson
- Centre for Host-Parasite Interaction (CHPI), Montreal, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Joseph F Urban
- United States Department of Agriculture, Beltsville, MD, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University in, St. Louis, MO, USA
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Armando Jardim
- Institute of Parasitology McGill University, Sainte-Anne-de-Bellevue, QC, Canada.
- Centre for Host-Parasite Interaction (CHPI), Montreal, Canada.
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17
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Host- and Helminth-Derived Endocannabinoids That Have Effects on Host Immunity Are Generated during Infection. Infect Immun 2018; 86:IAI.00441-18. [PMID: 30104215 DOI: 10.1128/iai.00441-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/07/2018] [Indexed: 02/07/2023] Open
Abstract
Helminths have coevolved with their hosts, resulting in the development of specialized host immune mechanisms and parasite-specific regulatory products. Identification of new pathways that regulate helminth infection could provide a better understanding of host-helminth interaction and may identify new therapeutic targets for helminth infection. Here we identify the endocannabinoid system as a new mechanism that influences host immunity to helminths. Endocannabinoids are lipid-derived signaling molecules that control important physiologic processes, such as feeding behavior and metabolism. Following murine infection with Nippostrongylus brasiliensis, an intestinal nematode with a life cycle similar to that of hookworms, we observed increased levels of endocannabinoids (2-arachidonoylglycerol [2-AG] or anandamide [AEA]) and the endocannabinoid-like molecule oleoylethanolamine (OEA) in infected lung and intestine. To investigate endocannabinoid function in helminth infection, we employed pharmacological inhibitors of cannabinoid subtype receptors 1 and 2 (CB1R and CB2R). Compared to findings for vehicle-treated mice, inhibition of CB1R but not CB2R resulted in increased N. brasiliensis worm burden and egg output, associated with significantly decreased expression of the T helper type 2 cytokine interleukin 5 (IL-5) in intestinal tissue and splenocyte cultures. Strikingly, bioinformatic analysis of genomic and transcriptome sequencing (RNA-seq) data sets identified putative genes encoding endocannabinoid biosynthetic and degradative enzymes in many parasitic nematodes. To test the novel hypothesis that helminth parasites produce their own endocannabinoids, we measured endocannabinoid levels in N. brasiliensis by mass spectrometry and quantitative PCR and found that N. brasiliensis parasites produced endocannabinoids, especially at the infectious larval stage. To our knowledge, this is the first report of helminth- and host-derived endocannabinoids that promote host immune responses and reduce parasite burden.
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18
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Ebner F, Kuhring M, Radonić A, Midha A, Renard BY, Hartmann S. Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development. Front Immunol 2018; 9:1868. [PMID: 30158930 PMCID: PMC6104121 DOI: 10.3389/fimmu.2018.01868] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/30/2018] [Indexed: 11/17/2022] Open
Abstract
Gastrointestinal nematodes are among the most prevalent parasites infecting humans and livestock worldwide. Infective larvae of the soil-transmitted nematode Ascaris spp. enter the host and start tissue migration by crossing the intestinal epithelial barrier. The initial interaction of the intestinal epithelium with the parasite, however, has received little attention. In a time-resolved interaction model of porcine intestinal epithelial cells (IPEC-J2) and infective Ascaris suum larvae, we addressed the early transcriptional changes occurring simultaneously in both organisms using dual-species RNA-Seq. Functional analysis of the host response revealed an overall induction of metabolic activity, without induction of immune responsive genes or immune signaling pathways and showing suppression of chemotactic genes like CXCL8/IL-8 or CHI3L1. Ascaris larvae, when getting in contact with the epithelium, showed induction of genes that orchestrate motor activity and larval development, such as myosin, troponin, myoglobin, and protein disulfide isomerase 2 (PDI-2). In addition, excretory-secretory products that likely facilitate parasite invasion were increased, among them, aspartic protease 6 or hyaluronidase. Integration of host and pathogen data in an interspecies gene co-expression network indicated links between nematode fatty acid biosynthesis and host ribosome assembly/protein synthesis. In summary, our study provides new molecular insights into the early factors of parasite invasion, while at the same time revealing host immunological unresponsiveness. Reproducible software for dual RNA-Seq analysis of non-model organisms is available at https://gitlab.com/mkuhring/project_asuum and can be applied to similar studies.
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Affiliation(s)
- Friederike Ebner
- Department of Veterinary Medicine, Institute of Immunology, Freie Universität Berlin, Berlin, Germany
| | - Mathias Kuhring
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany.,Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany.,Berlin Institute of Health Metabolomics Platform, Berlin Institute of Health (BIH), Berlin, Germany.,Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany
| | - Aleksandar Radonić
- Center for Biological Threats and Special Pathogens: Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Berlin, Germany
| | - Ankur Midha
- Department of Veterinary Medicine, Institute of Immunology, Freie Universität Berlin, Berlin, Germany
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Susanne Hartmann
- Department of Veterinary Medicine, Institute of Immunology, Freie Universität Berlin, Berlin, Germany
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19
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Tyagi R, Maddirala AR, Elfawal M, Fischer C, Bulman CA, Rosa BA, Gao X, Chugani R, Zhou M, Helander J, Brindley PJ, Tseng CC, Greig IR, Sakanari J, Wildman SA, Aroian R, Janetka JW, Mitreva M. Small Molecule Inhibitors of Metabolic Enzymes Repurposed as a New Class of Anthelmintics. ACS Infect Dis 2018; 4:1130-1145. [PMID: 29718656 PMCID: PMC6283408 DOI: 10.1021/acsinfecdis.8b00090] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The enormous prevalence of infections caused by parasitic nematodes worldwide, coupled to the rapid emergence of their resistance to commonly used anthelmintic drugs, presents an urgent need for the discovery of new drugs. Herein, we have identified several classes of small molecules with broad spectrum activity against these pathogens. Previously, we reported the identification of carnitine palmitoyltransferases (CPTs) as a representative class of enzymes as potential targets for metabolic chokepoint intervention that was elucidated from a combination of chemogenomic screening and experimental testing in nematodes. Expanding on these previous findings, we have discovered that several chemical classes of known small molecule inhibitors of mammalian CPTs have potent activity as anthelmintics. Cross-clade efficacy against a broad spectrum of adult parasitic nematodes was demonstrated for multiple compounds from different series. Several analogs of these initial hit compounds were designed and synthesized. The compounds we report represent a good starting point for further lead identification and optimization for development of new anthelmintic drugs with broad spectrum activity and a novel mechanism of action.
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Affiliation(s)
- Rahul Tyagi
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, Missouri 63108, USA
| | - Amarendar Reddy Maddirala
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8231, St. Louis, Missouri 63110, USA
| | - Mostafa Elfawal
- University of Massachusetts Medical School, Suite 219 Biotech 2, 373 Plantation St., Worcester, Massachusetts 01605, USA
| | - Chelsea Fischer
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St, San Francisco, California 94158, USA
| | - Christina A. Bulman
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St, San Francisco, California 94158, USA
| | - Bruce A. Rosa
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, Missouri 63108, USA
| | - Xin Gao
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, Missouri 63108, USA
| | - Ryan Chugani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8231, St. Louis, Missouri 63110, USA
| | - Mingzhou Zhou
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8231, St. Louis, Missouri 63110, USA
| | - Jon Helander
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8231, St. Louis, Missouri 63110, USA
| | - Paul J. Brindley
- Department of Microbiology, Immunology & Tropical Medicine, and Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Ross Hall, Room 521, 2300 Eye Street, NW, Washington, DC 20037, USA
| | - Chih-Chung Tseng
- Kosterlitz Centre for Therapeutics, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, U.K
| | - Iain R. Greig
- Kosterlitz Centre for Therapeutics, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, U.K
| | - Judy Sakanari
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St, San Francisco, California 94158, USA
| | - Scott A. Wildman
- UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin 53792, USA
| | - Raffi Aroian
- University of Massachusetts Medical School, Suite 219 Biotech 2, 373 Plantation St., Worcester, Massachusetts 01605, USA
| | - James W. Janetka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8231, St. Louis, Missouri 63110, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, Missouri 63108, USA
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, 4523 Clayton Ave., CB 8051, St. Louis MO, 63110, USA
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20
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Cavallero S, Lombardo F, Su X, Salvemini M, Cantacessi C, D'Amelio S. Tissue-specific transcriptomes of Anisakis simplex (sensu stricto) and Anisakis pegreffii reveal potential molecular mechanisms involved in pathogenicity. Parasit Vectors 2018; 11:31. [PMID: 29321072 PMCID: PMC5763927 DOI: 10.1186/s13071-017-2585-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/11/2017] [Indexed: 11/11/2022] Open
Abstract
Background Larval stages of the sibling species of parasitic nematodes Anisakis simplex (sensu stricto) (s.s.) (AS) and Anisakis pegreffii (AP) are responsible for a fish-borne zoonosis, known as anisakiasis, that humans aquire via the ingestion of raw or undercooked infected fish or fish-based products. These two species differ in geographical distribution, genetic background and peculiar traits involved in pathogenicity. However, thus far little is known of key molecules potentially involved in host-parasite interactions. Here, high-throughput RNA-Seq and bioinformatics analyses of sequence data were applied to the characterization of the whole sets of transcripts expressed by infective larvae of AS and AP, as well as of their pharyngeal tissues, in a bid to identify transcripts potentially involved in tissue invasion and host-pathogen interplay. Results Approximately 34,000,000 single-end reads were generated from cDNA libraries for each species. Transcripts identified in AS and AP encoded 19,403 and 10,424 putative peptides, respectively, and were classified based on homology searches, protein motifs, gene ontology and biological pathway mapping. Differential gene expression analysis yielded 226 and 339 transcripts upregulated in the pharyngeal regions of AS and AP, respectively, compared with their corresponding whole-larvae datasets. These included proteolytic enzymes, molecules encoding anesthetics, inhibitors of primary hemostasis and virulence factors, anticoagulants and immunomodulatory peptides. Conclusions This work provides the scientific community with a list of key transcripts expressed by AS and AP pharyngeal tissues and corresponding annotation information which represents a ready-to-use resource for future functional studies of biological pathways specifically involved in host-parasite interplay. Electronic supplementary material The online version of this article (10.1186/s13071-017-2585-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Serena Cavallero
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.
| | - Fabrizio Lombardo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Xiaopei Su
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Marco Salvemini
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Stefano D'Amelio
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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21
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Tool-Driven Advances in Neuropeptide Research from a Nematode Parasite Perspective. Trends Parasitol 2017; 33:986-1002. [DOI: 10.1016/j.pt.2017.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/10/2017] [Accepted: 08/21/2017] [Indexed: 01/21/2023]
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22
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Variation in gene expression within clones of the earthworm Dendrobaena octaedra. PLoS One 2017; 12:e0174960. [PMID: 28384196 PMCID: PMC5383104 DOI: 10.1371/journal.pone.0174960] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 03/19/2017] [Indexed: 12/23/2022] Open
Abstract
Gene expression is highly plastic, which can help organisms to both acclimate and adapt to changing environments. Possible variation in gene expression among individuals with the same genotype (among clones) is not widely considered, even though it could impact the results of studies that focus on gene expression phenotypes, for example studies using clonal lines. We examined the extent of within and between clone variation in gene expression in the earthworm Dendrobaena octaedra, which reproduces through apomictic parthenogenesis. Five microsatellite markers were developed and used to confirm that offspring are genetic clones of their parent. After that, expression of 12 genes was measured from five individuals each from six clonal lines after exposure to copper contaminated soil. Variation in gene expression was higher over all genotypes than within genotypes, as initially assumed. A subset of the genes was also examined in the offspring of exposed individuals in two of the clonal lines. In this case, variation in gene expression within genotypes was as high as that observed over all genotypes. One gene in particular (chymotrypsin inhibitor) also showed significant differences in the expression levels among genetically identical individuals. Gene expression can vary considerably, and the extent of variation may depend on the genotypes and genes studied. Ensuring a large sample, with many different genotypes, is critical in studies comparing gene expression phenotypes. Researchers should be especially cautious inferring gene expression phenotypes when using only a single clonal or inbred line, since the results might be specific to only certain genotypes.
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23
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Rosa BA, McNulty SN, Mitreva M, Jasmer DP. Direct experimental manipulation of intestinal cells in Ascaris suum, with minor influences on the global transcriptome. Int J Parasitol 2017; 47:271-279. [PMID: 28223178 DOI: 10.1016/j.ijpara.2016.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 12/24/2022]
Abstract
Ascaris suum provides a powerful model for studying parasitic nematodes, including individual tissues such as the intestine, an established target for anthelmintic treatments. Here, we add a valuable experimental component to our existing functional, proteomic, transcriptomic and phylogenomic studies of the Ascaris suum intestine, by developing a method to manipulate intestinal cell functions via direct delivery of experimental treatments (in this case, double-stranded (ds)RNA) to the apical intestinal membrane. We developed an intestinal perfusion method for direct, controlled delivery of dsRNA/heterogeneous small interfering (hsi) RNA into the intestinal lumen for experimentation. RNA-Seq (22 samples) was used to assess influences of the method on global intestinal gene expression. Successful mRNA-specific knockdown in intestinal cells of adult A. suum was accomplished with this new experimental method. Global transcriptional profiling confirmed that targeted transcripts were knocked down more significantly than any others, with only 12 (0.07% of all genes) or 238 (1.3%) off-target gene transcripts consistently differentially regulated by dsRNA treatment or the perfusion experimental design, respectively (after 24h). The system supports controlled, effective delivery of treatments (dsRNA/hsiRNA) to the apical intestinal membrane with relatively minor off-target effects, and builds on our experimental model to dissect A. suum intestinal cell functions with broad relevance to parasitic nematodes.
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Affiliation(s)
- Bruce A Rosa
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Samantha N McNulty
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Makedonka Mitreva
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA.
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Uygun S, Peng C, Lehti-Shiu MD, Last RL, Shiu SH. Utility and Limitations of Using Gene Expression Data to Identify Functional Associations. PLoS Comput Biol 2016; 12:e1005244. [PMID: 27935950 PMCID: PMC5147789 DOI: 10.1371/journal.pcbi.1005244] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/13/2016] [Indexed: 01/25/2023] Open
Abstract
Gene co-expression has been widely used to hypothesize gene function through guilt-by association. However, it is not clear to what degree co-expression is informative, whether it can be applied to genes involved in different biological processes, and how the type of dataset impacts inferences about gene functions. Here our goal is to assess the utility and limitations of using co-expression as a criterion to recover functional associations between genes. By determining the percentage of gene pairs in a metabolic pathway with significant expression correlation, we found that many genes in the same pathway do not have similar transcript profiles and the choice of dataset, annotation quality, gene function, expression similarity measure, and clustering approach significantly impacts the ability to recover functional associations between genes using Arabidopsis thaliana as an example. Some datasets are more informative in capturing coordinated expression profiles and larger data sets are not always better. In addition, to recover the maximum number of known pathways and identify candidate genes with similar functions, it is important to explore rather exhaustively multiple dataset combinations, similarity measures, clustering algorithms and parameters. Finally, we validated the biological relevance of co-expression cluster memberships with an independent phenomics dataset and found that genes that consistently cluster with leucine degradation genes tend to have similar leucine levels in mutants. This study provides a framework for obtaining gene functional associations by maximizing the information that can be obtained from gene expression datasets. There remain genes with no known function even in the most well studied, model species. One common way to hypothesize gene function is based on the assumption that genes with similar expression profiles tend to have similar functions. However, using datasets and biological pathway information from the model plant Arabidopsis thaliana as an example, we discovered that, although genes in the same pathways are functionally related, genes in only a subset of the pathways have highly similar expression patterns. In addition, our ability to hypothesize gene functions based on expression is significantly impacted by how the dataset is processed and combined as well as the methodology used to identify genes with similar expression. Therefore, multiple datasets and methods should be tested to maximize the functional information that we can get based on similarity in gene expression.
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Affiliation(s)
- Sahra Uygun
- Genetics Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Cheng Peng
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Melissa D. Lehti-Shiu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Robert L. Last
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Shin-Han Shiu
- Genetics Program, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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25
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Stoltzfus JD, Pilgrim AA, Herbert DR. Perusal of parasitic nematode 'omics in the post-genomic era. Mol Biochem Parasitol 2016; 215:11-22. [PMID: 27887974 DOI: 10.1016/j.molbiopara.2016.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 01/09/2023]
Abstract
The advent of high-throughput, next-generation sequencing methods combined with advances in computational biology and bioinformatics have greatly accelerated discovery within biomedical research. This "post-genomics" era has ushered in powerful approaches allowing one to quantify RNA transcript and protein abundance for every gene in the genome - often for multiple conditions. Herein, we chronicle how the post-genomics era has advanced our overall understanding of parasitic nematodes through transcriptomics and proteomics and highlight some of the important advances made in each major nematode clade. We primarily focus on organisms relevant to human health, given that nematode infections significantly impact disability-adjusted life years (DALY) scores within the developing world, but we also discuss organisms of veterinary importance as well as those used as laboratory models. As such, we envision that this review will serve as a comprehensive resource for those seeking a better understanding of basic parasitic nematode biology as well as those interested in targets for vaccination and pharmacological intervention.
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Affiliation(s)
- Jonathan D Stoltzfus
- Department of Biology, Millersville University, Millersville, PA, United States.
| | - Adeiye A Pilgrim
- Emory University School of Medicine MD/PhD Program, Atlanta, GA, United States
| | - De'Broski R Herbert
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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26
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Wei J, Damania A, Gao X, Liu Z, Mejia R, Mitreva M, Strych U, Bottazzi ME, Hotez PJ, Zhan B. The hookworm Ancylostoma ceylanicum intestinal transcriptome provides a platform for selecting drug and vaccine candidates. Parasit Vectors 2016; 9:518. [PMID: 27677574 PMCID: PMC5039805 DOI: 10.1186/s13071-016-1795-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/12/2016] [Indexed: 12/02/2022] Open
Abstract
Background The intestine of hookworms contains enzymes and proteins involved in the blood-feeding process of the parasite and is therefore a promising source of possible vaccine antigens. One such antigen, the hemoglobin-digesting intestinal aspartic protease known as Na-APR-1 from the human hookworm Necator americanus, is currently a lead candidate antigen in clinical trials, as is Na-GST-1 a heme-detoxifying glutathione S-transferase. Methods In order to discover additional hookworm vaccine antigens, messenger RNA was obtained from the intestine of male hookworms, Ancylostoma ceylanicum, maintained in hamsters. RNA-seq was performed using Illumina high-throughput sequencing technology. The genes expressed in the hookworm intestine were compared with those expressed in the whole worm and those genes overexpressed in the parasite intestine transcriptome were further analyzed. Results Among the lead transcripts identified were genes encoding for proteolytic enzymes including an A. ceylanicum APR-1, but the most common proteases were cysteine-, serine-, and metallo-proteases. Also in abundance were specific transporters of key breakdown metabolites, including amino acids, glucose, lipids, ions and water; detoxifying and heme-binding glutathione S-transferases; a family of cysteine-rich/antigen 5/pathogenesis-related 1 proteins (CAP) previously found in high abundance in parasitic nematodes; C-type lectins; and heat shock proteins. These candidates will be ranked for downstream antigen target selection based on key criteria including abundance, uniqueness in the parasite versus the vertebrate host, as well as solubility and yield of expression. Conclusion The intestinal transcriptome of A. ceylanicum provides useful information for the identification of proteins involved in the blood-feeding process, representing a first step towards a reverse vaccinology approach to a human hookworm vaccine. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1795-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junfei Wei
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ashish Damania
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xin Gao
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Zhuyun Liu
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rojelio Mejia
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.,Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Ulrich Strych
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maria Elena Bottazzi
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Biology, Baylor University, Waco, TX, 76706, USA
| | - Peter J Hotez
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Biology, Baylor University, Waco, TX, 76706, USA
| | - Bin Zhan
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
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27
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Gao X, Tyagi R, Magrini V, Ly A, Jasmer DP, Mitreva M. Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the nematode intestine. RNA Biol 2016; 14:1335-1352. [PMID: 27002534 DOI: 10.1080/15476286.2016.1166333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The intestine of parasitic nematodes has proven an important target for therapies aimed at prevention and treatment of diseases caused by these pathogens in humans, animals and plants. We have developed a unique research model with the intestine of Ascaris suum, the large round worm of swine and humans, that will enhance biological research on this tissue. To expand utility of this model, we quantitatively compared expression of 15,382 coding RNAs and 277 noncoding, micro RNAs (miRNAs) among 3 contiguous regions of the adult A. suum intestine. Differentially expressed transcripts were identified among regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. We further identified 64 exon splice variants (from 47 genes) that are differentially expressed among these regions. A total of 2,063 intestinal mRNA transcripts were predicted to be targeted by intestinal miRNA, and negative correlation coefficients for miRNA:mRNA abundances predicted 22 likely influential miRNAs and 503 likely associated miRNA:mRNA pairs. A. suum intestinal miRNAs were identified that are conserved with intestinal miRNAs from C. elegans (10 mature sequences and 13 seed sequences conserved), and prospective intestinal miRNAs from the murine gastrointestinal nematode, Heligmosomoides polygyrus (5 mature and 11 seeds). Most of the conserved intestinal miRNAs were also high abundance miRNAs. The data provide the most comprehensive compilation of constitutively and differentially expressed genes along the length of the intestine for any nematode species. The information will guide prospective development of many hypotheses on nematode intestinal functions encoded by mRNAs, miRNAs and interactions between these RNA populations.
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Affiliation(s)
- Xin Gao
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Rahul Tyagi
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Vincent Magrini
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Amy Ly
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Douglas P Jasmer
- b Department of Veterinary Microbiology and Pathology , Washington State University , Pullman , WA , USA
| | - Makedonka Mitreva
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA.,c Department of Internal Medicine , Washington University School of Medicine , St. Louis , MO , USA
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Vlaminck J, Supali T, Geldhof P, Hokke CH, Fischer PU, Weil GJ. Community Rates of IgG4 Antibodies to Ascaris Haemoglobin Reflect Changes in Community Egg Loads Following Mass Drug Administration. PLoS Negl Trop Dis 2016; 10:e0004532. [PMID: 26991326 PMCID: PMC4798312 DOI: 10.1371/journal.pntd.0004532] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/20/2016] [Indexed: 11/19/2022] Open
Abstract
Background Conventional diagnostic methods for human ascariasis are based on the detection of Ascaris lumbricoides eggs in stool samples. However, studies of ascariasis in pigs have shown that the prevalence and the number of eggs detected in the stool do not correlate well with exposure of the herd to the parasite. On the other hand, an ELISA test measuring antibodies to Ascaris suum haemoglobin (AsHb) has been shown to be useful for estimating transmission intensity on pig farms. In this study, we further characterized the AsHb antigen and screened samples from a population-based study conducted in an area that is endemic for Ascaris lumbricoides in Indonesia to assess changes in AsHb antibody rates and levels in humans following mass drug administration (MDA). Methodology/Principal findings We developed and evaluated an ELISA to detect human IgG4 antibodies to AsHb. We tested 1066 plasma samples collected at different times from 599 subjects who lived in a village in rural Indonesia that was highly endemic for ascariasis. The community received 6 rounds of MDA for lymphatic filariasis with albendazole plus diethylcarbamazine between 2002 and 2007. While the AsHb antibody assay was not sensitive for detecting all individuals with Ascaris eggs in their stools, the percentage of seropositive individuals decreased rapidly following MDA. Reductions in antibody rates reflected decreased mean egg output per person both at the community level and in different age groups. Two years after the last round of MDA the community egg output and antibody prevalence rate were reduced by 81.6% and 78.9% respectively compared to baseline levels. Conclusion/Significance IgG4 antibody levels to AsHb appear to reflect recent exposure to Ascaris. The antibody prevalence rate may be a useful indicator for Ascaris transmission intensity in communities that can be used to assess the impact of control measures on the force of transmission. Ascariasis is a neglected tropical disease caused by the intestinal nematode Ascaris lumbricoides that affects hundreds of millions of people in the developing world. Current methods for diagnosis of this infection are based on detecting eggs in the stool that are excreted by adult Ascaris worms. However, these methods have limited sensitivity for recent infections, and they do not detect infections with immature parasite stages that do not always result in the establishment of adult worms in the human intestine. We have previously shown that an assay for antibodies to Ascaris hemoglobin in pig serum is useful for assessing transmission of Ascaris infections on pig farms. In this study, we developed and evaluated a similar antibody assay that is based on the detection of human IgG4 antibodies to Ascaris haemoglobin (AsHb). Community antibody rates decreased rapidly following mass drug administration of the anthelmintic drug albendazole, and this decrease reflected reduced Ascaris egg excretion at the community level. This antibody test may be a useful tool for assessing the impact of control measures on the transmission of new Ascaris infections in endemic populations.
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Affiliation(s)
- Johnny Vlaminck
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
| | - Taniawati Supali
- Department of Parasitology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Peter Geldhof
- Laboratory for Parasitology, Department of Virology, Parasitology and Immunology, Ghent University, Merelbeke, Belgium
| | - Cornelis H. Hokke
- Department of Parasitology, Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter U. Fischer
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gary J. Weil
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
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29
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McNulty SN, Strübe C, Rosa BA, Martin JC, Tyagi R, Choi YJ, Wang Q, Hallsworth Pepin K, Zhang X, Ozersky P, Wilson RK, Sternberg PW, Gasser RB, Mitreva M. Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention. Sci Rep 2016; 6:20316. [PMID: 26856411 PMCID: PMC4746573 DOI: 10.1038/srep20316] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/26/2015] [Indexed: 11/12/2022] Open
Abstract
The bovine lungworm, Dictyocaulus viviparus (order Strongylida), is an important parasite of livestock that causes substantial economic and production losses worldwide. Here we report the draft genome, variome, and developmental transcriptome of D. viviparus. The genome (161 Mb) is smaller than those of related bursate nematodes and encodes fewer proteins (14,171 total). In the first genome-wide assessment of genomic variation in any parasitic nematode, we found a high degree of sequence variability in proteins predicted to be involved host-parasite interactions. Next, we used extensive RNA sequence data to track gene transcription across the life cycle of D. viviparus, and identified genes that might be important in nematode development and parasitism. Finally, we predicted genes that could be vital in host-parasite interactions, genes that could serve as drug targets, and putative RNAi effectors with a view to developing functional genomic tools. This extensive, well-curated dataset should provide a basis for developing new anthelmintics, vaccines, and improved diagnostic tests and serve as a platform for future investigations of drug resistance and epidemiology of the bovine lungworm and related nematodes.
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Affiliation(s)
- Samantha N McNulty
- The McDonnell Genome Institute, Washington University in St Louis, MO 63108, USA
| | - Christina Strübe
- Institute for Parasitology, University of Veterinary Medicine Hannover, Hannover 30559, Germany
| | - Bruce A Rosa
- The McDonnell Genome Institute, Washington University in St Louis, MO 63108, USA
| | - John C Martin
- The McDonnell Genome Institute, Washington University in St Louis, MO 63108, USA
| | - Rahul Tyagi
- The McDonnell Genome Institute, Washington University in St Louis, MO 63108, USA
| | - Young-Jun Choi
- The McDonnell Genome Institute, Washington University in St Louis, MO 63108, USA
| | - Qi Wang
- The McDonnell Genome Institute, Washington University in St Louis, MO 63108, USA
| | | | - Xu Zhang
- The McDonnell Genome Institute, Washington University in St Louis, MO 63108, USA
| | - Philip Ozersky
- The McDonnell Genome Institute, Washington University in St Louis, MO 63108, USA
| | - Richard K Wilson
- The McDonnell Genome Institute, Washington University in St Louis, MO 63108, USA
| | - Paul W Sternberg
- HHMI, Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Makedonka Mitreva
- The McDonnell Genome Institute, Washington University in St Louis, MO 63108, USA.,Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
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30
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Luck AN, Anderson KG, McClung CM, VerBerkmoes NC, Foster JM, Michalski ML, Slatko BE. Tissue-specific transcriptomics and proteomics of a filarial nematode and its Wolbachia endosymbiont. BMC Genomics 2015; 16:920. [PMID: 26559510 PMCID: PMC4642636 DOI: 10.1186/s12864-015-2083-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 10/15/2015] [Indexed: 11/12/2022] Open
Abstract
Background Filarial nematodes cause debilitating human diseases. While treatable, recent evidence suggests drug resistance is developing, necessitating the development of novel targets and new treatment options. Although transcriptomic and proteomic studies around the nematode life cycle have greatly enhanced our knowledge, whole organism approaches have not provided spatial resolution of gene expression, which can be gained by examining individual tissues. Generally, due to their small size, tissue dissection of human-infecting filarial nematodes remains extremely challenging. However, canine heartworm disease is caused by a closely related and much larger filarial nematode, Dirofilaria immitis. As with many other filarial nematodes, D. immitis contains Wolbachia, an obligate bacterial endosymbiont present in the hypodermis and developing oocytes within the uterus. Here, we describe the first concurrent tissue-specific transcriptomic and proteomic profiling of a filarial nematode (D. immitis) and its Wolbachia (wDi) in order to better understand tissue functions and identify tissue-specific antigens that may be used for the development of new diagnostic and therapeutic tools. Methods Adult D. immitis worms were dissected into female body wall (FBW), female uterus (FU), female intestine (FI), female head (FH), male body wall (MBW), male testis (MT), male intestine (MI), male head (MH) and 10.1186/s12864-015-2083-2 male spicule (MS) and used to prepare transcriptomic and proteomic libraries. Results Transcriptomic and proteomic analysis of several D. immitis tissues identified many biological functions enriched within certain tissues. Hierarchical clustering of the D. immitis tissue transcriptomes, along with the recently published whole-worm adult male and female D. immitis transcriptomes, revealed that the whole-worm transcriptome is typically dominated by transcripts originating from reproductive tissue. The uterus appeared to have the most variable transcriptome, possibly due to age. Although many functions are shared between the reproductive tissues, the most significant differences in gene expression were observed between the uterus and testis. Interestingly, wDi gene expression in the male and female body wall is fairly similar, yet slightly different to that of Wolbachia gene expression in the uterus. Proteomic methods verified 32 % of the predicted D. immitis proteome, including over 700 hypothetical proteins of D. immitis. Of note, hypothetical proteins were among some of the most abundant Wolbachia proteins identified, which may fulfill some important yet still uncharacterized biological function. Conclusions The spatial resolution gained from this parallel transcriptomic and proteomic analysis adds to our understanding of filarial biology and serves as a resource with which to develop future therapeutic strategies against filarial nematodes and their Wolbachia endosymbionts. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2083-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ashley N Luck
- Genome Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Kathryn G Anderson
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
| | - Colleen M McClung
- Chemical Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Nathan C VerBerkmoes
- Chemical Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Jeremy M Foster
- Genome Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Michelle L Michalski
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
| | - Barton E Slatko
- Genome Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA.
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Wang Q, Rosa BA, Nare B, Powell K, Valente S, Rotili D, Mai A, Marshall GR, Mitreva M. Targeting Lysine Deacetylases (KDACs) in Parasites. PLoS Negl Trop Dis 2015; 9:e0004026. [PMID: 26402733 PMCID: PMC4581690 DOI: 10.1371/journal.pntd.0004026] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/02/2015] [Indexed: 12/30/2022] Open
Abstract
Due to an increasing problem of drug resistance among almost all parasites species ranging from protists to worms, there is an urgent need to explore new drug targets and their inhibitors to provide new and effective parasitic therapeutics. In this regard, there is growing interest in exploring known drug leads of human epigenetic enzymes as potential starting points to develop novel treatments for parasitic diseases. This approach of repurposing (starting with validated targets and inhibitors) is quite attractive since it has the potential to reduce the expense of drug development and accelerate the process of developing novel drug candidates for parasite control. Lysine deacetylases (KDACs) are among the most studied epigenetic drug targets of humans, and a broad range of small-molecule inhibitors for these enzymes have been reported. In this work, we identify the KDAC protein families in representative species across important classes of parasites, screen a compound library of 23 hydroxamate- or benzamide-based small molecules KDAC inhibitors, and report their activities against a range of parasitic species, including the pathogen of malaria (Plasmodium falciparum), kinetoplastids (Trypanosoma brucei and Leishmania donovani), and nematodes (Brugia malayi, Dirofilaria immitis and Haemonchus contortus). Compound activity against parasites is compared to that observed against the mammalian cell line (L929 mouse fibroblast) in order to determine potential parasite-versus-host selectivity). The compounds showed nanomolar to sub-nanomolar potency against various parasites, and some selectivity was observed within the small panel of compounds tested. The possible binding modes of the active compounds at the different protein target sites within different species were explored by docking to homology models to help guide the discovery of more selective, parasite-specific inhibitors. This current work supports previous studies that explored the use of KDAC inhibitors in targeting Plasmodium to develop new anti-malarial treatments, and also pioneers experiments with these KDAC inhibitors as potential new anthelminthics. The selectivity observed begins to address the challenges of targeting specific parasitic diseases while limiting host toxicity. Due to pandemic drug resistance in the treatment of parasitic infections, there is an urgent need to identify novel drug targets and their associated drug compounds. Although “drug repurposing”, i.e. the application of known drugs and compounds to new indications such as infectious diseases, provides a cost effective approach in the development of novel therapeutics, selectivity is one of the major obstacles to overcome in getting such compounds into clinical trials as anti-parasitic drugs. Using the lysine deacetylases (KDACs) as an example, we explored the activities of a panel of known inhibitors against the KDAC targets in a range of parasitic organisms. The computational study of their binding modes to the targets (by docking the compounds to the homology models within different organisms in comparison with the human proteins) helps to rationalize the different activities observed and provide insight on the optimization of lead compounds to improve selectivity. Our work provides support of “drug repurposing” in the treatment of parasitic diseases, and demonstrates the necessity of optimizing these leads for the ultimate goal of preparing them for clinical use.
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Affiliation(s)
- Qi Wang
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bruce A. Rosa
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bakela Nare
- SCYNEXIS, Inc, Research Triangle Park, North Carolina, United States of America
| | - Kerrie Powell
- SCYNEXIS, Inc, Research Triangle Park, North Carolina, United States of America
| | - Sergio Valente
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, Roma, Italy
| | - Dante Rotili
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, Roma, Italy
| | - Antonello Mai
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma “La Sapienza”, Roma, Italy
| | - Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Makedonka Mitreva
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Departments of Genetics and of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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32
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Morris CP, Bennuru S, Kropp LE, Zweben JA, Meng Z, Taylor RT, Chan K, Veenstra TD, Nutman TB, Mitre E. A Proteomic Analysis of the Body Wall, Digestive Tract, and Reproductive Tract of Brugia malayi. PLoS Negl Trop Dis 2015; 9:e0004054. [PMID: 26367142 PMCID: PMC4569401 DOI: 10.1371/journal.pntd.0004054] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 08/14/2015] [Indexed: 12/18/2022] Open
Abstract
Filarial worms are parasitic nematodes that cause devastating diseases such as lymphatic filariasis (LF) and onchocerciasis. Filariae are nematodes with complex anatomy including fully developed digestive tracts and reproductive organs. To better understand the basic biology of filarial parasites and to provide insights into drug targets and vaccine design, we conducted a proteomic analysis of different anatomic fractions of Brugia malayi, a causative agent of LF. Approximately 500 adult female B. malayi worms were dissected, and three anatomical fractions (body wall, digestive tract, and reproductive tract) were obtained. Proteins from each anatomical fraction were extracted, desalted, trypsinized, and analyzed by microcapillary reverse-phase liquid chromatography-tandem-mass spectrometry. In total, we identified 4,785 B. malayi proteins. While 1,894 were identified in all three anatomic fractions, 396 were positively identified only within the digestive tract, 114 only within the body wall, and 1,011 only within the reproductive tract. Gene set enrichment analysis revealed a bias for transporters to be present within the digestive tract, suggesting that the intestine of adult filariae is functional and important for nutrient uptake or waste removal. As expected, the body wall exhibited increased frequencies of cytoskeletal proteins, and the reproductive tract had increased frequencies of proteins involved in nuclear regulation and transcription. In assessing for possible vaccine candidates, we focused on proteins sequestered within the digestive tract, as these could possibly represent “hidden antigens” with low risk of prior allergic sensitization. We identified 106 proteins that are enriched in the digestive tract and are predicted to localize to the surface of cells in the the digestive tract. It is possible that some of these proteins are on the luminal surface and may be accessible by antibodies ingested by the worm. A subset of 27 of these proteins appear especially promising vaccine candidates as they contain significant non-cytoplasmic domains, only 1–2 transmembrane domains, and a high degree of homology to W. bancrofti and/or O. volvulus. Filarial worms are parasitic worms that can live for years within humans and cause diseases such as elephantiasis and river blindness. In this study, we identified the proteins that exist within the worm's digestive tract, reproductive tract, and body wall. In addition to increasing our understanding of the basic biology of these parasites, this information is valuable for predicting which proteins may be candidates for vaccine development and rational drug design. Specifically, by analyzing which intestinal proteins are likely expressed on the surface of cells contained within the parasite's digestive tract and have little similarity to human proteins, we identified 27 possible vaccine candidates that warrant further study.
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Affiliation(s)
- C. Paul Morris
- Department of Microbiology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sasisekhar Bennuru
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Laura E. Kropp
- Department of Microbiology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Jesse A. Zweben
- Department of Microbiology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Zhaojing Meng
- Protein Characterization Laboratory Cancer Research Technology Program, Leidos Biomedical Research inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Rebekah T. Taylor
- Department of Biology, Frostburg State University, Frostburg, Maryland, United States of America
| | - King Chan
- Protein Characterization Laboratory Cancer Research Technology Program, Leidos Biomedical Research inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Timothy D. Veenstra
- Protein Characterization Laboratory Cancer Research Technology Program, Leidos Biomedical Research inc., Frederick National Laboratory, Frederick, Maryland, United States of America
| | - Thomas B. Nutman
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Edward Mitre
- Department of Microbiology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- * E-mail:
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Ma GX, Zhou RQ, Song ZH, Zhu HH, Zhou ZY, Zeng YQ. Molecular mechanism of serine/threonine protein phosphatase 1 (PP1cα-PP1r7) in spermatogenesis of Toxocara canis. Acta Trop 2015; 149:148-54. [PMID: 26026715 DOI: 10.1016/j.actatropica.2015.05.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 05/20/2015] [Accepted: 05/25/2015] [Indexed: 01/21/2023]
Abstract
Toxocariasis is one of the most important, but neglected, zoonoses, which is mainly caused by Toxocara canis. To better understand the role of serine/threonine protein phosphatase 1 (PP1) in reproductive processes of male adult T. canis, differential expression analysis was used to reveal the profiles of PP1 catalytic subunit α (PP1cα) gene Tc-stp-1 and PP1 regulatory subunit 7 (PP1r7) gene TcM-1309. Indirect fluorescence immunocytochemistry was carried out to determine the subcellular distribution of PP1cα. Double-stranded RNA interference (RNAi) assays were employed to illustrate the function and mechanism of PP1cα in male adult reproduction. Real-time quantitative PCR (qPCR) showed transcriptional consistency of Tc-stp-1 and TcM-1309 in sperm-producing germline tissues and localization research showed cytoplasmic distribution of PP1cα in sf9 cells, which indicated relevant involvements of PP1cα and PP1r7 in spermatogenesis. Moreover, spatiotemporal transcriptional differences of Tc-stp-1 were determined by gene knockdown analysis, which revealed abnormal morphologies and blocked meiotic divisions of spermatocytes by phenotypic aberration scanning, thereby highlighting the crucial involvement of PP1cα in spermatogenesis. These results revealed a PP1cα-PP1r7 mechanism by which PP1 regulates kinetochore-microtubule interactions in spermatogenesis and provided important clues to identify novel drug or vaccine targets for toxocariasis control.
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Affiliation(s)
- Guang Xu Ma
- Department of Veterinary Medicine, Rongchang Campus, Southwest University, Chongqing 402460, People's Republic of China
| | - Rong Qiong Zhou
- Department of Veterinary Medicine, Rongchang Campus, Southwest University, Chongqing 402460, People's Republic of China.
| | - Zhen Hui Song
- Department of Veterinary Medicine, Rongchang Campus, Southwest University, Chongqing 402460, People's Republic of China
| | - Hong Hong Zhu
- Department of Veterinary Medicine, Rongchang Campus, Southwest University, Chongqing 402460, People's Republic of China
| | - Zuo Yong Zhou
- Department of Veterinary Medicine, Rongchang Campus, Southwest University, Chongqing 402460, People's Republic of China
| | - Yuan Qin Zeng
- College of Life Sciences, Southwest University, Chongqing 402460, People's Republic of China
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Wang Q, Rosa BA, Jasmer DP, Mitreva M. Pan-Nematoda Transcriptomic Elucidation of Essential Intestinal Functions and Therapeutic Targets With Broad Potential. EBioMedicine 2015; 2:1079-89. [PMID: 26501106 PMCID: PMC4587998 DOI: 10.1016/j.ebiom.2015.07.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/22/2015] [Accepted: 07/22/2015] [Indexed: 01/22/2023] Open
Abstract
The nematode intestine is continuous with the outside environment, making it easily accessible to anthelmintics for parasite control, but the development of new therapeutics is impeded by limited knowledge of nematode intestinal cell biology. We established the most comprehensive nematode intestinal functional database to date by generating transcriptional data from the dissected intestines of three parasitic nematodes spanning the phylum, and integrating the results with the whole proteomes of 10 nematodes (including 9 pathogens of humans or animals) and 3 host species and 2 outgroup species. We resolved 10,772 predicted nematode intestinal protein families (IntFams), and studied their presence and absence within the different lineages (births and deaths) among nematodes. Conserved intestinal cell functions representing ancestral functions of evolutionary importance were delineated, and molecular features useful for selective therapeutic targeting were identified. Molecular patterns conserved among IntFam proteins demonstrated large potential as therapeutic targets to inhibit intestinal cell functions with broad applications towards treatment and control of parasitic nematodes.
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Affiliation(s)
- Qi Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruce A. Rosa
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Douglas P. Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Division of Infectious Disease, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
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Tyagi R, Rosa BA, Lewis WG, Mitreva M. Pan-phylum Comparison of Nematode Metabolic Potential. PLoS Negl Trop Dis 2015; 9:e0003788. [PMID: 26000881 PMCID: PMC4441503 DOI: 10.1371/journal.pntd.0003788] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/24/2015] [Indexed: 01/12/2023] Open
Abstract
Nematodes are among the most important causative pathogens of neglected tropical diseases. The increased availability of genomic and transcriptomic data for many understudied nematode species provides a great opportunity to investigate different aspects of their biology. Increasingly, metabolic potential of pathogens is recognized as a critical determinant governing their development, growth and pathogenicity. Comparing metabolic potential among species with distinct trophic ecologies can provide insights on overall biology or molecular adaptations. Furthermore, ascertaining gene expression at pathway level can help in understanding metabolic dynamics over development. Comparison of biochemical pathways (or subpathways, i.e. pathway modules) among related species can also retrospectively indicate potential mistakes in gene-calling and functional annotation. We show with numerous illustrative case studies that comparisons at the level of pathway modules have the potential to uncover biological insights while remaining computationally tractable. Here, we reconstruct and compare metabolic modules found in the deduced proteomes of 13 nematodes and 10 non-nematode species (including hosts of the parasitic nematode species). We observed that the metabolic potential is, in general, concomitant with phylogenetic and/or ecological similarity. Varied metabolic strategies are required among the nematodes, with only 8 out of 51 pathway modules being completely conserved. Enzyme comparison based on topology of metabolic modules uncovered diversification between parasite and host that can potentially guide therapeutic intervention. Gene expression data from 4 nematode species were used to study metabolic dynamics over their life cycles. We report unexpected differential metabolism between immature and mature microfilariae of the human filarial parasite Brugia malayi. A set of genes potentially important for parasitism is also reported, based on an analysis of gene expression in C. elegans and the human hookworm Necator americanus. We illustrate how analyzing and comparing metabolism at the level of pathway modules can improve existing knowledge of nematode metabolic potential and can provide parasitism related insights. Our reconstruction and comparison of nematode metabolic pathways at a pan-phylum and inter-phylum level enabled determination of phylogenetic restrictions and differential expression of pathways. A visualization of our results is available at http://nematode.net and the program for identification of module completeness (modDFS) is freely available at SourceForge. The methods reported will help biologists to predict biochemical potential of any organism with available deduced proteome, to direct experiments and test hypotheses. We reconstructed metabolic pathways of 23 organisms including 13 nematode species, using their complete deduced protein coding sequences and compared them to 10 non-nematodes. We observed that metabolic potential availability is concomitant with phylogenetic and/or ecological similarity, with the exceptions providing interesting case studies. We also studied changes in metabolic profiles under different developmental stages of 4 nematode species using stage-specific transcriptomic data. A comparison of the variation patterns in these profiles led to recognition of modules that share metabolic profiles at various life-cycle stages or during development. The undertaken analysis improved genome annotation and the obtained results provided insight into parasitism, resulting in identification of taxonomically-restricted pathways and enzymes that may provide new mechanisms for control of nematode infections.
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Affiliation(s)
- Rahul Tyagi
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bruce A. Rosa
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Warren G. Lewis
- Division of Infectious Disease, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Makedonka Mitreva
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Disease, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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Rosa BA, Townsend R, Jasmer DP, Mitreva M. Functional and phylogenetic characterization of proteins detected in various nematode intestinal compartments. Mol Cell Proteomics 2015; 14:812-27. [PMID: 25609831 DOI: 10.1074/mcp.m114.046227] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 12/13/2022] Open
Abstract
The parasitic nematode intestine is responsible for nutrient digestion and absorption, and many other processes essential for reproduction and survival, making it a valuable target for anthelmintic drug treatment. However, nematodes display extreme biological diversity (including occupying distinct trophic habitats), resulting in limited knowledge of intestinal cell/protein functions of fundamental or adaptive significance. We developed a perfusion model for isolating intestinal proteins in Ascaris suum (a parasite of humans and swine), allowing for the identification of over 1000 intestinal A. suum proteins (using mass spectrometry), which were assigned to several different intestinal cell compartments (intestinal tissue, the integral and peripheral intestinal membranes, and the intestinal lumen). A multi-omics analysis approach identified a large diversity of biological functions across intestinal compartments, based on both functional enrichment analysis (identifying terms related to detoxification, proteolysis, and host-parasite interactions) and regulatory binding sequence analysis to identify putatively active compartment-specific transcription factors (identifying many related to intestinal sex differentiation or lifespan regulation). Orthologs of A. suum proteins in 15 other nematodes species, five host species, and two outgroups were identified and analyzed. Different cellular compartments demonstrated markedly different levels of protein conservation; e.g. integral intestinal membrane proteins were the most conserved among nematodes (up to 96% conservation), whereas intestinal lumen proteins were the most diverse (only 6% conservation across all nematodes, and 71% with no host orthologs). Finally, this integrated multi-omics analysis identified conserved nematode-specific intestinal proteins likely performing essential functions (including V-type ATPases and ABC transporters), which may serve as promising anthelmintic drug or vaccine targets in future research. Collectively, the findings provide valuable new insights on conserved and adaptive features of nematode intestinal cells, membranes and the intestinal lumen, and potential targets for parasite treatment and control.
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Affiliation(s)
- Bruce A Rosa
- From the ‡The Genome Institute, Washington University in St Louis, Missouri 63108
| | - Reid Townsend
- §Department of Cell Biology & Physiology and Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Douglas P Jasmer
- ¶Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington 99164
| | - Makedonka Mitreva
- From the ‡The Genome Institute, Washington University in St Louis, Missouri 63108; ‖Department of Medicine and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108
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Jasmer DP, Rosa BA, Mitreva M. Peptidases compartmentalized to the Ascaris suum intestinal lumen and apical intestinal membrane. PLoS Negl Trop Dis 2015; 9:e3375. [PMID: 25569475 PMCID: PMC4287503 DOI: 10.1371/journal.pntd.0003375] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/27/2014] [Indexed: 11/17/2022] Open
Abstract
The nematode intestine is a tissue of interest for developing new methods of therapy and control of parasitic nematodes. However, biological details of intestinal cell functions remain obscure, as do the proteins and molecular functions located on the apical intestinal membrane (AIM), and within the intestinal lumen (IL) of nematodes. Accordingly, methods were developed to gain a comprehensive identification of peptidases that function in the intestinal tract of adult female Ascaris suum. Peptidase activity was detected in multiple fractions of the A. suum intestine under pH conditions ranging from 5.0 to 8.0. Peptidase class inhibitors were used to characterize these activities. The fractions included whole lysates, membrane enriched fractions, and physiological- and 4 molar urea-perfusates of the intestinal lumen. Concanavalin A (ConA) was confirmed to bind to the AIM, and intestinal proteins affinity isolated on ConA-beads were compared to proteins from membrane and perfusate fractions by mass spectrometry. Twenty-nine predicted peptidases were identified including aspartic, cysteine, and serine peptidases, and an unexpectedly high number (16) of metallopeptidases. Many of these proteins co-localized to multiple fractions, providing independent support for localization to specific intestinal compartments, including the IL and AIM. This unique perfusion model produced the most comprehensive view of likely digestive peptidases that function in these intestinal compartments of A. suum, or any nematode. This model offers a means to directly determine functions of these proteins in the A. suum intestine and, more generally, deduce the wide array functions that exist in these cellular compartments of the nematode intestine. Past research has demonstrated that the nematode intestine has value for developing new methods of therapy and control of parasitic nematodes, as related to both vaccines and other anthelmintics. Yet, information related to basic intestinal cell biology is very limited. Research progress reported here moves towards the comprehensive identification of proteins (peptidases and others), and hence functions, that are sited on the apical intestinal membrane and within the intestinal lumen of adult female Ascaris suum. These advances provide an unprecedented research model to determine critical functions sited at these locations and to develop approaches to inhibit those functions. Comparative analysis among diverse parasitic species raises expectations that the results from A. suum can be applied to many parasitic nematodes for which similar research is technically impossible to perform.
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Affiliation(s)
- Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
| | - Bruce A Rosa
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Makedonka Mitreva
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Medicine and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Systems biology studies of adult paragonimus lung flukes facilitate the identification of immunodominant parasite antigens. PLoS Negl Trop Dis 2014; 8:e3242. [PMID: 25329661 PMCID: PMC4199545 DOI: 10.1371/journal.pntd.0003242] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/04/2014] [Indexed: 01/05/2023] Open
Abstract
Background Paragonimiasis is a food-borne trematode infection acquired by eating raw or undercooked crustaceans. It is a major public health problem in the far East, but it also occurs in South Asia, Africa, and in the Americas. Paragonimus worms cause chronic lung disease with cough, fever and hemoptysis that can be confused with tuberculosis or other non-parasitic diseases. Treatment is straightforward, but diagnosis is often delayed due to a lack of reliable parasitological or serodiagnostic tests. Hence, the purpose of this study was to use a systems biology approach to identify key parasite proteins that may be useful for development of improved diagnostic tests. Methodology/Principal Findings The transcriptome of adult Paragonimus kellicotti was sequenced with Illumina technology. Raw reads were pre-processed and assembled into 78,674 unique transcripts derived from 54,622 genetic loci, and 77,123 unique protein translations were predicted. A total of 2,555 predicted proteins (from 1,863 genetic loci) were verified by mass spectrometric analysis of total worm homogenate, including 63 proteins lacking homology to previously characterized sequences. Parasite proteins encoded by 321 transcripts (227 genetic loci) were reactive with antibodies from infected patients, as demonstrated by immunoaffinity purification and high-resolution liquid chromatography-mass spectrometry. Serodiagnostic candidates were prioritized based on several criteria, especially low conservation with proteins in other trematodes. Cysteine proteases, MFP6 proteins and myoglobins were abundant among the immunoreactive proteins, and these warrant further study as diagnostic candidates. Conclusions The transcriptome, proteome and immunolome of adult P. kellicotti represent a major advance in the study of Paragonimus species. These data provide a powerful foundation for translational research to develop improved diagnostic tests. Similar integrated approaches may be useful for identifying novel targets for drugs and vaccines in the future. Paragonimiasis is a food-borne trematode infection that people acquire when they eat raw or undercooked crustaceans. Disease symptoms (including cough, fever, blood in sputum, etc.) can be similar to those observed in patients with tuberculosis or bacterial pneumonia, frequently resulting in misdiagnosis. Although the infection is relatively easy to treat, diagnosis is complicated. Available diagnostic assays rely on total parasite homogenate to facilitate the detection of Paragonimus-specific antibodies in patients. Though these blot-based assays have shown high sensitivity and specificity, they are inconvenient because total parasite homogenate is not readily available. This study used next generation genomic and proteomic methods to identify transcripts and proteins expressed in adult Paragonimus flukes. We then used sera from patients infected with P. kellicotti to isolate immunoreactive proteins, and these were analyzed by mass spectrometry. The annotated transcriptome and the associated proteome of the antibody immune response represent a significant advance in research on Paragonimus. This information will be a valuable resource for further research on Paragonimus and paragonimiasis. Thus this project illustrates the potential power of employing systems biology for translational research in parasitology.
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Abubucker S, McNulty SN, Rosa BA, Mitreva M. Identification and characterization of alternative splicing in parasitic nematode transcriptomes. Parasit Vectors 2014; 7:151. [PMID: 24690220 PMCID: PMC3997825 DOI: 10.1186/1756-3305-7-151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/14/2014] [Indexed: 12/05/2022] Open
Abstract
Background Alternative splicing (AS) of mRNA is a vital mechanism for enhancing genomic complexity in eukaryotes. Spliced isoforms of the same gene can have diverse molecular and biological functions and are often differentially expressed across various tissues, times, and conditions. Thus, AS has important implications in the study of parasitic nematodes with complex life cycles. Transcriptomic datasets are available from many species, but data must be revisited with splice-aware assembly protocols to facilitate the study of AS in helminthes. Methods We sequenced cDNA from the model worm Caenorhabditis elegans using 454/Roche technology for use as an experimental dataset. Reads were assembled with Newbler software, invoking the cDNA option. Several combinations of parameters were tested and assembled transcripts were verified by comparison with previously reported C. elegans genes and transcript isoforms and with Illumina RNAseq data. Results Thoughtful adjustment of program parameters increased the percentage of assembled transcripts that matched known C. elegans sequences, decreased mis-assembly rates (i.e., cis- and trans-chimeras), and improved the coverage of the geneset. The optimized protocol was used to update de novo transcriptome assemblies from nine parasitic nematode species, including important pathogens of humans and domestic animals. Our assemblies indicated AS rates in the range of 20-30%, typically with 2-3 transcripts per AS locus, depending on the species. Transcript isoforms from the nine species were translated and searched for similarity to known proteins and functional domains. Some 21 InterPro domains, including several involved in nucleotide and chromatin binding, were statistically correlated with AS genetic loci. In most cases, the Roche/454 data explored in this study are the only sequences available from the species in question; however, the recently published genome of the human hookworm Necator americanus provided an additional opportunity to validate our results. Conclusions Our optimized assembly parameters facilitated the first survey of AS among parasitic nematodes. The nine transcriptome assemblies, their protein translations, and basic annotations are available from Nematode.net as a resource for the research community. These should be useful for studies of specific genes and gene families of interest as well as for curating draft genome assemblies as they become available.
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Affiliation(s)
| | | | | | - Makedonka Mitreva
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Boulevard, St, Louis, MO 63108, USA.
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