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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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Thawornkuno C, Nogrado K, Adisakwattana P, Thiangtrongjit T, Reamtong O. Identification and profiling of Trichinella spiralis circulating antigens and proteins in sera of mice with trichinellosis. PLoS One 2022; 17:e0265013. [PMID: 35271623 PMCID: PMC8912135 DOI: 10.1371/journal.pone.0265013] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Trichinellosis is a zoonotic disease caused by the ingestion of the Trichinella nematode. With a worldwide incidence of approximately 10,000 cases per year, Trichinella spiralis is responsible for most human infections. There are no specific signs or symptoms of this parasitic infection. Muscle biopsy is the gold diagnostic standard for trichinellosis, but the technique is invasive and unable to detect the early stage of infection. Although immunodiagnostics are also available, antibody detection usually occurs after 3 weeks and prolonged up to 19 years after the acute phase. Therefore, additional diagnostic biomarkers must be identified to improve trichinellosis diagnosis. This study aimed to measure concentration changes in mouse serum proteins prior to T. spiralis infection and 2, 4 and 8 weeks after infection, and to identify T. spiralis circulating proteins and antigens using mass spectrometry-based proteomics. Mouse muscle-related proteins including inter-alpha-trypsin inhibitor heavy chain H2, a protein involved in the response to muscle tissue damage, were up-regulated in mouse sera during the T. spiralis larvae invasion. Additionally, 33 circulatory parasite proteins were identified in infected mouse sera. Notably, T. spiralis long-chain fatty acid transport protein 1 could be detected in the early stage of infection and peroxidasin-like protein was identified 2, 4 and 8 weeks after infection. Seventeen T. spiralis circulating antigens were detected in mouse immune complexes, with PX domain protein being found 2, 4 and 8 weeks after infection. Because peroxidasin-like protein and PX domain protein were detected at all post-infection time points, sequence alignments of these proteins were performed, which showed they are conserved among Trichinella spp. and have less similarity to the human and murine sequences. Integrative analysis of T. spiralis biomarkers throughout the course of infection may reveal additional diagnostic targets to improve early diagnosis of trichinellosis.
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Affiliation(s)
- Charin Thawornkuno
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kathyleen Nogrado
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tipparat Thiangtrongjit
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- * E-mail:
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Noack S, Harrington J, Carithers DS, Kaminsky R, Selzer PM. Heartworm disease - Overview, intervention, and industry perspective. Int J Parasitol Drugs Drug Resist 2021; 16:65-89. [PMID: 34030109 PMCID: PMC8163879 DOI: 10.1016/j.ijpddr.2021.03.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Dirofilaria immitis, also known as heartworm, is a major parasitic threat for dogs and cats around the world. Because of its impact on the health and welfare of companion animals, heartworm disease is of huge veterinary and economic importance especially in North America, Europe, Asia and Australia. Within the animal health market many different heartworm preventive products are available, all of which contain active components of the same drug class, the macrocyclic lactones. In addition to compliance issues, such as under-dosing or irregular treatment intervals, the occurrence of drug-resistant heartworms within the populations in the Mississippi River areas adds to the failure of preventive treatments. The objective of this review is to provide an overview of the disease, summarize the current disease control measures and highlight potential new avenues and best practices for treatment and prevention.
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Affiliation(s)
- Sandra Noack
- Boehringer Ingelheim Animal Health, Binger Str. 173, 55216, Ingelheim am Rhein, Germany
| | - John Harrington
- Boehringer Ingelheim Animal Health, 1730 Olympic Drive, 30601, Athens, GA, USA
| | - Douglas S Carithers
- Boehringer Ingelheim Animal Health, 3239 Satellite Blvd, 30096, Duluth, GA, USA
| | - Ronald Kaminsky
- paraC Consulting, Altenstein 13, 79685, Häg-Ehrsberg, Germany
| | - Paul M Selzer
- Boehringer Ingelheim Animal Health, Binger Str. 173, 55216, Ingelheim am Rhein, Germany.
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Zawistowska-Deniziak A, Powązka K, Pękacz M, Basałaj K, Klockiewicz M, Wiśniewski M, Młocicki D. Immunoproteomic Analysis of Dirofilaria repens Microfilariae and Adult Parasite Stages. Pathogens 2021; 10:pathogens10020174. [PMID: 33562513 PMCID: PMC7914743 DOI: 10.3390/pathogens10020174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 12/19/2022] Open
Abstract
Dirofilariarepens is a parasitic nematode causing a vector-borne zoonotic infection (dirofilariosis), considered an emerging problem in human and veterinary medicine. Currently, diagnosis is based on the detection of the adult parasite and microfilariae in the host tissues. However, the efficacy of tests relying on microfilariae detection is limited by microfilariae periodic occurrence. Therefore, a new reliable and affordable serological diagnostic method is needed. Better characteristic of the parasite biology and its interaction with host immune system should help to achieve this goal. This study analyzes adult and microfilariae proteomes, and the use of one-dimensional electrophoresis (1-DE) and two-dimensional electrophoresis (2-DE) proteomics, immunoproteomics, and LC-MS/MS mass spectrometry allowed us to identify 316 potentially immunogenic proteins (75 belong to adult stage, 183 to microfilariae, and 58 are common for both). Classified by their ontology, the proteins showed important similarities and differences between both parasite stages. The most frequently identified proteins are structural, metabolic, and heat shock proteins. Additionally, real-time PCR analysis of some immunogenic targets revealed significant differences between microfilariae and adult life stages. We indicated molecules involved in parasite-host interactions and discussed their importance in parasite biology, which may help to reveal potential diagnostic antigens or select drug and vaccine targets.
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Affiliation(s)
- Anna Zawistowska-Deniziak
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, 00-818 Warsaw, Poland; (K.P.); (M.P.); (K.B.); (D.M.)
- Correspondence: ; Tel.: +48-22-697-89-66
| | - Katarzyna Powązka
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, 00-818 Warsaw, Poland; (K.P.); (M.P.); (K.B.); (D.M.)
| | - Mateusz Pękacz
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, 00-818 Warsaw, Poland; (K.P.); (M.P.); (K.B.); (D.M.)
- Division of Parasitology, Department of Preclinical Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-786 Warsaw, Poland; (M.K.); (M.W.)
| | - Katarzyna Basałaj
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, 00-818 Warsaw, Poland; (K.P.); (M.P.); (K.B.); (D.M.)
| | - Maciej Klockiewicz
- Division of Parasitology, Department of Preclinical Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-786 Warsaw, Poland; (M.K.); (M.W.)
| | - Marcin Wiśniewski
- Division of Parasitology, Department of Preclinical Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-786 Warsaw, Poland; (M.K.); (M.W.)
| | - Daniel Młocicki
- Witold Stefański Institute of Parasitology, Polish Academy of Sciences, 00-818 Warsaw, Poland; (K.P.); (M.P.); (K.B.); (D.M.)
- Department of General Biology and Parasitology, Medical University of Warsaw, 02-004 Warsaw, Poland
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Lefoulon E, Clark T, Guerrero R, Cañizales I, Cardenas-Callirgos JM, Junker K, Vallarino-Lhermitte N, Makepeace BL, Darby AC, Foster JM, Martin C, Slatko BE. Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm. Microb Genom 2020; 6:mgen000487. [PMID: 33295865 PMCID: PMC8116671 DOI: 10.1099/mgen.0.000487] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/14/2020] [Indexed: 01/13/2023] Open
Abstract
Wolbachia are alpha-proteobacteria symbionts infecting a large range of arthropod species and two different families of nematodes. Interestingly, these endosymbionts are able to induce diverse phenotypes in their hosts: they are reproductive parasites within many arthropods, nutritional mutualists within some insects and obligate mutualists within their filarial nematode hosts. Defining Wolbachia 'species' is controversial and so they are commonly classified into 17 different phylogenetic lineages, termed supergroups, named A-F, H-Q and S. However, available genomic data remain limited and not representative of the full Wolbachia diversity; indeed, of the 24 complete genomes and 55 draft genomes of Wolbachia available to date, 84 % belong to supergroups A and B, exclusively composed of Wolbachia from arthropods. For the current study, we took advantage of a recently developed DNA-enrichment method to produce four complete genomes and two draft genomes of Wolbachia from filarial nematodes. Two complete genomes, wCtub and wDcau, are the smallest Wolbachia genomes sequenced to date (863 988 bp and 863 427 bp, respectively), as well as the first genomes representing supergroup J. These genomes confirm the validity of this supergroup, a controversial clade due to weaknesses of the multilocus sequence typing approach. We also produced the first draft Wolbachia genome from a supergroup F filarial nematode representative (wMhie), two genomes from supergroup D (wLsig and wLbra) and the complete genome of wDimm from supergroup C. Our new data confirm the paradigm of smaller Wolbachia genomes from filarial nematodes containing low levels of transposable elements and the absence of intact bacteriophage sequences, unlike many Wolbachia from arthropods, where both are more abundant. However, we observe differences among the Wolbachia genomes from filarial nematodes: no global co-evolutionary pattern, strong synteny between supergroup C and supergroup J Wolbachia, and more transposable elements observed in supergroup D Wolbachia compared to the other supergroups. Metabolic pathway analysis indicates several highly conserved pathways (haem and nucleotide biosynthesis, for example) as opposed to more variable pathways, such as vitamin B biosynthesis, which might be specific to certain host-symbiont associations. Overall, there appears to be no single Wolbachia-filarial nematode pattern of co-evolution or symbiotic relationship.
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Affiliation(s)
- Emilie Lefoulon
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
- Present address: School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Travis Clark
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
| | - Ricardo Guerrero
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Israel Cañizales
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
- Ediciones La Fauna KPT SL, Madrid, Spain
| | - Jorge Manuel Cardenas-Callirgos
- Neotropical Parasitology Research Network - NEOPARNET, Asociación Peruana de Helmintología e Invertebrados Afines – APHIA, Peru
| | - Kerstin Junker
- Epidemiology, Parasites and Vectors, ARC-Onderstepoort Veterinary Institute, Onderstepoort 0110, South Africa
| | - Nathaly Vallarino-Lhermitte
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Benjamin L. Makepeace
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alistair C. Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jeremy M. Foster
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
| | - Coralie Martin
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum National d’Histoire Naturelle, CNRS, Paris, France
| | - Barton E. Slatko
- Molecular Parasitology Group, New England Biolabs, Ipswich, MA, USA
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A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts. G3-GENES GENOMES GENETICS 2020; 10:3243-3260. [PMID: 32718933 PMCID: PMC7467002 DOI: 10.1534/g3.120.401534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Wolbachia is a genus containing obligate, intracellular endosymbionts with arthropod and nematode hosts. Numerous studies have identified differentially expressed transcripts in Wolbachia endosymbionts that potentially inform the biological interplay between these endosymbionts and their hosts, albeit with discordant results. Here, we re-analyze previously published Wolbachia RNA-Seq transcriptomics data sets using a single workflow consisting of the most up-to-date algorithms and techniques, with the aim of identifying trends or patterns in the pan-Wolbachia transcriptional response. We find that data from one of the early studies in filarial nematodes did not allow for robust conclusions about Wolbachia differential expression with these methods, suggesting the original interpretations should be reconsidered. Across datasets analyzed with this unified workflow, there is a general lack of global gene regulation with the exception of a weak transcriptional response resulting in the upregulation of ribosomal proteins in early larval stages. This weak response is observed across diverse Wolbachia strains from both nematode and insect hosts suggesting a potential pan-Wolbachia transcriptional response during host development that diverged more than 700 million years ago.
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Elucidating the molecular and developmental biology of parasitic nematodes: Moving to a multiomics paradigm. ADVANCES IN PARASITOLOGY 2020; 108:175-229. [PMID: 32291085 DOI: 10.1016/bs.apar.2019.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the past two decades, significant progress has been made in the sequencing, assembly, annotation and analyses of genomes and transcriptomes of parasitic worms of socioeconomic importance. This progress has somewhat improved our knowledge and understanding of these pathogens at the molecular level. However, compared with the free-living nematode Caenorhabditis elegans, the areas of functional genomics, transcriptomics, proteomics and metabolomics of parasitic nematodes are still in their infancy, and there are major gaps in our knowledge and understanding of the molecular biology of parasitic nematodes. The information on signalling molecules, molecular pathways and microRNAs (miRNAs) that are known to be involved in developmental processes in C. elegans and the availability of some molecular resources (draft genomes, transcriptomes and some proteomes) for selected parasitic nematodes provide a basis to start exploring the developmental biology of parasitic nematodes. Indeed, some studies have identified molecules and pathways that might associate with developmental processes in related, parasitic nematodes, such as Haemonchus contortus (barber's pole worm). However, detailed information is often scant and 'omics resources are limited, preventing a proper integration of 'omic data sets and comprehensive analyses. Moreover, little is known about the functional roles of pheromones, hormones, signalling pathways and post-transcriptional/post-translational regulations in the development of key parasitic nematodes throughout their entire life cycles. Although C. elegans is an excellent model to assist molecular studies of parasitic nematodes, its use is limited when it comes to explorations of processes that are specific to parasitism within host animals. A deep understanding of parasitic nematodes, such as H. contortus, requires substantially enhanced resources and the use of integrative 'omics approaches for analyses. The improved genome and well-established in vitro larval culture system for H. contortus provide unprecedented opportunities for comprehensive studies of the transcriptomes (mRNA and miRNA), proteomes (somatic, excretory/secretory and phosphorylated proteins) and lipidomes (e.g., polar and neutral lipids) of this nematode. Such resources should enable in-depth explorations of its developmental biology at a level, not previously possible. The main aims of this review are (i) to provide a background on the development of nematodes, with a particular emphasis on the molecular aspects involved in the dauer formation and exit in C. elegans; (ii) to critically appraise the current state of knowledge of the developmental biology of parasitic nematodes and identify key knowledge gaps; (iii) to cover salient aspects of H. contortus, with a focus on the recent advances in genomics, transcriptomics, proteomics and lipidomics as well as in vitro culturing systems; (iv) to review recent advances in our knowledge and understanding of the molecular and developmental biology of H. contortus using an integrative multiomics approach, and discuss the implications of this approach for detailed explorations of signalling molecules, molecular processes and pathways likely associated with nematode development, adaptation and parasitism, and for the identification of novel intervention targets against these pathogens. Clearly, the multiomics approach established recently is readily applicable to exploring a wide range of interesting and socioeconomically significant parasitic worms (including also trematodes and cestodes) at the molecular level, and to elucidate host-parasite interactions and disease processes.
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Comparative Genomics Guides Elucidation of Vitamin B 12 Biosynthesis in Novel Human-Associated Akkermansia Strains. Appl Environ Microbiol 2020; 86:AEM.02117-19. [PMID: 31757822 PMCID: PMC6974653 DOI: 10.1128/aem.02117-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
There is significant interest in the therapeutic and probiotic potential of the common gut bacterium Akkermansia muciniphila. However, knowledge of both the genomic and physiological diversity of this bacterial lineage is limited. Using a combination of genomic, molecular biological, and traditional microbiological approaches, we identified at least four species-level phylogroups with differing functional potentials that affect how these bacteria interact with both their human host and other members of the human gut microbiome. Specifically, we identified and isolated Akkermansia strains that were able to synthesize vitamin B12. The ability to synthesize this important cofactor broadens the physiological capabilities of human-associated Akkermansia strains, fundamentally altering our understanding of how this important bacterial lineage may affect human health. Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most humans and is considered a “next-generation probiotic.” However, knowledge of the genomic and physiological diversity of human-associated Akkermansia sp. strains is limited. Here, we reconstructed 35 metagenome-assembled genomes and combined them with 40 publicly available genomes for comparative genomic analysis. We identified at least four species-level phylogroups (AmI to AmIV), with distinct functional potentials. Most notably, we identified genes for cobalamin (vitamin B12) biosynthesis within the AmII and AmIII phylogroups. To verify these predictions, 10 Akkermansia strains were isolated from adults and screened for vitamin B12 biosynthesis genes via PCR. Two AmII strains were positive for the presence of cobalamin biosynthesis genes, while all 9 AmI strains tested were negative. To demonstrate vitamin B12 biosynthesis, we measured the production of acetate, succinate, and propionate in the presence and absence of vitamin supplementation in representative strains of the AmI and AmII phylogroups, since cobalamin is an essential cofactor in propionate metabolism. Results showed that the AmII strain produced acetate and propionate in the absence of supplementation, which is indicative of vitamin B12 biosynthesis. In contrast, acetate and succinate were the main fermentation products for the AmI strains when vitamin B12 was not supplied in the culture medium. Lastly, two bioassays were used to confirm vitamin B12 production by the AmII phylogroup. This novel physiological trait of human-associated Akkermansia strains may affect how these bacteria interact with the human host and other members of the human gut microbiome. IMPORTANCE There is significant interest in the therapeutic and probiotic potential of the common gut bacterium Akkermansia muciniphila. However, knowledge of both the genomic and physiological diversity of this bacterial lineage is limited. Using a combination of genomic, molecular biological, and traditional microbiological approaches, we identified at least four species-level phylogroups with differing functional potentials that affect how these bacteria interact with both their human host and other members of the human gut microbiome. Specifically, we identified and isolated Akkermansia strains that were able to synthesize vitamin B12. The ability to synthesize this important cofactor broadens the physiological capabilities of human-associated Akkermansia strains, fundamentally altering our understanding of how this important bacterial lineage may affect human health.
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O’Connell EM, Kamenyeva O, Lustigman S, Bell A, Nutman TB. Defining the target and the effect of imatinib on the filarial c-Abl homologue. PLoS Negl Trop Dis 2017; 11:e0005690. [PMID: 28727765 PMCID: PMC5538754 DOI: 10.1371/journal.pntd.0005690] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 08/01/2017] [Accepted: 06/08/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Previously we demonstrated the micro- and macrofilaricidal properties of imatinib in vitro. Here we use electron and multiphoton microscopy to define the target of imatinib in the adult and microfilarial stages of Brugia malayi and assess the effects of pharmacologically relevant levels of imatinib on the adult parasites. METHODS After fixation of adult B. malayi males and females, sections were stained with polyclonal rabbit anti-c-Abl antibody (or isotype control) and imaged with multiphoton fluorescent microscopy. Microfilariae were fixed and labeled with rabbit anti-c-Abl IgG primary antibody followed by anti-rabbit gold conjugated secondary antibody and imaged using transmission electron microscopy (TEM; immunoEM). In addition, adult B. malayi males and females were exposed to 0 or 10μM of imatinib for 7 days following which they were prepared for transmission electron microscopy (TEM) to assess the drug's effect on filarial ultrastructure. RESULTS Fluorescent localization of anti-c-Abl antibody demonstrated widespread uptake in the adult filariae, but the most intense signal was seen in the reproductive organs, muscle, and intestine of both male and female worms. Fluorescence was significantly more intense in the early microfilarial stage (i.e. early morula) compared with later development stages (i.e. pretzel). Anti-c-Abl antibody in the microfilariae localized to the nuclei. Based on TEM assessment following imatinib exposure, imatinib appeared to be detrimental to embryogenesis in the adult female B. malayi. CONCLUSIONS At pharmacologically achievable concentrations of imatinib, embryogenesis is impaired and possibly halted in adult filariae. Imatinib is likely a slow microfilaricide due to interference in intra-nuclear processes, which are slowly detrimental to the parasite and not immediately lethal, and thus may be used to lower the levels of L. loa microfilariae before they are treated within the context of conventional mass drug administration.
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Affiliation(s)
- Elise M. O’Connell
- Laboratory of Parasitic Diseases, Helminth Immunology Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
- * E-mail:
| | - Olena Kamenyeva
- Research Technologies Branch, Biological Imaging Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, New York City, New York, United States of America
| | - Aaron Bell
- Laboratory of Electron Microscopy, Lindsley F. Kimball Research Institute, New York Blood Center, New York City, New York, United States of America
| | - Thomas B. Nutman
- Laboratory of Parasitic Diseases, Helminth Immunology Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
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Affiliation(s)
- Sara Lustigman
- Molecular Parasitology, New York Blood Center, New York, NY, United States of America
- * E-mail:
| | - Alexandra Grote
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, United States of America
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, United States of America
- College of Global Public Health, New York University, New York, NY, United States of America
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Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq. PLoS Negl Trop Dis 2017; 11:e0005357. [PMID: 28358880 PMCID: PMC5373514 DOI: 10.1371/journal.pntd.0005357] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/26/2017] [Indexed: 01/08/2023] Open
Abstract
Background Filarial nematodes currently infect up to 54 million people worldwide, with millions more at risk for infection, representing the leading cause of disability in the developing world. Brugia malayi is one of the causative agents of lymphatic filariasis and remains the only human filarial parasite that can be maintained in small laboratory animals. Many filarial nematode species, including B. malayi, carry an obligate endosymbiont, the alpha-proteobacteria Wolbachia, which can be eliminated through antibiotic treatment. Elimination of the endosymbiont interferes with development, reproduction, and survival of the worms within the mamalian host, a clear indicator that the Wolbachia are crucial for survival of the parasite. Little is understood about the mechanism underlying this symbiosis. Methodology/ Principle findings To better understand the molecular interplay between these two organisms we profiled the transcriptomes of B. malayi and Wolbachia by dual RNA-seq across the life cycle of the parasite. This helped identify functional pathways involved in this essential symbiotic relationship provided by the co-expression of nematode and bacterial genes. We have identified significant stage-specific and gender-specific differential expression in Wolbachia during the nematode’s development. For example, during female worm development we find that Wolbachia upregulate genes involved in ATP production and purine biosynthesis, as well as genes involved in the oxidative stress response. Conclusions/ Significance This global transcriptional analysis has highlighted specific pathways to which both Wolbachia and B. malayi contribute concurrently over the life cycle of the parasite, paving the way for the development of novel intervention strategies. Filarial nematodes currently infect millions of people worldwide and represent a leading cause of disability. Currently available medications are insufficient in reaching elimination of these parasites. Many filarial nematodes, including Brugia malayi, have an Achilles heel of sorts—that is their obligate symbiotic relationship with the bacteria Wolbachia. While it is known that the nematode and the bacteria are co-dependent, the molecular basis of this relationship remains poorly understood. Using deep sequencing, we profiled the transcriptomes of B. malayi and Wolbachia across the life cycle of the parasite to determine the functional pathways necessary for parasite survival provided by the co-expression of nematode and bacterial genes. Defining the mechanisms of endosymbiosis between these two organisms will allow for the exploitation of this relationship for the development of new intervention strategies.
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Luck AN, Slatko BE, Foster JM. Removing the needle from the haystack: Enrichment of Wolbachia endosymbiont transcripts from host nematode RNA by Cappable-seq™. PLoS One 2017; 12:e0173186. [PMID: 28291780 PMCID: PMC5349465 DOI: 10.1371/journal.pone.0173186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/16/2017] [Indexed: 11/18/2022] Open
Abstract
Efficient transcriptomic sequencing of microbial mRNA derived from host-microbe associations is often compromised by the much lower relative abundance of microbial RNA in the mixed total RNA sample. One solution to this problem is to perform extensive sequencing until an acceptable level of transcriptome coverage is obtained. More cost-effective methods include use of prokaryotic and/or eukaryotic rRNA depletion strategies, sometimes in conjunction with depletion of polyadenylated eukaryotic mRNA. Here, we report use of Cappable-seq™ to specifically enrich, in a single step, Wolbachia endobacterial mRNA transcripts from total RNA prepared from the parasitic filarial nematode, Brugia malayi. The obligate Wolbachia endosymbiont is a proven drug target for many human filarial infections, yet the precise nature of its symbiosis with the nematode host is poorly understood. Insightful analysis of the expression levels of Wolbachia genes predicted to underpin the mutualistic association and of known drug target genes at different life cycle stages or in response to drug treatments is typically challenged by low transcriptomic coverage. Cappable-seq resulted in up to ~ 5-fold increase in the number of reads mapping to Wolbachia. On average, coverage of Wolbachia transcripts from B. malayi microfilariae was enriched ~40-fold by Cappable-seq. Additionally, this method has an additional benefit of selectively removing abundant prokaryotic ribosomal RNAs.The deeper microbial transcriptome sequencing afforded by Cappable-seq facilitates more detailed characterization of gene expression levels of pathogens and symbionts present in animal tissues.
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Affiliation(s)
- Ashley N. Luck
- Genome Biology Division, New England Biolabs, Inc., Ipswich, MA, United States of America
| | - Barton E. Slatko
- Genome Biology Division, New England Biolabs, Inc., Ipswich, MA, United States of America
| | - Jeremy M. Foster
- Genome Biology Division, New England Biolabs, Inc., Ipswich, MA, United States of America
- * E-mail:
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Grote A, Lustigman S, Ghedin E. Lessons from the genomes and transcriptomes of filarial nematodes. Mol Biochem Parasitol 2017; 215:23-29. [PMID: 28126543 DOI: 10.1016/j.molbiopara.2017.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 01/21/2017] [Indexed: 12/20/2022]
Abstract
Human filarial infections are a leading cause of morbidity in the developing world. While a small arsenal of drugs exists to treat these infections, there remains a tremendous need for the development of additional interventions. Recent genome sequences and transcriptome analyses of filarial nematodes have provided novel biological insight and allowed for the prediction of novel drug targets as well as potential vaccine candidates. In this review, we discuss the currently available data, insights gained into the metabolism of these organisms, and how the filaria field can move forward by leveraging these data.
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Affiliation(s)
- Alexandra Grote
- Center for Genomics and Systems Biology, Department of Biology, New York University, USA
| | | | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, USA.
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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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Luck AN, Yuan X, Voronin D, Slatko BE, Hamza I, Foster JM. Heme acquisition in the parasitic filarial nematode Brugia malayi. FASEB J 2016; 30:3501-3514. [PMID: 27363426 PMCID: PMC5024691 DOI: 10.1096/fj.201600603r] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/21/2016] [Indexed: 11/11/2022]
Abstract
Nematodes lack a heme biosynthetic pathway and must acquire heme from exogenous sources. Given the indispensable role of heme, this auxotrophy may be exploited to develop drugs that interfere with heme uptake in parasites. Although multiple heme-responsive genes (HRGs) have been characterized within the free-living nematode Caenorhabditis elegans, we have undertaken the first study of heme transport in Brugia malayi, a causative agent of lymphatic filariasis. Through functional assays in yeast, as well as heme analog, RNAi, and transcriptomic experiments, we have shown that the heme transporter B. malayi HRG-1 (BmHRG-1) is indeed functional in B. malayi In addition, BmHRG-1 localizes both to the endocytic compartments and cell membrane when expressed in yeast cells. Transcriptomic sequencing revealed that BmHRG-1, BmHRG-2, and BmMRP-5 (all orthologs of HRGs in C. elegans) are down-regulated in heme-treated B. malayi, as compared to non-heme-treated control worms. Likely because of short gene lengths, multiple exons, other HRGs in B. malayi (BmHRG-3-6) remain unidentified. Although the precise mechanisms of heme homeostasis in a nematode with the ability to acquire heme remains unknown, this study clearly demonstrates that the filarial nematode B. malayi is capable of transporting exogenous heme.-Luck, A. N., Yuan, X., Voronin, D., Slatko, B. E., Hamza, I., Foster, J. M. Heme acquisition in the parasitic filarial nematode Brugia malayi.
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Affiliation(s)
- Ashley N Luck
- New England BioLabs, Incorporated, Genome Biology Division, Ipswich, Massachusetts, USA
| | - Xiaojing Yuan
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA; and
| | - Denis Voronin
- New York Blood Center, Lindsley F. Kimball Research Institute, New York, New York, USA
| | - Barton E Slatko
- New England BioLabs, Incorporated, Genome Biology Division, Ipswich, Massachusetts, USA
| | - Iqbal Hamza
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA; and
| | - Jeremy M Foster
- New England BioLabs, Incorporated, Genome Biology Division, Ipswich, Massachusetts, USA;
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