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Hibsh D, Schori H, Efroni S, Shefi O. De novo transcriptome assembly databases for the central nervous system of the medicinal leech. Sci Data 2015; 2:150015. [PMID: 25977819 PMCID: PMC4412018 DOI: 10.1038/sdata.2015.15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/03/2015] [Indexed: 01/17/2023] Open
Abstract
The study of non-model organisms stands to benefit greatly from genetic and genomic data. For a better understanding of the molecular mechanisms driving neuronal development, and to characterize the entire leech Hirudo medicinalis central nervous system (CNS) transcriptome we combined Trinity for de-novo assembly and Illumina HiSeq2000 for RNA-Seq. We present a set of 73,493 de-novo assembled transcripts for the leech, reconstructed from RNA collected, at a single ganglion resolution, from the CNS. This set of transcripts greatly enriches the available data for the leech. Here, we share two databases, such that each dataset allows a different type of search for candidate homologues. The first is the raw set of assembled transcripts. This set allows a sequence-based search. A comprehensive analysis of which revealed 22,604 contigs with high e-values, aligned versus the Swiss-Prot database. This analysis enabled the production of the second database, which includes correlated sequences to annotated transcript names, with the confidence of BLAST best hit.
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Affiliation(s)
- Dror Hibsh
- Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
- Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Hadas Schori
- Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Sol Efroni
- Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Orit Shefi
- Faculty of Engineering, Bar Ilan University, Ramat Gan 5290002, Israel
- Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan 5290002, Israel
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Drago F, Sautière PE, Le Marrec-Croq F, Accorsi A, Van Camp C, Salzet M, Lefebvre C, Vizioli J. Microglia of medicinal leech (Hirudo medicinalis) express a specific activation marker homologous to vertebrate ionized calcium-binding adapter molecule 1 (Iba1/alias aif-1). Dev Neurobiol 2014; 74:987-1001. [PMID: 24723370 DOI: 10.1002/dneu.22179] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 04/07/2014] [Indexed: 01/13/2023]
Abstract
The Ionized calcium-Binding Adapter molecule 1 (Iba1), also known as Allograft Inflammatory Factor 1 (AIF-1), is a 17 kDa cytokine-inducible protein, produced by activated macrophages during chronic transplant rejection and inflammatory reactions in Vertebrates. In mammalian central nervous system (CNS), Iba1 is a sensitive marker associated with activated macrophages/microglia and is upregulated following neuronal death or brain lesions. The medicinal leech Hirudo medicinalis is able to regenerate its CNS after injury, leading to a complete functional repair. Similar to Vertebrates, leech neuroinflammatory processes are linked to microglia activation and recruitment at the lesion site. We identified a gene, named Hmiba1, coding a 17.8 kDa protein showing high similarity with Vertebrate AIF-1. The present work constitutes the first report on an Iba1 protein in the nervous system of an invertebrate. Immunochemistry and gene expression analyses showed that HmIba1, like its mammalian counterpart, is modulated in leech CNS by mechanical injury or chemical stimuli (ATP). We presently demonstrate that most of leech microglial cells migrating and accumulating at the lesion site specifically expressed the activation marker HmIba1. While the functional role of Iba1, whatever species, is still unclear in reactive microglia, this molecule appeared as a good selective marker of activated cells in leech and presents an interesting tool to investigate the functions of these cells during nerve repair events.
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Affiliation(s)
- Francesco Drago
- Université Lille 1, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée, EA4550, Villeneuve d'Ascq, 59655, France
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Hibsh D, Schori H, Efroni S, Shefi O. Spatial regulation dominates gene function in the ganglia chain. ACTA ACUST UNITED AC 2013; 30:310-6. [PMID: 24085568 DOI: 10.1093/bioinformatics/btt570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MOTIVATION To understand the molecular mechanisms of neurons, it is imperative to identify genomic dissimilarities within the heterogeneity of the neural system. This is especially true for neuronal disorders in which spatial considerations are of critical nature. For this purpose, Hirudo medicinalis provides here an ideal system in which we are able to follow gene expression along the central nervous system, to affiliate location with gene behavior. RESULTS In all, 221.1 million high-quality short reads were sequenced on the Illumina Hiseq2000 platform at the single ganglion level. Thereafter, a de novo assembly was performed using two state-of-the-art assemblers, Trinity and Trans-ABySS, to reconstruct a comprehensive de novo transcriptome. Classification of Trinity and Trans-ABySS transcripts produced a non-redundant set of 76 845 and 268 355 transcripts (>200 bp), respectively. Remarkably, using Trinity, 82% of the published medicinal leech messenger RNAs was identified. For the innexin family, all of the 21 recently reported genes were identified. Spatial regulation analysis across three ganglia throughout the entire central nervous system revealed distinct patterns of gene expression. These transcriptome data were combined with expression distribution to produce a spatio-transcripto map along the ganglia chain. This study provides a resource for gene discovery and gene regulation in future studies.
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Affiliation(s)
- Dror Hibsh
- Faculty of Life Sciences, Faculty of Engineering and Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel 52900
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Meriaux C, Arafah K, Tasiemski A, Wisztorski M, Bruand J, Boidin-Wichlacz C, Desmons A, Debois D, Laprévote O, Brunelle A, Gaasterland T, Macagno E, Fournier I, Salzet M. Multiple changes in peptide and lipid expression associated with regeneration in the nervous system of the medicinal leech. PLoS One 2011; 6:e18359. [PMID: 21526169 PMCID: PMC3081291 DOI: 10.1371/journal.pone.0018359] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 02/28/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The adult medicinal leech central nervous system (CNS) is capable of regenerating specific synaptic circuitry after a mechanical lesion, displaying evidence of anatomical repair within a few days and functional recovery within a few weeks. In the present work, spatiotemporal changes in molecular distributions during this phenomenon are explored. Moreover, the hypothesis that neural regeneration involves some molecular factors initially employed during embryonic neural development is tested. RESULTS Imaging mass spectrometry coupled to peptidomic and lipidomic methodologies allowed the selection of molecules whose spatiotemporal pattern of expression was of potential interest. The identification of peptides was aided by comparing MS/MS spectra obtained for the peptidome extracted from embryonic and adult tissues to leech transcriptome and genome databases. Through the parallel use of a classical lipidomic approach and secondary ion mass spectrometry, specific lipids, including cannabinoids, gangliosides and several other types, were detected in adult ganglia following mechanical damage to connected nerves. These observations motivated a search for possible effects of cannabinoids on neurite outgrowth. Exposing nervous tissues to Transient Receptor Potential Vanilloid (TRPV) receptor agonists resulted in enhanced neurite outgrowth from a cut nerve, while exposure to antagonists blocked such outgrowth. CONCLUSION The experiments on the regenerating adult leech CNS reported here provide direct evidence of increased titers of proteins that are thought to play important roles in early stages of neural development. Our data further suggest that endocannabinoids also play key roles in CNS regeneration, mediated through the activation of leech TRPVs, as a thorough search of leech genome databases failed to reveal any leech orthologs of the mammalian cannabinoid receptors but revealed putative TRPVs. In sum, our observations identify a number of lipids and proteins that may contribute to different aspects of the complex phenomenon of leech nerve regeneration, establishing an important base for future functional assays.
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Affiliation(s)
- Céline Meriaux
- Université Lille Nord de France, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée (FABMS), EA 4550, Université Lille 1, Villeneuve d'Ascq, France
| | - Karim Arafah
- Université Lille Nord de France, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée (FABMS), EA 4550, Université Lille 1, Villeneuve d'Ascq, France
| | - Aurélie Tasiemski
- Université Lille Nord de France, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée (FABMS), EA 4550, Université Lille 1, Villeneuve d'Ascq, France
| | - Maxence Wisztorski
- Université Lille Nord de France, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée (FABMS), EA 4550, Université Lille 1, Villeneuve d'Ascq, France
| | - Jocelyne Bruand
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Céline Boidin-Wichlacz
- Université Lille Nord de France, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée (FABMS), EA 4550, Université Lille 1, Villeneuve d'Ascq, France
| | - Annie Desmons
- Université Lille Nord de France, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée (FABMS), EA 4550, Université Lille 1, Villeneuve d'Ascq, France
| | - Delphine Debois
- Institut de Chimie des Substances Naturelles, Centre de Recherche de Gif, Gif-sur-Yvette, France
| | - Olivier Laprévote
- Institut de Chimie des Substances Naturelles, Centre de Recherche de Gif, Gif-sur-Yvette, France
- Chimie Toxicologie Analytique et Cellulaire, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Paris, France
| | - Alain Brunelle
- Institut de Chimie des Substances Naturelles, Centre de Recherche de Gif, Gif-sur-Yvette, France
| | - Terry Gaasterland
- Marine Biology Research Division, Scripps Institution of Oceanography, Division of Biological Sciences, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Eduardo Macagno
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Isabelle Fournier
- Université Lille Nord de France, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée (FABMS), EA 4550, Université Lille 1, Villeneuve d'Ascq, France
| | - Michel Salzet
- Université Lille Nord de France, Laboratoire de Spectrométrie de Masse Biologique Fondamentale et Appliquée (FABMS), EA 4550, Université Lille 1, Villeneuve d'Ascq, France
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Macagno ER, Gaasterland T, Edsall L, Bafna V, Soares MB, Scheetz T, Casavant T, Da Silva C, Wincker P, Tasiemski A, Salzet M. Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. BMC Genomics 2010; 11:407. [PMID: 20579359 PMCID: PMC2996935 DOI: 10.1186/1471-2164-11-407] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 06/25/2010] [Indexed: 11/17/2022] Open
Abstract
Background The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the Hirudo transcriptome that is available to the scientific community. Results A total of ~133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions. Conclusions The sequences obtained for Hirudo transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of Helobdella robusta, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with Capitella capitata (a polychaete) and 56% with Aplysia californica (a mollusk), as well as 58% with Schistosoma mansoni (a platyhelminth). Phylogenetic comparisons of putative Hirudo innate immune response genes present within the Hirudo transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.
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Affiliation(s)
- Eduardo R Macagno
- Division of Biological Sciences, University of California, San Diego, CA, USA.
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Mary J, Rogniaux H, Rees JF, Zal F. Response of Alvinella pompejana to variable oxygen stress: A proteomic approach. Proteomics 2010; 10:2250-8. [DOI: 10.1002/pmic.200900394] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Tasiemski A, Salzet M. Leech Immunity: From Brain to Peripheral Responses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 708:80-104. [DOI: 10.1007/978-1-4419-8059-5_5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Tahtouh M, Croq F, Vizioli J, Sautiere PE, Van Camp C, Salzet M, Daha MR, Pestel J, Lefebvre C. Evidence for a novel chemotactic C1q domain-containing factor in the leech nerve cord. Mol Immunol 2009; 46:523-31. [DOI: 10.1016/j.molimm.2008.07.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 07/15/2008] [Accepted: 07/15/2008] [Indexed: 10/21/2022]
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