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Bail K, Notz Q, Rovituso DM, Schampel A, Wunsch M, Koeniger T, Schropp V, Bharti R, Scholz CJ, Foerstner KU, Kleinschnitz C, Kuerten S. Differential effects of FTY720 on the B cell compartment in a mouse model of multiple sclerosis. J Neuroinflammation 2017; 14:148. [PMID: 28738885 PMCID: PMC5525315 DOI: 10.1186/s12974-017-0924-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/14/2017] [Indexed: 12/11/2022] Open
Abstract
Background MP4-induced experimental autoimmune encephalomyelitis (EAE) is a mouse model of multiple sclerosis (MS), which enables targeted research on B cells, currently much discussed protagonists in MS pathogenesis. Here, we used this model to study the impact of the S1P1 receptor modulator FTY720 (fingolimod) on the autoreactive B cell and antibody response both in the periphery and the central nervous system (CNS). Methods MP4-immunized mice were treated orally with FTY720 for 30 days at the peak of disease or 50 days after EAE onset. The subsequent disease course was monitored and the MP4-specific B cell/antibody response was measured by ELISPOT and ELISA. RNA sequencing was performed to determine any effects on B cell-relevant gene expression. S1P1 receptor expression by peripheral T and B cells, B cell subset distribution in the spleen and B cell infiltration into the CNS were studied by flow cytometry. The formation of B cell aggregates and of tertiary lymphoid organs (TLOs) was evaluated by histology and immunohistochemistry. Potential direct effects of FTY720 on B cell aggregation were studied in vitro. Results FTY720 significantly attenuated clinical EAE when treatment was initiated at the peak of EAE. While there was a significant reduction in the number of T cells in the blood after FTY720 treatment, B cells were only slightly diminished. Yet, there was evidence for the modulation of B cell receptor-mediated signaling upon FTY720 treatment. In addition, we detected a significant increase in the percentage of B220+ B cells in the spleen both in acute and chronic EAE. Whereas acute treatment completely abrogated B cell aggregate formation in the CNS, the numbers of infiltrating B cells and plasma cells were comparable between vehicle- and FTY720-treated mice. In addition, there was no effect on already developed aggregates in chronic EAE. In vitro B cell aggregation assays suggested the absence of a direct effect of FTY720 on B cell aggregation. However, FTY720 impacted the evolution of B cell aggregates into TLOs. Conclusions The data suggest differential effects of FTY720 on the B cell compartment in MP4-induced EAE. Electronic supplementary material The online version of this article (doi:10.1186/s12974-017-0924-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathrin Bail
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Quirin Notz
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Damiano M Rovituso
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Andrea Schampel
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Marie Wunsch
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Tobias Koeniger
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Verena Schropp
- Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Richa Bharti
- Core Unit Systems Medicine, University Hospitals of Würzburg, Würzburg, Germany
| | - Claus-Juergen Scholz
- Core Unit Systems Medicine, University Hospitals of Würzburg, Würzburg, Germany.,LIMES Institute, University of Bonn, Bonn, Germany
| | - Konrad U Foerstner
- Core Unit Systems Medicine, University Hospitals of Würzburg, Würzburg, Germany
| | - Christoph Kleinschnitz
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany.,Department of Neurology, University Hospital Essen, Essen, Germany
| | - Stefanie Kuerten
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany. .,Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
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Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P. Enterotypes of the human gut microbiome. Nature 2011; 473:174-80. [PMID: 21508958 DOI: 10.1038/nature09944] [Citation(s) in RCA: 4496] [Impact Index Per Article: 345.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 12/18/2010] [Indexed: 02/06/2023]
Abstract
Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.
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Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P. SmashCommunity: a metagenomic annotation and analysis tool: Fig. 1. Bioinformatics 2010; 26:2977-8. [DOI: 10.1093/bioinformatics/btq536] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
Bacterial nitrile hydratase (NHases) are important industrial catalysts and waste water remediation tools. In a global computational screening of conventional and metagenomic sequence data for NHases, we detected the two usually separated NHase subunits fused in one protein of the choanoflagellate Monosiga brevicollis, a recently sequenced unicellular model organism from the closest sister group of Metazoa. This is the first time that an NHase is found in eukaryotes and the first time it is observed as a fusion protein. The presence of an intron, subunit fusion and expressed sequence tags covering parts of the gene exclude contamination and suggest a functional gene. Phylogenetic analyses and genomic context imply a probable ancient horizontal gene transfer (HGT) from proteobacteria. The newly discovered NHase might open biotechnological routes due to its unconventional structure, its new type of host and its apparent integration into eukaryotic protein networks.
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Affiliation(s)
| | - Tobias Doerks
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jean Muller
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jeroen Raes
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
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Hooper SD, Raes J, Foerstner KU, Harrington ED, Dalevi D, Bork P. A molecular study of microbe transfer between distant environments. PLoS One 2008; 3:e2607. [PMID: 18612393 PMCID: PMC2442867 DOI: 10.1371/journal.pone.0002607] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 05/28/2008] [Indexed: 11/18/2022] Open
Abstract
Background Environments and their organic content are generally not static and isolated, but in a constant state of exchange and interaction with each other. Through physical or biological processes, organisms, especially microbes, may be transferred between environments whose characteristics may be quite different. The transferred microbes may not survive in their new environment, but their DNA will be deposited. In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances. Methodology By studying synonymous nucleotide composition, oligomer frequency and orthology between predicted genes in metagenomics data from two environments, terrestrial and aquatic, and by correlating with phylogenetic mappings, we find that both environments are likely to contain trace amounts of microbes which have been far removed from their original habitat. We also suggest a bias in direction from soil to sea, which is consistent with the cycles of planetary wind and water. Conclusions Our findings support the Baas-Becking hypothesis formulated in 1934, which states that due to dispersion and population sizes, microbes are likely to be found in widely disparate environments. Furthermore, the availability of genetic material from distant environments is a possible font of novel gene functions for lateral gene transfer.
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Affiliation(s)
- Sean D. Hooper
- Department of Energy Joint Genome Institute (DOE-JGI), Walnut Creek, California, United States of America
| | | | | | | | - Daniel Dalevi
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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Danckwardt S, Kaufmann I, Gentzel M, Foerstner KU, Gantzert AS, Gehring NH, Neu-Yilik G, Bork P, Keller W, Wilm M, Hentze MW, Kulozik AE. Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals. EMBO J 2007; 26:2658-69. [PMID: 17464285 PMCID: PMC1888663 DOI: 10.1038/sj.emboj.7601699] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Accepted: 04/02/2007] [Indexed: 12/26/2022] Open
Abstract
The prothrombin (F2) 3' end formation signal is highly susceptible to thrombophilia-associated gain-of-function mutations. In its unusual architecture, the F2 3' UTR contains an upstream sequence element (USE) that compensates for weak activities of the non-canonical cleavage site and the downstream U-rich element. Here, we address the mechanism of USE function. We show that the F2 USE contains a highly conserved nonameric core sequence, which promotes 3' end formation in a position- and sequence-dependent manner. We identify proteins that specifically interact with the USE, and demonstrate their function as trans-acting factors that promote 3' end formation. Interestingly, these include the splicing factors U2AF35, U2AF65 and hnRNPI. We show that these splicing factors not only modulate 3' end formation via the USEs contained in the F2 and the complement C2 mRNAs, but also in the biocomputationally identified BCL2L2, IVNS and ACTR mRNAs, suggesting a broader functional role. These data uncover a novel mechanism that functionally links the splicing and 3' end formation machineries of multiple cellular mRNAs in an USE-dependent manner.
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Affiliation(s)
- Sven Danckwardt
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL and University of Heidelberg, Heidelberg, Germany
| | | | - Marc Gentzel
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Anne-Susan Gantzert
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL and University of Heidelberg, Heidelberg, Germany
| | - Niels H Gehring
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL and University of Heidelberg, Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL and University of Heidelberg, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Matthias Wilm
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthias W Hentze
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
- European Molecular Biology Laboratory, Meyerhof str. 1, 69117 Heidelberg, Germany. Tel.: +49 6221 387501; Fax: +49 6221 387518; E-mail:
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL and University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 156, 69120 Heidelberg, Germany. Tel.: +49 6221 564555; Fax: +49 6221 564559; E-mail:
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Abstract
Environmental sequencing, also dubbed metagenomics, is increasingly being used to obtain insights into organismal communities in diverse habitats, and has a variety of potential applications foreseeable in biotechnology and medicine. The first public large-scale data provide already a wealth of information hidden in vast amounts of fragmented pieces of DNA from unknown species residing in these environments. Comparative sequence analysis is essential for the interpretation of such data. However, different layers of complexity that are intrinsic to each sample require the establishment of some baselines for comparison: how to normalize for the differences in phylogenetic and functional diversity, how to avoid biases from incomplete data, and how to deal with differences in species dominance or genome sizes? Here we discuss a few of these items and delineate some simple discriminative sequence properties for four distinct habitats.
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Affiliation(s)
- Konrad U Foerstner
- European Molecular Biology LaboratoryMeyerhofstrasse 1, Heidelberg 69117, Germany
| | - Christian von Mering
- European Molecular Biology LaboratoryMeyerhofstrasse 1, Heidelberg 69117, Germany
| | - Peer Bork
- European Molecular Biology LaboratoryMeyerhofstrasse 1, Heidelberg 69117, Germany
- Max-Delbrück-Centre for Molecular MedicineRobert-Rössle-Strasse 10, Berlin 13092, Germany
- Author for correspondence ()
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Foerstner KU, von Mering C, Hooper SD, Bork P. Environments shape the nucleotide composition of genomes. EMBO Rep 2006; 6:1208-13. [PMID: 16200051 PMCID: PMC1369203 DOI: 10.1038/sj.embor.7400538] [Citation(s) in RCA: 190] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 08/15/2005] [Accepted: 08/19/2005] [Indexed: 11/09/2022] Open
Abstract
To test the impact of environments on genome evolution, we analysed the relative abundance of the nucleotides guanine and cytosine ('GC content') of large numbers of sequences from four distinct environmental samples (ocean surface water, farm soil, an acidophilic mine drainage biofilm and deep-sea whale carcasses). We show that the GC content of complex microbial communities seems to be globally and actively influenced by the environment. The observed nucleotide compositions cannot be easily explained by distinct phylogenetic origins of the species in the environments; the genomic GC content may change faster than was previously thought, and is also reflected in the amino-acid composition of the proteins in these habitats.
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Affiliation(s)
- Konrad U Foerstner
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christian von Mering
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Sean D Hooper
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Max-Delbrück Centre for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany
- Tel: +49 6221 387 8526; Fax: +49 6221 387 517; E-mail:
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