Bacterial membrane vesicles
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ABSTRACT:
PROVIDER: PRJEB80775 | ENA |
REPOSITORIES: ENA
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Project description:We have investigated the genomic and epigenetic consequences of co-culturing colorectal carcinoma cells with membrane vesicles from pathogenic bacteria Vibrio cholerae and non-pathogenic commensal bacteria Escherichia coli. Our study has revealed that membrane vesicles from pathogenic and commensal bacteria have a global impact on the gene expression of coloncarcinoma cells. The changes in gene expression correlated positively with both epigenetic changes and chromatin accessibility of promoters at transcription start sites of genes induced by both types of membrane vesicles. Moreover, we have demonstrated that membrane vesicles obtained only from V. cholerae induced the expression of genes associated with tumour differentiation. Altogether, our study suggests that the observed genomic changes in host cells might be due to specific components of membrane vesicles and does not require communication by direct contact with the bacteria.
2017-08-23 | GSE102923 | GEO
Project description:Extracellularly released particles, including membrane vesicles, have increasingly been recognized as important for bacterial community functions and host-interaction processes, but their compositions and functional roles differ between species and also between strains of the same species. In this study, we have determined the composition of membrane vesicles and protein particles identified in the cell-free pellets of two strains of Apilactobacillus kunkeei, a defensive symbiont of honeybees. The membrane vesicles were separated from the extracellular particles using density gradient ultracentrifugation. The peaks of the RNA and protein distributions were separated from each other and the highest concentration of RNA was observed in the fractions that contained the membrane vesicles while the highest protein concentration coincided with the fractions that contained extracellular particles. A comparative proteomics analysis by LC-MS/MS showed that 37 proteins with type-I signal peptides were consistently identified across the fractionated samples obtained from the cell-free pellets, of which 29 were orthologs detected in both strains. Functional predictions of the extracellular proteins revealed the presence of glycoside hydrolases, glycosyltransferases, giant proteins and peptidases. The extracellular transcriptomes mapped to a broad set of genes with a similar functional profile as the whole cell transcriptome. This study provides insights into the composition of membrane vesicles and extracellular proteins of a bee-associated symbiont.
2023-06-09 | GSE205998 | GEO
Project description:We performed comparative transcriptomic analysis of the outer membrane vesicles (OMVs) released from B. burgdorferi. We identified a total of ~1200 unique transcripts with at least one mapped read from the bacterial cell and its OMVs.
2018-06-21 | GSE114368 | GEO
Project description:Microbial molecules have evolved to promote transient and/or permanent associations with mammals. Although numerous examples of secretion systems employed by pathogens have been described, mechanisms by which commensal bacteria export molecules during symbiosis remain unknown. The human gut mutualist Bacteroides fragilis produces a capsular polysaccharide (PSA) that directs host immune development. We reveal herein that outer membrane vesicles (OMVs) deliver PSA to dendritic cells (DCs), promoting regulatory T cells and inducing anti-inflammatory cytokines during protection from intestinal disease. In addition, we found that TLR2 signaling by DCs is required for OMV sensing. Following internalization into DCs and engagement of TLR2, OMVs initiate a gene expression program that results in IL-10 production by DCs. Although it is known that the outcome of PSA sensing by the immune system is Treg induction, nothing is known about the intracellular signaling pathway(s) activated by PSA within DCs. We analyzed the gene expression profile of DCs treated with OMVs to uncover factors that are expressed in a PSA-dependent, TLR2-dependent manner. Our findings demonstrate DC-induced protection from disease via OMV-delivery of a beneficial microbial molecule, uncovering a novel paradigm for inter-kingdom communication between the microbiota and mammals. RNA samples (1ug total RNA) from BMDCs were labeled with fluorescent dyes using the Quick Amp Labeling Kit (Agilent). Microarray (AgilentWhole Mouse Genome chip) hybridizations (65M-BM-0C for 16 hours) and washes were performed with Agilent reagents following standard protocols. Microarrays were analyzed using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 10.1.1.1. Significant genes were selected based on p< 0.01 and fold change >2.0.
2012-07-22 | E-GEOD-39563 | biostudies-arrayexpress
Project description:Microbial molecules have evolved to promote transient and/or permanent associations with mammals. Although numerous examples of secretion systems employed by pathogens have been described, mechanisms by which commensal bacteria export molecules during symbiosis remain unknown. The human gut mutualist Bacteroides fragilis produces a capsular polysaccharide (PSA) that directs host immune development. We reveal herein that outer membrane vesicles (OMVs) deliver PSA to dendritic cells (DCs), promoting regulatory T cells and inducing anti-inflammatory cytokines during protection from intestinal disease. In addition, we found that TLR2 signaling by DCs is required for OMV sensing. Following internalization into DCs and engagement of TLR2, OMVs initiate a gene expression program that results in IL-10 production by DCs. Although it is known that the outcome of PSA sensing by the immune system is Treg induction, nothing is known about the intracellular signaling pathway(s) activated by PSA within DCs. We analyzed the gene expression profile of DCs treated with OMVs to uncover factors that are expressed in a PSA-dependent, TLR2-dependent manner. Our findings demonstrate DC-induced protection from disease via OMV-delivery of a beneficial microbial molecule, uncovering a novel paradigm for inter-kingdom communication between the microbiota and mammals.
2012-07-23 | GSE39563 | GEO
Project description:miRNA-sequencing of cell membrane-based vesicles derived from gingiva-derived mesenchymal stem cells and fusion nanovesicles. We then performed gene expression profiling analysis to explore the miRNAs of cell membrane-based vesicles derived from gingiva-derived mesenchymal stem cells , and the retention rate of miRNAs after membrane fusion
2023-10-26 | GSE223577 | GEO
Project description:Comparison of bacterial species in gut microbiome and circulating extracellular vesicles
2023-02-24 | GSE225873 | GEO
Project description:Similar to bacterial proteins that are targeted to distinct macrophages organelles via extracellular vesicles, we propose that these vesicles also traffic small RNAs to modulate specific host factors. To test this, we aim to sequence extracellular vesicle derived sRNA, and whole bacterial small RNAs to determine selectivity, and to identify their bacterial and mammalian targets (Experimental Plan in Table-1). For this we will collect highly purified vesicles from N. gonorrhoeae (strain MS11A). We will also treat mouse derived primary macrophages with extracellular vesicles and compare their RNA response to untreated macrophages (Table-2). This will provide novel insights into how macrophages respond to N. gonorrhoeae infections. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2016-03-01 | E-ERAD-439 | biostudies-arrayexpress
Project description:Asthma is the most common chronic respiratory disease. Asthma that cannot be well controlled by steroid treatment is called steroid-resistant asthma. Steroid-resistant asthma accounts for only 5% of all asthma cases, but it accounts for 80% of asthma healthcare costs. Nontypeable Haemophilus influenzae (NTHi), as a Gram-negative bacterium, can release outer membrane vesicles (OMVs) and transfer biomolecules to host cells and the external environment by carrying lipopolysaccharides, proteins, peptidoglycans, outer membrane proteins, cell wall components, proteins, nucleic acids, ion metabolites, and signaling molecules. Thus, it plays a role in obtaining nutrition, stress, toxin delivery, adhesion, host immune surveillance evasion, and host immune response regulation. It becomes an essential way in bacterial pathogenesis. To further clarify whether NTHi OMVs could be inhaled to induce steroid-resistant asthma, we isolated and purified NTHi OMVs. In vivo experiments showed that NTHi OMVs could be inhaled and enter airway epithelial cells. Cosensitization with OVA induces steroid-resistant asthma in mice. Furthermore, through high-throughput sequencing, we found that the NTHi OMVs and OVA co-sensitized mice had significantly enriched inflammatory and immune-related signaling pathways, and the transcription and secretion of IL-1β were increased was the potential cause of SRA.
2023-07-18 | GSE222546 | GEO
Project description:Helicobacter pylori, a bacterium that colonizes the human stomach, like all Gram-negative bacteria spontaneously shed outer membrane vesicles (OMVs). OMVs, which act as a delivery system for bacterial components, are involved in bacterial-host interactions and thus contribute to pathogenesis. In this study, to understand the gene expression changes that human gastric epithelial cells might undergo when exposed to H. pylori-OMVs, we profiled the transcriptomic changes of the MKN74 gastric cell line induced by OMVs compared to control cells and H. pylori-infected cells, using the Ion AmpliSeq™ Transcriptome Human Gene Expression Panel. The top enriched pathways in the OMVs challenge condition included amino acid-related metabolic pathways, mitogen-activated protein kinase signaling, autophagy, and ferroptosis. The cell cycle, DNA replication, and repair pathways were the top diminished pathways. The transcriptomic changes induced by OMVs were largely consistent with those of the bacteria, although often at low expression levels, suggesting that their effects will mostly reinforce those of the bacterium itself. Our data provide a valuable portrayal of the transcriptomic remodeling of gastric cells by H. pylori-OMVs, which can be further dissected regarding the underlying molecular mediators and explored to understand the pathobiology of the full-spectrum of H. pylori-mediated diseases.
2024-04-03 | GSE229512 | GEO