Homo sapiens
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-23630
PROVIDER: PRJNA129929 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Background: In the last decade, much attention has been drawn to probiotic bacteria in the context of inflammatory bowel disease (IBD), since the potential of certain strains to attenuate inflammation was demonstrated in several animal experiments and clinical studies. Data in humans elucidating the molecular mechanism of probiotic action are still scarce. To this end, we used an organ culture system of human colon mucosa and investigated the gene expression profiles after treatment with different probiotic bacteria in phorbol 12-myristate 13-acetate (PMA)/ionomycin (IO)) stimulated samples using whole genome microarrays. Moreover, we analyzed changes occurring in the intestinal explants cultured for 8 hours when compared to fresh, directly frozen mucosa, in order to infer the suitability of the system to study an inflammatory stimulus and likely antiinflammatory responses. Results: Culturing intestinal colon fragments during 8 hours elicited differential gene expression in 283 genes, 229 upregulated and 54 downregulated. Upregulated genes were predominantly related to apoptosis, whereas downregulated genes encoded mitochondrial proteins. No specific enrichment of genes related to inflammation or immune response could be detected, confirming the suitability of the system to further study the inmunomodulatory/anti-inflammatory properties of Lactobacillus casei BL23 (BL23), L.plantarum 299v (LP299v) and L.plantarum 299v (A-) (LP299v (A-)), a mutant strain with reduced adhesive properties to enterocytes. Intestinal explants were stimulated with PMA/IO for 3 hours and subsequently incubated with probiotic bacteria for 4 h. ANOVA analysis (p ? 0,01) revealed 205 differentially expressed genes between Control, PMA/IO (Inflamed), and the 3 bacterial treatments. Most importantly, a number of PMA/IO induced genes related to immune response and immune system process such as IL-2, IFN-?, IL17A and pro-inflammatory cytokines CXCL9 and CXCL11 were downregulated by BL23, LP299v and LP299v (A-). The behaviour of the three Lactobacillus strains was quite similar, although their presence induced differential expression of a small number of genes in a strain dependent manner. Conclusion: The human colon organ culture was found to be a suitable model for the study of inflammatory/anti-inflammatory stimuli, and therefore it constitutes a valuable tool to determine the inmunomodulatory effect of probiotic bacteria. The global transcriptional profile evoked by strains BL23, LP299v and LP299v (A-) in artificially inflamed tissue indicated a clear homeostasis restoring effect, including a decrease of the signals produced by activated T cells. Macroscopically healthy colonic intestinal tissue was obtained at surgery from 3 patients. Intestinal explants were treated with PMA and ionomycin for 3 h to induce pro-inflammatory conditions. Then, culture medium was changed and replaced with either medium or medium containing either Lactobacillus casei BL23, Lactobacillus plantarum 299v, or a nonadherent mutant of L. plantarum 299v (A-) and incubated for further 4 hours. In parallel, control intestinal explants were cultured without any treatment of PMA/ionomycin or probiotic bacteria and compared to directly frozen tissue in order to evaluate changes in gene expression which are due solely to the culture conditions.
2012-06-19 | E-GEOD-23630 | biostudies-arrayexpress
Project description:Background: In the last decade, much attention has been drawn to probiotic bacteria in the context of inflammatory bowel disease (IBD), since the potential of certain strains to attenuate inflammation was demonstrated in several animal experiments and clinical studies. Data in humans elucidating the molecular mechanism of probiotic action are still scarce. To this end, we used an organ culture system of human colon mucosa and investigated the gene expression profiles after treatment with different probiotic bacteria in phorbol 12-myristate 13-acetate (PMA)/ionomycin (IO)) stimulated samples using whole genome microarrays. Moreover, we analyzed changes occurring in the intestinal explants cultured for 8 hours when compared to fresh, directly frozen mucosa, in order to infer the suitability of the system to study an inflammatory stimulus and likely antiinflammatory responses. Results: Culturing intestinal colon fragments during 8 hours elicited differential gene expression in 283 genes, 229 upregulated and 54 downregulated. Upregulated genes were predominantly related to apoptosis, whereas downregulated genes encoded mitochondrial proteins. No specific enrichment of genes related to inflammation or immune response could be detected, confirming the suitability of the system to further study the inmunomodulatory/anti-inflammatory properties of Lactobacillus casei BL23 (BL23), L.plantarum 299v (LP299v) and L.plantarum 299v (A-) (LP299v (A-)), a mutant strain with reduced adhesive properties to enterocytes. Intestinal explants were stimulated with PMA/IO for 3 hours and subsequently incubated with probiotic bacteria for 4 h. ANOVA analysis (p ≤ 0,01) revealed 205 differentially expressed genes between Control, PMA/IO (Inflamed), and the 3 bacterial treatments. Most importantly, a number of PMA/IO induced genes related to immune response and immune system process such as IL-2, IFN-γ, IL17A and pro-inflammatory cytokines CXCL9 and CXCL11 were downregulated by BL23, LP299v and LP299v (A-). The behaviour of the three Lactobacillus strains was quite similar, although their presence induced differential expression of a small number of genes in a strain dependent manner. Conclusion: The human colon organ culture was found to be a suitable model for the study of inflammatory/anti-inflammatory stimuli, and therefore it constitutes a valuable tool to determine the inmunomodulatory effect of probiotic bacteria. The global transcriptional profile evoked by strains BL23, LP299v and LP299v (A-) in artificially inflamed tissue indicated a clear homeostasis restoring effect, including a decrease of the signals produced by activated T cells.
2012-06-20 | GSE23630 | GEO
Project description:Escherichia coli Nissle 1917 (EcN) is a probiotic used for treatment of intestinal disorders. EcN improves gastrointestinal homeostasis and microbiota balance; however little is known about how this probiotic delivers effector molecules to the host. Outer membrane vesicles (OMVs) are constitutively produced by gram-negative bacteria and have a relevant role in bacteria-host interactions. Here we performed proteomic analysis of EcN OMVs. Using 1D SDSD-PAGE and highly sensitive LC-MS/MS analysis we identified 192 EcN vesicular proteins with high confidence in three independent experiments. Of these proteins, 18 were encoded by strain-linked genes and 57 were common to pathogen-derived OMVs. These proteins may contribute to the ability of this probiotic to colonize the human gut as they fulfil functions related to adhesion to host tissues, immune modulation or bacterial survival in host niches. This study describes the first global OMV proteome of a probiotic strain and provides evidence that probiotic-derived OMVs contain proteins that can target these vesicles to the host and mediate their beneficial effects on intestinal function.
2013-12-19 | PXD000367 | Pride
Project description:Transcription profiling by array of human intestinal colon explants stimulated by phorbol 12-myristate 13-acetate (PMA)/ionomycin (IO)) and co-cultured with different strains of Lactobacillus probiotic bacteria
2014-10-15 | E-GEOD-23630 | ExpressionAtlas
Project description:Identification of factors in conditioned media of first-trimester placental villous explants. Explants were cultured under hypoxia (2% O2), 5% CO2 in serum-free DMEM/F12 and treated with recombinant galectin-7 (1ug/ml) or vehicle control (BSA) for 72h. Identification of factors in conditioned media of first-trimester placental villous explants. Explants were cultured under superoxia (20% O2), 5% CO2 in serum-free DMEM/F12 and treated with recombinant galectin-7 (1ug/ml) or vehicle control (BSA) for 72h.
2021-04-20 | PXD019331 | Pride
Project description:Probiotic bacteria may render mice resistant to the development of various inflammatory and infectious diseases. This study aimed to identify underlying mechanisms by which probiotic bacteria may influence intestinal immune homeostasis in non-inflammatory conditions. To this end, we studied the effect of short term (3 days) and long term (28 days) oral administration of VSL#3, a mixture of 8 probiotic bacteria, to healthy BALB/c and C57BL/6 mice, with dominant humoral or cellular immunity, respectively. Long-term treatment with VSL#3 resulted in an increase of B cells and a decrease of CD4+ T cells in the Peyer’s patches (PP) and mesenteric lymph nodes (MLN) of both mouse strains, compared to untreated mice. However, genome wide gene expression profiling using micro-arrays revealed that prolonged administration of VSL#3 to BALB/c and C57BL/6 mice was associated with host-specific modulation of gene expression in colon and small intestine. Whereas VSL#3 treatment resulted in down-regulation of Il13 and Epx, and up-regulation of Il12rb1, Ccr5, Cxcr3 and Cxcl10 in BALB/c mice, such effects were not observed in C57BL/6 mice. In BALB/c mice, a 2-fold increase in CD103+ CD11c+ dendritic cells was found both in PP and in MLN, 18 hours after the first treatment with VSL#3. Prolonged treatment with VSL#3 was associated with increased numbers of Th17 cells and Foxp3+ regulatory T cells in the MLN of these mice. In conclusion, these experiments in healthy mice show that probiotic bacteria may alter the immunological phenotype of the host; the nature of these effects is dependent on mouse strain. In conclusion, these experiments in healthy mice show that probiotic bacteria may alter the immunological phenotype of the host; the nature of these effects is dependent on mouse strain. 40 samples (4 experimental groups, 5 biological replicates), performed in two inbred mice strains
2014-10-23 | E-GEOD-62619 | biostudies-arrayexpress
Project description:Probiotic bacteria, specific representatives of bacterial species that are a common part of the human microbiota, are proposed to deliver health benefits to the consumer by modulation of intestinal function via largely unknown molecular mechanisms. To explore in vivo mucosal responses of healthy adults to probiotics, we obtained transcriptomes in an intervention study following a double-blind placebo-controlled cross-over design. In the mucosa of the proximal small intestine of healthy volunteers, probiotic strains from the species Lactobacillus acidophilus, L. casei and L. rhamnosus each induced differential gene regulatory networks and pathways in the human mucosa. Comprehensive analyses revealed that these transcriptional networks regulate major basal mucosal processes, and uncovered remarkable similarity to response profiles obtained for specific bioactive molecules and drugs. This study elucidates how intestinal mucosa of healthy humans perceive different probiotics and provides avenues for rationally designed tests of clinical applications. Keywords: mucosal response of healthy adult humans to lactic acid bacteria
2010-09-08 | GSE18741 | GEO
Project description:Transcriptional profiling of small intestinal explants cultured in the absence or in the presence of Ibuprofen (100 µM). Two-condition experiment, control intestinal explants vs Ibuprofen intestinal explants
2019-01-07 | GSE108369 | GEO
Project description:Probiotic bacteria may render mice resistant to the development of various inflammatory and infectious diseases. This study aimed to identify underlying mechanisms by which probiotic bacteria may influence intestinal immune homeostasis in non-inflammatory conditions. To this end, we studied the effect of short term (3 days) and long term (28 days) oral administration of VSL#3, a mixture of 8 probiotic bacteria, to healthy BALB/c and C57BL/6 mice, with dominant humoral or cellular immunity, respectively. Long-term treatment with VSL#3 resulted in an increase of B cells and a decrease of CD4+ T cells in the Peyer’s patches (PP) and mesenteric lymph nodes (MLN) of both mouse strains, compared to untreated mice. However, genome wide gene expression profiling using micro-arrays revealed that prolonged administration of VSL#3 to BALB/c and C57BL/6 mice was associated with host-specific modulation of gene expression in colon and small intestine. Whereas VSL#3 treatment resulted in down-regulation of Il13 and Epx, and up-regulation of Il12rb1, Ccr5, Cxcr3 and Cxcl10 in BALB/c mice, such effects were not observed in C57BL/6 mice. In BALB/c mice, a 2-fold increase in CD103+ CD11c+ dendritic cells was found both in PP and in MLN, 18 hours after the first treatment with VSL#3. Prolonged treatment with VSL#3 was associated with increased numbers of Th17 cells and Foxp3+ regulatory T cells in the MLN of these mice. In conclusion, these experiments in healthy mice show that probiotic bacteria may alter the immunological phenotype of the host; the nature of these effects is dependent on mouse strain. In conclusion, these experiments in healthy mice show that probiotic bacteria may alter the immunological phenotype of the host; the nature of these effects is dependent on mouse strain.
2014-10-23 | GSE62619 | GEO
Project description:Probiotic bacteria, specific representatives of bacterial species that are a common part of the human microbiota, are proposed to deliver health benefits to the consumer by modulation of intestinal function via largely unknown molecular mechanisms. To explore in vivo mucosal responses of healthy adults to probiotics, we obtained transcriptomes in an intervention study following a double-blind placebo-controlled cross-over design. In the mucosa of the proximal small intestine of healthy volunteers, probiotic strains from the species Lactobacillus acidophilus, L. casei and L. rhamnosus each induced differential gene regulatory networks and pathways in the human mucosa. Comprehensive analyses revealed that these transcriptional networks regulate major basal mucosal processes, and uncovered remarkable similarity to response profiles obtained for specific bioactive molecules and drugs. This study elucidates how intestinal mucosa of healthy humans perceive different probiotics and provides avenues for rationally designed tests of clinical applications. Keywords: mucosal response of healthy adult humans to lactic acid bacteria This study was set up according to a randomised double-blind cross-over placebo-controlled design. It contains transcriptional profiles from biopsies from 7 healthy individuals after oral intake of three different Lactobacillus species or placebo control. In total, this study includes data from 7 individuals x 4 treatments=28 arrays.
2010-09-08 | E-GEOD-18741 | biostudies-arrayexpress