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Transcriptomic response of immune signaling pathways in intestinal epithelial cells exposed to commensals, pathogens and probiotics

ABSTRACT: In order to understand the appropriate use of potentially beneficial Gram positive microbes through their introduction in the gut microbiome, it is necessary to understand the influence of individual bacteria on the host response system at a cellular level. In the present study we showed that lipopolysaccharide (LPS), flagellated Gram negative bacteria, potentially beneficial Gram positive bacteria and yeast interact differently with human intestinal enterocytes (IEC) with a custom-designed expression microarray evaluating 17 specific host-response pathways. Only, LPS and flagellated Gram negative bacteria induced inflammatory response, while a subset of Gram positive microbes had anti-inflammatory potential. The main outcome from the study was the differential regulation of the central MAPK signaling pathway by these Gram positive microbes versus commensal/pathogenic Gram negative bacteria. The microarray was efficient to highlight the impact of individual bacteria on IEC response, but q-RT-PCR validation demonstrated some underestimation for down regulated genes by the microarray. This Immune Array will allow us to better understand the mechanisms underlying pathogen-induced host immune responses, aid in the selection potentially probiotic microbes and perhaps select biomarkers for future clinical studies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE31394 | GEO | 2011/12/31

SECONDARY ACCESSION(S): PRJNA145879

REPOSITORIES: GEO

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Transcriptomic response of immune signaling pathways in intestinal epithelial cells exposed to commensals, pathogens and probiotics

Project description:In order to understand the appropriate use of potentially beneficial Gram positive microbes through their introduction in the gut microbiome, it is necessary to understand the influence of individual bacteria on the host response system at a cellular level. In the present study we showed that lipopolysaccharide (LPS), flagellated Gram negative bacteria, potentially beneficial Gram positive bacteria and yeast interact differently with human intestinal enterocytes (IEC) with a custom-designed expression microarray evaluating 17 specific host-response pathways. Only, LPS and flagellated Gram negative bacteria induced inflammatory response, while a subset of Gram positive microbes had anti-inflammatory potential. The main outcome from the study was the differential regulation of the central MAPK signaling pathway by these Gram positive microbes versus commensal/pathogenic Gram negative bacteria. The microarray was efficient to highlight the impact of individual bacteria on IEC response, but q-RT-PCR validation demonstrated some underestimation for down regulated genes by the microarray. This Immune Array will allow us to better understand the mechanisms underlying pathogen-induced host immune responses, aid in the selection potentially probiotic microbes and perhaps select biomarkers for future clinical studies. In this study, human immune response was assessed by stimulating HT-29 intestinal epithelial cells (IEC) with different microorganisms (or LPS) individually. For each of the 12 different treatments, between 4 and 8 biological replicates were performed, analyzed with dye-swaps and hybridized against control or untreated cells. Genes that were showing a 1.3 mRNA transcript abundance fold change and a P-value below 0.05 were considered to be differentially expressed.

2011-12-31 | E-GEOD-31394 | biostudies-arrayexpress

Dietary heme modulates microbiota and mucosa of mouse colon without significant host-microbe cross talk

Project description:Previously, we showed that dietary heme injured the colonic surface epithelium and induced hyperproliferation by changing the surface to crypt signaling. In this study we investigated whether bacteria play a role in this changed signaling. Dietary heme increased the Bacteroidetes and decreased the Firmicutes in colonic content. This shift was caused by a selective susceptibility of Gram-positive bacteria to the heme cytotoxic fecal waters, which is not observed for Gram-negative bacteria allowing expansion of the Gram-negative community. The increased amount of Gram-negative bacteria increased LPS exposure to colonocytes, however, there is no appreciable immune response detected in the heme-fed mice. There were no signs of sensing of the bacteria by the mucosa, as changes in TLR signaling were not present. This lack of microbe-host cross talk indicated that the changes in microbiota do not play a causal role in the heme-induced hyperproliferation.

2013-07-18 | GSE34253 | GEO

G-quadruplex DNA as a target for pathogenic bacteria: efficacy of an extended naphthalene diimide ligand and mode of action

Project description:Guanidine DNA quadruplex (G4-DNA) structures convey a distinctive layer of epigenetic information that is critical for the regulation of key biological activities and processes as genome transcription regulation, replication and repair. Despite several works that have been published recently, the information regarding their role and possible use as therapeutic drug targets in bacteria is still scarce. Here, we tested the biological activity of a small G4-DNA ligand library based on the naphthalene diimide (NDI) pharmacophore, against both Gram-positive and Gram-negative bacteria. For the best compound identified, NDI-10, the action mechanism was further characterized. Gram-negative bacteria were more resistant altogether due to the presence of the outer membrane, although the activity of the G4-Ligand was generally bactericidal, while it was bacteriostatic for Gram-positive bacteria. This asymmetric activity could be related to the different prevalence of putative G4-DNA structures in each group, the influence that they can exert on the gene expression (which was found more severe for the Gram-negative bacteria) and the role of the G4 structures in these bacteria, that seems to be more related to promote transcription in Gram-positive bacteria and repress transcription in Gram-negative.

2022-12-10 | GSE178890 | GEO

Dietary heme modulates microbiota and mucosa of mouse colon without significant host-microbe cross talk

2013-07-18 | E-GEOD-34253 | biostudies-arrayexpress

Profiling the circulating miRNAs in mice exposed to gram-positive and gram-negative bacteria by Illumina small RNA deep sequencing

Project description:We profiled the expression of circulating microRNAs (miRNAs) in mice exposed to gram-positive and gram-negative bacteria using Illumina small RNA deep sequencing. Recombinant-specific gram-negative pathogen Escherichia coli (Xen14) and gram-positive pathogen Staphylococcus aureus (Xen29) were used to induce bacterial infection in mice at a concentration of 1 × 108 bacteria/100 μL of phosphate buffered saline (PBS). Small RNA libraries generated from the serum of mice after exposure to PBS, Xen14, Xen29, and Xen14+Xen29 via the routes of subcutaneous injection (I), cut wound (C), or under grafted skin (S) were analyzed using an Illumina HiSeq2000 Sequencer. Following exposure to gram-negative bacteria alone, no differentially expressed miRNA was found in the injection, cut, or skin graft models. Exposure to mixed bacteria induced a similar expression pattern of the circulating miRNAs to that induced by gram-positive bacterial infection. Upon gram-positive bacterial infection, 9 miRNAs (mir-193b-3p, mir-133a-1-3p, mir-133a-2-3p, mir-133a-1-5p, mir-133b-3p, mir-434-3p, mir-127-3p, mir-676-3p, mir-215-5p) showed upregulation greater than 4-fold with a p-value < 0.01. Among them, mir-193b-3p, mir-133a-1-3p, and mir-133a-2-3p presented the most common miRNA targets expressed in the mice exposed to gram-positive bacterial infection.

2014-08-19 | GSE60492 | GEO

Bacteria

Project description:Genome sequencing of mcr-positive Gram-negative bacteria

| PRJDB10296 | ENA

Project description:Gram-positive Bacteria

| PRJNA754713 | ENA

RNA-seq of intestinal epithelial cells isolated from DSS colitis model mice

Project description:In the present study, we demonstrated that mice deficient in chemerin or IEC-specific CMKLR1 expression were highly susceptible to DSS-induced colitis and subsequent tumorigenesis, which was reversed by suppressing colonic neutrophilic inflammation using CXCR2 inhibitor. Surprisingly, we found that lack of the Chemerin-CMKLR1 signaling specifically reduced colonic epithelial expression of lactoperoxidase (LPO), an epithelial peroxidase which could utilize H2O2 to oxidase thiocyanates to antibiotic compound (Bafort et al., 2014). Importantly, we demonstrated that impaired epithelial LPO expression accounted for outgrowth of potentially pathogenic Gram-negative bacteria following epithelial injury, which led to overproduction of CXCL1/2 and pathological neutrophilic inflammation in mice with epithelial Chemerin-CMKLR1 signaling deficiency. Finally, lack of epithelial Chemerin-CMKLR1 signaling impaired early host defense against enteric bacteria, which was reversed by LPO supplementation. Taken together, our study uncovers a critical role of epithelial Chemerin-CMKLR1 signaling in restricting pathological colonic neutrophilia via potentiating LPO-mediated epithelial innate defense, thereby rendering protection against microbiota-driven colitis and tumorigenesis.

2022-06-30 | GSE178308 | GEO

Circulating miRNA expression after subcutaneous injection of Gram negative and positive bacteria in the mice

Project description:To explore the circulating miRNA expression after subcutaneous injection of Gram negative and positive bacteria in the mice

2014-01-01 | GSE49189 | GEO

Gene expression in Drosophila melanogaster in response to bacterial infection

Project description:The goal of this study was to generate a high-quality dataset of gene expression in Drosophila melanogaster 3 hours after infection with Gram-positive (M luteus) or Gram-negative (E coli) bacteria.

2023-10-31 | GSE216042 | GEO

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