MicroRNA-146 function in the innate immune response of zebrafish embryos to Salmonella typhimurium infection [miRNA profile]
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE45409 | GEO | 2013/09/16
SECONDARY ACCESSION(S): PRJNA194604
REPOSITORIES: GEO
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Project description:This study reports on infection-inducible miRNAs in zebrafish. Using a custom-designed microarray platform for miRNA expression we found that miRNAs of the miR-21, miR-29, and miR-146 families were commonly induced by infection of zebrafish embryos with Salmonella typhimurium and by infection of adult fish with Mycobacterium marinum. A custom-designed Agilent zebrafish 8x15k miRNA platform was used to profile miRNA expression in zebrafish embryos infected with Salmonella typhimurium strain SL1027 and adult zebrafish infected with Mycobacterium marinum strain Mma20 . The 15k design contained a duplicate of 7604 probes of 60-oligonucleotide length. The probes consisted of 2x22 nucleotide sequences antisense to mature miRNAs separated by a spacer of 8 nucleotides (CGATCTTT) and with a second spacer with the same sequence at the end. From 7604 probes 546 were designed for left (5') and right (3') arms of the hairpins of zebrafish miRNAs known in miRBase, while the remainder 7058 probes corresponded to predicted hairpin structures in the zebrafish genome that might include additional miRNAs but were not considered in this study. Zebrafish embryos were infected at 28 hours post fertilization (hpf) by injecting 200-250 colony forming units of Salmonella typhimurium into the caudal vein and miRNA profiles of infected embryos were compared to control embryos injected with PBS (phosphate buffered saline) at 8 hours post-infection (hpi; 3 biological replicates and 2 technical replicates per each sample). Adult zebrafish were infected with 10000 colony forming units of Mycobacterium marinum and miRNA profiles were compared to PBS-injected control fish at 6 days post infection (dpi; 3 biological replicates). For dual color hybridization of the Agilent chips miRNA samples from infected zebrafish were labeled with Hy3 and samples from control fish were labeled with Hy5.
2013-09-16 | E-GEOD-45409 | biostudies-arrayexpress
Project description:We used zebrafish embryos as an in vivo system to investigate the role of the microRNA-146 family (consisting of 2 members miR-146a and miR-146b) in the innate immune response to S. typhimurium infection. To determine the role of miR-146 microRNAs in the response to S. typhimurium infection we used Illumina RNA sequencing to compare the mRNA expression profiles of control embryos versus embryos with knockdown of miR-146a and miR-146b. RNA sequencing analysis of miR-146 knockdown embryos showed no major effects on pro-inflammatory gene expression or on the expression of transcriptional regulators and signal transduction components of the immune response. In contrast, apoliprotein-mediated lipid transport emerged as an infection-inducible pathway under miR-146 knockdown conditions, suggesting a function of miR-146 in regulating lipid metabolism during inflammation.
2013-09-16 | GSE45209 | GEO
Project description:We used zebrafish embryos as an in vivo system to investigate the role of the microRNA-146 family (consisting of 2 members miR-146a and miR-146b) in the innate immune response to S. typhimurium infection. To determine the role of miR-146 microRNAs in the response to S. typhimurium infection we used Illumina RNA sequencing to compare the mRNA expression profiles of control embryos versus embryos with knockdown of miR-146a and miR-146b. RNA sequencing analysis of miR-146 knockdown embryos showed no major effects on pro-inflammatory gene expression or on the expression of transcriptional regulators and signal transduction components of the immune response. In contrast, apoliprotein-mediated lipid transport emerged as an infection-inducible pathway under miR-146 knockdown conditions, suggesting a function of miR-146 in regulating lipid metabolism during inflammation. Embryos were injected at the one cell stage with a combination of two morpholinos targeting miR-146a and miR-146b, or with the standard control morpholino from GeneTools. Subsequently, at 28 hours post fertilzation (hpf) they were infected by injecting 200-250 colony forming units of S. typhimurium strain SL1027 into the caudal vein, or mock-injected with PBS. RNA was isolated at 8 hours post injection (hpi) for Illumina RNAseq analysis. Two independent experiments were performed for RNAseq analysis of biological duplicates.
2013-09-16 | E-GEOD-45209 | biostudies-arrayexpress
Project description:Characterization of the zebrafish embryonic host response to systemic bacterial infection with Salmonella typhimurium wild type strain (SL1027) and its isogenic LPS O-antigen mutant Ra (SF1592) by means of a time-resolved global expression analysis.
2009-03-02 | GSE13994 | GEO
Project description:Both embryonic and adult zebrafish Mycobacterium marinum infection studies have contributed to our knowledge of the development and function of tuberculous granulomas, which are typical for mycobacterial pathogenesis. In this review we discuss how transcriptome profiling studies have helped to characterize this infection process and we include new RNA sequencing (RNA-Seq) data that reveals three main phases in the host response to M. marinum during the early stages of granuloma development in zebrafish embryos and larvae. The late-phase response shares common components with the strong and acute host transcriptome response that has previously been reported for S. typhimurium infection in zebrafish embryos. In contrast, the early/mid-phase response to M. marinum infection, characterized by suppressed pro-inflammatory signaling, is strikingly different from the acute response to S. typhimurium infection. Furthermore, M. marinum infection shows a collective and strongly fluctuating regulation of lipoproteins, while S. typhimurium infection has pronounced effects on amino acid metabolism and glycolysis.
2016-06-01 | GSE76499 | GEO
Project description:MicroRNA-146 function in the innate immune response of zebrafish embryos to Salmonella typhimurium infection
| PRJNA194603 | ENA
Project description:Characterization of the zebrafish embryonic host response to systemic bacterial infection with Salmonella typhimurium wild type strain (SL1027) and its isogenic LPS O-antigen mutant Ra (SF1592) by means of a time-resolved global expression analysis. All infection experiments were performed using mixed egg clutches from three tanks of AB strain zebrafish. Embryos were staged at 27 hours post fertilization (hpf) by morphological criteria (Kimmel et al., 1995) and approximately 250 cfu of DsRed expressing S. typhimurium wt and Ra mutant bacteria were injected into the caudal vein close to the urogenital opening. As a control an equal volume of PBS was likewise injected. Injections were controlled using a Leica MZ Fluo 3 stereomicroscope with epifluorescence attachment together with a Femtojet microinjector (Eppendorf) and a micromanipulator with pulled microcapillary pipettes. Pools of 20-40 embryos were collected at 2, 5, 8 and 24 hours post infection (hpi). For the microarray analysis, the whole infection procedure was preformed in triplicate on separate days. The triplicates are marked A,B and C. The order of injecting wt bacteria, Ra bacteria and PBS control was randomized in the different experiments. The general reference sample is a mixture of all RNA samples from this infection study and it is named Common Reference (CR).
2010-05-22 | E-GEOD-13994 | biostudies-arrayexpress
Project description:Both embryonic and adult zebrafish Mycobacterium marinum infection studies have contributed to our knowledge of the development and function of tuberculous granulomas, which are typical for mycobacterial pathogenesis. In this review we discuss how transcriptome profiling studies have helped to characterize this infection process and we include new RNA sequencing (RNA-Seq) data that reveals three main phases in the host response to M. marinum during the early stages of granuloma development in zebrafish embryos and larvae. The late-phase response shares common components with the strong and acute host transcriptome response that has previously been reported for S. typhimurium infection in zebrafish embryos. In contrast, the early/mid-phase response to M. marinum infection, characterized by suppressed pro-inflammatory signaling, is strikingly different from the acute response to S. typhimurium infection. Furthermore, M. marinum infection shows a collective and strongly fluctuating regulation of lipoproteins, while S. typhimurium infection has pronounced effects on amino acid metabolism and glycolysis. Embryos were infected at 28 hpf by injecting 250 colony forming units of M. marinum Mma20 in 2%PVP into the caudal vein, or mock-injected with PBS/2%PVP. After injections, embryos were transferred into fresh egg water containing 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich) to prevent melanization and incubated at 28°C. After the incubation period, infected and uninfected groups of 30 embryos were snap-frozen in liquid nitrogen and RNA was isolated for Illumina RNAseq analysis. Samples were taken at the following timepoints: 2, 4, 6, 8 hpi and 1, 2, 3, 4, 5 dpi.
2016-06-01 | E-GEOD-76499 | biostudies-arrayexpress
Project description:Salmonella enterica serovar Typhimurium (S. typhimurium) bacteria cause an inflammatory and lethal infection in zebrafish embryos. To characterize the embryonic innate host response at the transcriptome level, we have extended and validated previous microarray data by Illumina next-generation sequencing analysis. Comparison of tag-based sequencing (DGE or Tag-Seq) with full transcript sequencing (RNA-Seq) showed a strong correlation of sequence read counts per transcript and an overlap of 241 transcripts differentially expressed in response to infection. A slightly lower overlap of 165 transcripts was observed with previous microarray data. Based on the combined sequencing-based and microarray-based transcriptome data we compiled an annotated reference set of infection-responsive genes in zebrafish embryos, encoding transcription factors, signal transduction proteins, cytokines and chemokines, complement factors, proteins involved in apoptosis and proteolysis, proteins with anti-microbial activities, as well as many known or novel proteins not previously linked to the immune response. Furthermore, by comparison of the deep sequencing data of S. typhimurium infection in zebrafish embryos with previous deep sequencing data of Mycobacterium marinum infection in adult zebrafish we derived a common set of innate host defense genes that are expressed both in the absence and presence of a fully developed adaptive immune system and that provide a valuable reference for future studies of host-pathogen interactions using zebrafish infection models.
2010-10-26 | GSE22472 | GEO
Project description:Although ectopic overexpression of miRNAs can influence mammary normal and cancer stem cells (SCs/CSCs), their physiological relevance remains uncertain. Here, we found that the miR-146 family is linked to SC identity, since: i) their expression is very high in SCs/CSCs from human/mouse primary mammary tissues; correlates with the basal-like breast cancer subtype, which typically has a high CSC content; and specifically distinguishes cells with SC/CSC identity; ii) miR-146 depletion reduces SC/CSC self-renewal in vitro and the number of tumor-initiating cells in vivo. Analysis of the transcriptional effects of miR-146 in breast SC-like cells revealed a complex network of highly connected miR-146 targets related to quiescence, transcription and metabolic pathways (one-carbon pool, purine synthesis and folate metabolism). As predicted by our analysis, SCs/CSCs display innate resistance to anti-folate therapy that can be reversed by miR-146 depletion, unmasking a “hidden vulnerability” that could be exploited for the development of anti-CSC therapies.
2020-01-21 | GSE131876 | GEO