Pathogen recognition and activation of the innate immune response in zebrafish
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE35474 | GEO | 2012/11/01
SECONDARY ACCESSION(S): PRJNA152357
REPOSITORIES: GEO
Similar Datasets
Project description:We use the zebrafish embryo model to study the similarities and differences in the innate immune response against three different bacterial pathogens. Therefore, we injected E. tarda, Salmonella, or M. marinum into the caudal vein of 28 hours post fertilization (hpf) zebrafish embryos and analysed their gene expression profile at 8 hours or 4 days after infection by microarrays. The results show that infections with the gram-negative bacteria E. tarda and S. typhimurium, which are lethal within 1-2 days, induce a strong early immune response at 8 hours after infection. In contrast, infection with M. marinum leads to a chronic infection that only induces a strong response at 4 days post infection. This microarray study was designed to determine the gene expression profile during infection with Salmonella typhimurium, Mycobacterium marinum, and Edwardsiella tarda. RNA was isolated from single embryos and each treatment group consisted of three embryos: (1) Wildtypes injected with PBS 8 hours post infection (hpi), (2) S. typhimurium-infected wildtypes 8hpi, (3) wildtypes injected with PBS/2%PVP 8hpi , (4) M. marinum-infected wildtypes 8hpi, (5) wildtypes injected with PBS/2%PVP 4 days post infection (dpi), (6) M. marinum-infected wildtypes 4dpi, (7) wildtypes injected with PBS 8hpi (E. tarda control), (8) E. tarda-infected wildtypes 8hpi. Embryos were grown at 28.5M-bM-^@M-^S30M-BM-0C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of S. typhimurium SL1027, E. tarda or Mycobacteria marinum M20 bacteria into the caudal vein, or were mock-injected with buffer as a control. After injections embryos were transferred into fresh egg water and incubated for 8 h or 4 days at 28M-BM-0C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for microarray analysis. All treatment groups were analyzed using a common reference approach.
2012-11-01 | E-GEOD-35474 | biostudies-arrayexpress
Project description:We use the Tlr2 mutant of zebrafish embryos model to study the transcriptome response to Mycobacterium marinum infection. We injected M.marinum into the caudal vein at 28 hours post fertilization and took samples at 4 days post infection.
2018-01-01 | GSE102766 | GEO
Project description:Transcriptional profiling of the zebrafish embryonic host response to infection by injection of 200 CFUs of Edwardsiella tarda (strain FL6-60) All infection experiments were performed using mixed egg clutches of Albino strain zebrafish. Embryos were staged at 28 hours post fertilization (hpf) by morphological criteria and approximately 200 cfu of mCherry expressing E. tarda bacteria were injected into the caudal vein close to the urogenital opening. As a control an equal volume of PBS was likewise injected. Single embryos of the infected and control group were collected 8 hours post infection (hpi).
2011-09-30 | E-GEOD-28485 | biostudies-arrayexpress
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: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:Zebrafish Mycobacterium marinum infection has been widely used to model human tuberculosis because these two diseases share common features, e.g. latency, granuloma formation and reactivation. Here we infected adult zebrafish with a low dose of M. marinum, which usually leads to a chronic infection. At 14 days post infection we performed microarray analysis to characterize the immune response against this infection. Analysis was done using total RNA extracted from the abdominal organs of zebrafish. Our aim was to find novel genes underlying host defense mechanisms against M. marinum infection in zebrafish, and thus to produce novel information that is valuable when developing new treatments for human tuberculosis.
2019-02-01 | GSE120552 | GEO
Project description:MyD88 is an adaptor protein in Toll-like receptor and interleukin 1 receptor mediated signaling pathways that plays an essential role in activation of immune responses following pathogen recognition. We investigate that role in the zebrafish embryo model by using a zebrafish mutant line that contains a premature stop condon in the gene encoding MyD88, leading to a truncated protein that lacks domains important for its normal function. We infected these MyD88 mutants and wildtype individuals with Mycobacterium marinum to compare the resulting immune response by transcriptome profiling on total RNA isolated from single embryos. Autophagy regulator dram1 was identified as one of the MyD88-dependent genes. This RNAseq analysis was used to determine the effect of a truncation of the MyD88 protein on the innate immune response of zebrafish embryos during infection with Mycobacterium marinum. Myd88 mutant and wild type embryos were derived by incrossing homozygous myd88 mutant parents (allele hu3568, van der Vaart et al., 2013, Disease models & mechanisms 6, 841-854) or their wildtype siblings. RNA was isolated from pools of 20 embryos at 4 days post infection (4 dpi). The following treatment groups were used: homozygous mutants mock-injected with PBS/2%PVP 4 dpi, (2) wildtype siblings mock-injected with PBS/2%PVP 4dpi, (3) M. marinum-infected homozygous mutants 4dpi, (4) M. marinum-infected wildtype siblings 4dpi. Embryos were grown at 28.5M-bM-^@M-^S30M-BM-0C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of Mycobacterium marinum Mma20 bacteria into the caudal vein, or were mock-injected with buffer (PBS/2%PVP) as a control. After injections embryos were transferred into fresh egg water and incubated for 4 days at 28M-BM-0C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for RNAseq analysis.
2014-06-01 | E-GEOD-49186 | biostudies-arrayexpress
Project description:MyD88 is an adaptor protein in Toll-like receptor and interleukin 1 receptor mediated signaling pathways that plays an essential role in activation of immune responses following pathogen recognition. We investigate that role in the zebrafish embryo model by using a zebrafish mutant line that contains a premature stop condon in the gene encoding MyD88, leading to a truncated protein that lacks domains important for its normal function. We infected these MyD88 mutants and wildtype individuals with S Mycobacterium marinum to compare the resulting immune response by transcriptome profiling on total RNA isolated from single embryos. Autophagy regulator dram1 was identified as one of the MyD88-dependent genes. This microarray study was designed to determine the effect of a truncation of the MyD88 protein on the innate immune response of zebrafish embryos during infection with Mycobacterium marinum. Embryos used in this study are derived from an incross between parents heterozygous for the mutation. Both homozygous mutants and their wildtype siblings were selected by genotyping after being injected with the bacteria or PBS as control. RNA was isolated from single embryos at 4 days post infection (4 dpi) and each treatment group consisted of three embryos: (1) Homozygous mutants mock-injected with PBS/2%PVP 4 dpi, (2) wildtype siblings mock-injected with PBS/2%PVP 4dpi, (3) M. marinum-infected homozygous mutants 4dpi, (4) M. marinum-infected wildtype siblings 4dpi. Embryos were grown at 28.5M-bM-^@M-^S30M-BM-0C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of Mycobacterium marinum Mma20 bacteria into the caudal vein, or were mock-injected with buffer (PBS/2%PVP) as a control. After injections embryos were transferred into fresh egg water and incubated for 4 days at 28M-BM-0C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for microarray analysis. The treatment groups were analyzed using a common reference approach.
2014-06-01 | E-GEOD-49187 | biostudies-arrayexpress
Project description:We use the zebrafish embryo model to study the innate immune response against Mycobacterium marinum. Therefore, we injected M. marinum into the yolk at the 64 cell stage and took samples at 5 days post injection. This deep sequence study was designed to determine the gene expression profile by Mycobacterium marinum infection. RNA was isolated from embryos at 5 days post injection. Wildtypes zebrafish embryos were micro-injected into the yolk (64 cell stage) with 40 CFU of Mycobacterium marinum E11 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone), or Non-injected as a control. After injections embryos were transferred into fresh egg water and incubated at 28M-BM-0C. At 5 days post injection 50 embryos per group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.
2014-12-11 | E-GEOD-57792 | biostudies-arrayexpress
Project description:Mycobacterium marinum infection in zebrafish (Danio rerio) has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole-genome level transcriptome analysis. In addition, we carried out a medium-scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen, we identified a mutant zebrafish line with impaired resistance to a low-dose M. marinum infection. In this line, the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation.
2019-10-16 | GSE118350 | GEO