RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection
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PROVIDER: PRJNA1213790 | ENA |
REPOSITORIES: ENA
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Project description:Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish (Danio rerio) has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish lines. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu5 mutation revealed differentially expressed genes compared to WT controls. Genes associated with neutrophil degranulation, haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls.
2025-02-07 | GSE287594 | GEO
Project description:Inflammasome regulates the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of M. marinum infection in adult zebrafish (Danio rerio) has similar features than the course of tuberculosis in human. Here we have investigated the role of the inflammasome adaptor pycard in M. marinum infection in zebrafish with two CRISPR/Cas9 mutagenesis generated zebrafish line. Adult zebrafish devoid of pycard showed impaired survival and increased bacterial burden in M. marinum infection. Transcriptome analysis with RNA sequencing of a kidney derived neutrophils of M. marinum infected fish homozygous for pycardptu4 mutation revealed differentially expressed genes compared to WT controls. Differentially expressed genes were associated with neutrophil degranulation, haematopoiesis and PI3K signalling are differentially expressed in the pycard deficient neutrophils when compared to wild type controls.
2024-07-03 | GSE270136 | GEO
Project description:Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis, as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up- or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA-seq was conducted using a low dose infection (approximately 30 CFU) at 4 weeks post infection, from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria.
2024-07-04 | GSE189627 | GEO
Project description:RNA seq analysis from the kidney neutrophils of pycard mutant adult zebrafish in Mycobacterium marinum infection
| PRJNA1125316 | ENA
Project description:RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection
| PRJNA783915 | ENA
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:Novel high-throughput deep sequencing technology has dramatically changed the way that the functional complexity of transcriptomes can be studied. Here we report on the first use of this technology to gain insight into the wide range of transcriptional alterations that are associated with an infectious disease process. Using Solexa/IlluminaM-bM-^@M-^Ys digital gene expression (DGE) system, a tag-based transcriptome sequencing method, we investigated mycobacterium-induced transcriptome changes in a model vertebrate species, the zebrafish. Our DGE data substantiate recent RNA-seq results from other models indicating a much larger extent of genome transcription than previously thought, and demonstrate that the host response to bacterial infection adds a further degree of complexity to the transcriptome. We obtained a sequencing depth of over 5 million tags per sample with strong correlation between replicates. Tag mapping indicated that mycobacterium-infected adult zebrafish express over 70% of all genes represented in transcript databases. Comparison of our DGE data with a previous multiplatform microarray analysis showed that both types of technologies identified regulation of similar functional groups of genes, more specifically the up-regulation of different classes of immune response genes concomitant with a broad down-regulation of metabolic genes. However, the unbiased nature of DGE analysis provided insights that microarray analysis could not have achieved. As demonstrated here, DGE data are useful for the verification of predicted gene models and allowed us to detect mycobacterium-regulated switching between different transcript isoforms. Moreover, genomic mapping of infection-induced DGE tags revealed novel transcript forms for which any previous EST-based evidence of expression was lacking. Adult male zebrafish were infected by intraperitoneal inoculation with approximately 1x 10-3 M. marinum bacteria. All four infected fish were sacrificed when they showed overt signs of fish tuberculosis, including lethargy, skin ulcers and extensive granuloma formation in organs such as liver and kidney. Histological examination of fish from the same experiments confirmed that the pathology of infected fish corresponded to fish tuberculosis and that no characteristics of the disease were present in the control fish. For DGE analysis RNA samples from the four control adult zebrafish (c1,c2,c3,c4) were pooled, and RNA samples from the four M.marinum-infected adult zebrafish (i1,i2,i3,i4) were pooled. Before pooling the individual RNA samples had been checked by microarray analysis for correlation between biological replicates.
2009-06-29 | E-GEOD-14782 | biostudies-arrayexpress
Project description:Mycobacteria infect macrophages that aggregate with additional macrophages and lymphocytes to form granulomas. We have used a functional genomics approach to identify immune response genes expressed during granuloma formation in Mycobacterium marinum-infected transparent zebrafish larvae where individual infection steps can be viewed in real time. We assessed RNA expression profiles from zebrafish larvae that were either infected with Mycobacterium marinum or mock-infected. Zebrafish infections were performed at 1 day post-fertilization (dpf), and samples were derived from pools of 6dpf zebrafish larvae. Keywords: host response to infection
2008-01-01 | GSE8846 | GEO
Project description:Mycobacteria infect macrophages that aggregate with additional macrophages and lymphocytes to form granulomas. We have used a functional genomics approach to identify immune response genes expressed during granuloma formation in Mycobacterium marinum-infected transparent zebrafish larvae where individual infection steps can be viewed in real time. We assessed RNA expression profiles from zebrafish larvae that were either infected with Mycobacterium marinum, mock-infected, or uninfected. Zebrafish infections were performed at 1 day post-fertilization (dpf), and samples were derived from pools of 6dpf zebrafish larvae. Keywords: host response to infection
2008-01-01 | GSE8327 | GEO