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PROVIDER: PRJNA193776 | ENA |
REPOSITORIES: ENA
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Project description:Comparative transcriptomics of infectious spores from the fungal pathogen Histoplasma capsulatum G186AR
| PRJNA193985 | ENA
Project description:Comparative transcriptomics of infectious spores from the fungal pathogen Histoplasma capsulatum G217B
| PRJNA193984 | ENA
Project description:The fungal pathogen Histoplasma capsulatum is thought to be the most common cause of fungal respiratory infections in immunocompetent humans, yet little is known about its biology. Here we provide the first genome-wide studies to experimentally validate its genome annotation. A functional interrogation of the Histoplasma genome provides critical support for continued investigation into the biology and pathogenesis of H. capsulatum and related fungi. We employed a three-pronged approach to provide a functional annotation for the H. capsulatum G217B strain. First, we probed high-density tiling arrays with labeled cDNAs from cells grown under diverse conditions. These data defined 6,172 transcriptionally active regions (TARs), providing validation of 6,008 gene predictions. Interestingly, 22% of these predictions showed evidence of anti-sense transcription. Additionally, we detected transcription of 264 novel genes not present in the original gene predictions. To further enrich our analysis, we incorporated expression data from whole-genome oligonucleotide microarrays. These expression data included profiling under growth conditions that were not represented in the tiling experiment, and validated an additional 2,249 gene predictions. Finally, we compared the G217B gene predictions to other available fungal genomes, and observed that an additional 254 gene predictions had an ortholog in a different fungal species, suggesting that they represent genuine coding sequences. These analyses yielded a high confidence set of validated gene predictions for H. capsulatum. The transcript sets resulting from this study are a valuable resource for further experimental characterization of this ubiquitous fungal pathogen. The data is available for interactive exploration at http://histo.ucsf.edu. The non-redundant genome sequence of Histoplasma capsulatum G217B was tiled over a set of 93 CombiMatrix arrays, which were then hybridized with labeled cDNA samples from yeast-form (red channel) or mycelial-form (green channel) Histoplasma. Due to low yields from the mycelial samples, only the red channel intensities were analyzed (and the red foreground intensities are, therefore, reported in the VALUE column for each sample). Rather than normalizing intensities across arrays, each probe was evaluated as detected or undetected relative to the negative control intensities on the corresponding array, and the density of detected probes as a function of genome position was used for the remaining analysis.
2011-08-11 | E-GEOD-31155 | biostudies-arrayexpress
Project description:The fungal pathogen Histoplasma capsulatum is thought to be the most common cause of fungal respiratory infections in immunocompetent humans, yet little is known about its biology. Here we provide the first genome-wide studies to experimentally validate its genome annotation. A functional interrogation of the Histoplasma genome provides critical support for continued investigation into the biology and pathogenesis of H. capsulatum and related fungi. We employed a three-pronged approach to provide a functional annotation for the H. capsulatum G217B strain. First, we probed high-density tiling arrays with labeled cDNAs from cells grown under diverse conditions. These data defined 6,172 transcriptionally active regions (TARs), providing validation of 6,008 gene predictions. Interestingly, 22% of these predictions showed evidence of anti-sense transcription. Additionally, we detected transcription of 264 novel genes not present in the original gene predictions. To further enrich our analysis, we incorporated expression data from whole-genome oligonucleotide microarrays. These expression data included profiling under growth conditions that were not represented in the tiling experiment, and validated an additional 2,249 gene predictions. Finally, we compared the G217B gene predictions to other available fungal genomes, and observed that an additional 254 gene predictions had an ortholog in a different fungal species, suggesting that they represent genuine coding sequences. These analyses yielded a high confidence set of validated gene predictions for H. capsulatum. The transcript sets resulting from this study are a valuable resource for further experimental characterization of this ubiquitous fungal pathogen. The data is available for interactive exploration at http://histo.ucsf.edu.
2011-08-12 | GSE31155 | GEO
Project description:Innate immune cells shape the host response to microbial pathogens. Here we studied the role of TLR7/9 in dendritic cell (DC) responses to Histoplasma capsulatum, an intracellular fungal pathogen of humans. Whereas macrophages succumbed to Histoplasma infection, TLR7/9 were critical for DCs to produce Type I interferons (IFN-I), restrict fungal growth, and survive fungal infection. In the mouse model of infection, optimal IFN-I and IFN gamma production, host survival, and restriction of cerebral fungal burden were also dependent on TLR7/9. Interestingly, CD103+ conventional DCs were the major producer of IFN-I in the lungs of infected mice, revealing a previously unknown role for these cells and uncovering their pivotal function in modulating the host immune response to endemic fungi.
2016-06-28 | GSE70505 | GEO
Project description:To identify signaling pathways that are induced by macrophages infected with Histoplasma capsulatum, we examined the whole genome expression profile of murine bone marrow derived macrophages infected with conidia, the natural infectious particle of Histoplasma. Conidia induced the expression of signature Type I interferon response genes. The induction of a Type I interferon response was specific to conidia, yeast cells did not trigger the response. Macrophages that lack the Type I interferon receptor, IFNAR1, were infected and compared to wild-type macrophages. The expression of some Type I IFN response genes are dependent upon Keywords: Murine bone marrow derived macrophage transcriptional response to infection with Histoplasma capsulatum conidia
2010-03-01 | GSE20022 | GEO
Project description:Innate immune cells shape the host response to microbial pathogens. Here we studied the role of TLR7/9 in dendritic cell (DC) responses to Histoplasma capsulatum, an intracellular fungal pathogen of humans. Whereas macrophages succumbed to Histoplasma infection, TLR7/9 were critical for DCs to produce Type I interferons (IFN-I), restrict fungal growth, and survive fungal infection. In the mouse model of infection, optimal IFN-I and IFN gamma production, host survival, and restriction of cerebral fungal burden were also dependent on TLR7/9. Interestingly, CD103+ conventional DCs were the major producer of IFN-I in the lungs of infected mice, revealing a previously unknown role for these cells and uncovering their pivotal function in modulating the host immune response to endemic fungi. In 6-well tissue culture treated dishes, 1 x 10 6 BMDCs or BMMs were subjected to either mock infection, infection with UV-treated Histoplasma, or infection with live Histoplasma yeasts at an MOI of 4. UV-treated (UVT) yeasts were prepared by subjecting G217B to UV light (UV Stratalinker 1800) for 1 hour; these yeasts failed to generate colonies when plated on HMM agarose.
2016-06-28 | E-GEOD-70505 | biostudies-arrayexpress
Project description:Histoplasma capsulatum is a fungal pathogen that infects both healthy and immunocompromised hosts. In endemic regions, H. capsulatum grows in the soil and causes respiratory and systemic disease when inhaled by humans. An interesting aspect of H. capsulatum biology is that it adopts specialized developmental programs in response to its environment. In the soil, it grows as filamentous chains of cells (mycelia) that produce asexual spores (conidia). When the soil is disrupted, conidia aerosolize and are inhaled by mammalian hosts. Inside a host, conidia germinate into yeast-form cells that colonize immune cells and cause disease. Despite the ability of conidia to initiate infection and disease, they have not been explored on a molecular level. Here we develop methods to purify H. capsulatum conidia and show that these cells germinate into either filaments at room temperature or into yeast-form cells at 37C. Conidia internalized by macrophages germinate into the yeast form and proliferate within the macrophages, ultimately lysing the host cells. Similarly, infection of mice with purified conidia is sufficient to establish infection and yield viable yeast-form cells in vivo. To characterize conidia on a molecular level, we perform whole-genome expression profiling of conidia, yeast, and mycelia from two highly diverged H. capsulatum strains. In parallel, we use homology and protein domain analysis to manually annotate the predicted genes of both strains. Analyses of the resultant data define sets of transcripts that reflect the unique molecular states of H. capsulatum conidia, yeast and mycelia. This series gives the results for the G186AR strain.
2013-04-10 | GSE45416 | GEO
Project description:Histoplasma capsulatum is a fungal pathogen that infects both healthy and immunocompromised hosts. In endemic regions, H. capsulatum grows in the soil and causes respiratory and systemic disease when inhaled by humans. An interesting aspect of H. capsulatum biology is that it adopts specialized developmental programs in response to its environment. In the soil, it grows as filamentous chains of cells (mycelia) that produce asexual spores (conidia). When the soil is disrupted, conidia aerosolize and are inhaled by mammalian hosts. Inside a host, conidia germinate into yeast-form cells that colonize immune cells and cause disease. Despite the ability of conidia to initiate infection and disease, they have not been explored on a molecular level. Here we develop methods to purify H. capsulatum conidia and show that these cells germinate into either filaments at room temperature or into yeast-form cells at 37C. Conidia internalized by macrophages germinate into the yeast form and proliferate within the macrophages, ultimately lysing the host cells. Similarly, infection of mice with purified conidia is sufficient to establish infection and yield viable yeast-form cells in vivo. To characterize conidia on a molecular level, we perform whole-genome expression profiling of conidia, yeast, and mycelia from two highly diverged H. capsulatum strains. In parallel, we use homology and protein domain analysis to manually annotate the predicted genes of both strains. Analyses of the resultant data define sets of transcripts that reflect the unique molecular states of H. capsulatum conidia, yeast and mycelia. This series gives the results for the G217B strain.
2013-04-10 | GSE45415 | GEO
Project description:To identify signaling pathways that are induced by macrophages infected with Histoplasma capsulatum, we examined the whole genome expression profile of murine bone marrow derived macrophages infected with conidia, the natural infectious particle of Histoplasma. Conidia induced the expression of signature Type I interferon response genes. The induction of a Type I interferon response was specific to conidia, yeast cells did not trigger the response. Macrophages that lack the Type I interferon receptor, IFNAR1, were infected and compared to wild-type macrophages. The expression of some Type I IFN response genes are dependent upon Keywords: Murine bone marrow derived macrophage transcriptional response to infection with Histoplasma capsulatum conidia We analyzed a series of 24 MEEBO arrays on which were hybed RNA amplified from bone marrow derived macrophages from C57BL/6 (WT) or ifnar1-/- mice either mock infected or infected with H. capsulatum conidia or yeast cells.
2010-05-06 | E-GEOD-20022 | biostudies-arrayexpress