Expression data analysis of murine pulmonary cryptococcosis induced by Cryptococcus gattii and Cryptococcus neoformans
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE83594 | GEO | 2016/06/22
SECONDARY ACCESSION(S): PRJNA326448
REPOSITORIES: GEO
Similar Datasets
Project description:Our previous investigation indicated that high-virulence C. gattii (C. gattii R265) tend to reside in the alveoli, whereas low-virulence C. gattii (C. gattii 5815) tend to be washed out from the alveoli and move into the central side of the respiratory system of the mice. Furthermore, C. gattii R265 and 5815 infected mice showed much lesser macrophage response than C. neoformans H99 infected mice. To elucidate the mechanism of this phenomenon from the viewpoint of genetic analysis, we performed this microarray assay. C. gattii R265, C. gattii 5815, and C. neoformans H99 were prepared for the study. The mice were anesthetized and the spore suspension was intratracheally injected into each mouse. Mice were sacrificed 15 days after the infection and then examined. Lungs of the mice infected with C. gattii R265 (n=4), C. gattii 5815 (n=4), and C. neoformans H99 (n=3) and of a normal control (n=1) were obtained. RNA targets preparation was performed according to the manufacturer's protocol using GeneChip(R) 3' IVT Express Kit (Affymetrix). One hundred nanograms of total RNA were converted into double-stranded cDNA template for transcription. In vitro transcription synthesized amplified RNA (aRNA) and incorporated a biotin-conjugated nucleotide. After purification and fragmentation of aRNA, 12.5 ug of them was hybridized to GeneChip(R) Mouse Genome 430 2.0 Array (Affymetrix).The Probe Array was scanned using a GeneChip(R) Scanner 3000 7G.
2016-06-22 | E-GEOD-83594 | biostudies-arrayexpress
Project description:Our previous investigation indicated that high-virulence C. gattii (C. gattii TIMM 4097) tend to reside in the alveoli, whereas low-virulence C. gattii (C. gattii TIMM 4903) tend to be washed out from the alveoli and move into the central side of the respiratory system. To test this hypothesis, we performed microarray assay.
2013-07-08 | GSE48595 | GEO
Project description:Our previous investigation indicated that high-virulence C. gattii (C. gattii TIMM 4097) tend to reside in the alveoli, whereas low-virulence C. gattii (C. gattii TIMM 4903) tend to be washed out from the alveoli and move into the central side of the respiratory system. To test this hypothesis, we performed microarray assay. C. gattii TIMM 4097 and C. gattii TIMM 4903 were prepared for the study. The mice were anesthetized and the spore suspension was intratracheally injected into each mouse. Mice were sacrificed 15 days after the infection and then examined. Lung of the mice infected with C. gattii TIMM 4097 and C. gattii TIMM 4903 and normal controls were obtained (n=3, respectively. RNA targets preparation was performed according to the manufacturer's protocol using GeneChip(R) 3' IVT Express Kit (Affymetrix). One hundred nanograms of total RNA were converted into double-stranded cDNA template for transcription. In vitro transcription synthesized amplified RNA (aRNA) and incorporated a biotin-conjugated nucleotide. After purification and fragmentation of aRNA, 12.5 ug of them was hybridized to GeneChip(R) Mouse Genome 430 2.0 Array (Affymetrix).The Probe Array was scanned using a GeneChip(R) Scanner 3000 7G
2013-07-08 | E-GEOD-48595 | biostudies-arrayexpress
Project description:An array analysis of C. gattii (C. bacillosporus), intended to identify loci associated with the hypervirulence of the Vancouver Island Outbreak (VIO). 23 C. gattii isolates, representing both VIO strains and control strains, were grown for 24 hours in mammalian macrophages. RNA was isolated and gene expression for each strain quantified relative to pooled RNA from all 23 samples. Linear regression was used to identify loci showing positive or negative correlation with "intracellular proliferation rate", a proxy measure for virulence. Data from this analysis is included in Ma et al, 2009, PNAS 106(31) 12980-12985. The abstract is included below. In 1999, the population of Vancouver Island, Canada, began to experience an outbreak of a fatal fungal disease caused by a highly virulent lineage of Cryptococcus gattii. This organism has recently spread to the Canadian mainland and Pacific Northwest, but the molecular cause of the outbreak remains unknown. Here we show that the Vancouver Island outbreak (VIO) isolates have dramatically increased their ability to replicate within macrophages of the mammalian immune system in comparison with other C. gattii strains. We further demonstrate that such enhanced intracellular parasitism is directly linked to virulence in a murine model of cryptococcosis, suggesting that this phenotype may be the cause of the outbreak. Finally, microarray studies on 24 C. gattii strains reveals that the hypervirulence of the VIO isolates is characterized by the up-regulation of a large group of genes, many of which are encoded by mitochondrial genome or associated with mitochondrial activities. This expression profile correlates with an unusual mitochondrial morphology exhibited by the VIO strains after phagocytosis. Our data thus demonstrate that the intracellular parasitism of macrophages is a key driver of a human disease outbreak, a finding that has significant implications for a wide range of other human pathogens.
2009-08-07 | GSE17052 | GEO
Project description:An array analysis of C. gattii (C. bacillosporus), intended to identify loci associated with the hypervirulence of the Vancouver Island Outbreak (VIO). 23 C. gattii isolates, representing both VIO strains and control strains, were grown for 24 hours in mammalian macrophages. RNA was isolated and gene expression for each strain quantified relative to pooled RNA from all 23 samples. Linear regression was used to identify loci showing positive or negative correlation with "intracellular proliferation rate", a proxy measure for virulence. Data from this analysis is included in Ma et al, 2009, PNAS 106(31) 12980-12985. The abstract is included below. In 1999, the population of Vancouver Island, Canada, began to experience an outbreak of a fatal fungal disease caused by a highly virulent lineage of Cryptococcus gattii. This organism has recently spread to the Canadian mainland and Pacific Northwest, but the molecular cause of the outbreak remains unknown. Here we show that the Vancouver Island outbreak (VIO) isolates have dramatically increased their ability to replicate within macrophages of the mammalian immune system in comparison with other C. gattii strains. We further demonstrate that such enhanced intracellular parasitism is directly linked to virulence in a murine model of cryptococcosis, suggesting that this phenotype may be the cause of the outbreak. Finally, microarray studies on 24 C. gattii strains reveals that the hypervirulence of the VIO isolates is characterized by the up-regulation of a large group of genes, many of which are encoded by mitochondrial genome or associated with mitochondrial activities. This expression profile correlates with an unusual mitochondrial morphology exhibited by the VIO strains after phagocytosis. Our data thus demonstrate that the intracellular parasitism of macrophages is a key driver of a human disease outbreak, a finding that has significant implications for a wide range of other human pathogens. Dual-colour hybridization (each sample was hybridized against pooled RNA), one array per isolate, 23 biological samples, no technical replicates.
2010-05-15 | E-GEOD-17052 | biostudies-arrayexpress
Project description:Flucytosine (5-FC) is an antifungal drug commonly used for treatment of cryptococcosis and several other systemic mycoses. In fungal species, cytosine permease and cytosine deaminase are known to play major roles in flucytosine resistance by regulating uptake and deamination of 5-FC, respectively. Cryptococcus species have three paralogs of cytosine permease (FCY2, FCY3, and FCY4) and three paralogs of cytosine deaminase (FCY1, FCY5, and FCY6). Like in other fungi, we found Fcy1 and Fcy2 to be the primary cytosine deaminase and permease respectively in C. neoformans H99 (VNI), C. gattii R265 (VGIIa), and WM276 (VGI). However, when different amino acids were used as the sole nitrogen source, Fcy3 and Fcy6 functioned as the secondary cytosine permease and deaminase respectively in C. gattii. Transcriptome analysis using RNA-seq under three different nitrogen sources (NH4, Asn, and Pro) revealed that these permease and deaminase genes as well as two GATA family transcription factor genes, GAT1 and CIR1, were differentially expressed in WM276. In addition, deletion studies of GAT1 and CIR1 demonstrated that the expression of each permease and deaminase genes was under the regulation of GAT1 and CIR1 individually. Furthermore, the expression levels of FCY3 and FCY6 regulated by GAT1 and CIR1 contributed to the 5-FC susceptibility in fcy2Δ or fcy1Δ background under different amino acid conditions. This study offers an insight into the mechanism of 5-FC resistance in C. gattii which is orchestrated by cytosine permease and deaminase genes, and two GATA family transcription factor genes, GAT1 and CIR1, under diverse nitrogen conditions.
2023-01-11 | GSE215311 | GEO
Project description:We compared the interaction between Cryptococcus gattii species complex strain R265 and Cryptococcus neoformans species complex strain H99, molecular type VNI, with murine macrophages to ascertain similarities and differences in their intracellular pathogenic strategy. Parameters analyzed include non-lytic exocytosis using time-lapse microscopy, phagolysosomal pH by dual fluorescent microscopy, intracellular capsular growth, phagolysosomal membrane permeabilization by flow cytometry, and the macrophage transcriptional response by gene expression microarray analysis. Using microarrays, we compared the transcriptional response of Bone Marrow-derived macrophages (BMDM) infected with C. gattii species complex strain R265 or C. neoformans species complex strain H99, relative to uninfected BMDM collected from the same time intervals, 2hr and 24 hr post-infection. For analysis following normalization and summarization steps, a 2-way Analysis of Variance (ANOVA) with linear contrasts for treatment (infection/strain) and time (2 h or 24 h) vs. Control (uninfected) was performed with outputs of P value, Fold Change, and Mean Ratio. A linear contrast of uninfected controls (24 h uninfected vs 2 h uninfected) was also performed to generate a ‘time only’ gene list. Cutoff criteria for filtering gene lists was significant P values (p<0.01) with fold changes greater that 2 or less than –2. Ten genes from the filtered gene lists were selected for validation by qPCR, with four housekeeping genes for normalization and comparison.
2018-06-30 | GSE112668 | GEO
Project description:The gene expression of C. neoformans H99 treated with eltrombopag
2018-06-12 | GSE115570 | GEO
Project description:Wild type strain H99 compared to independent sir2 deletion mutants grown to mid-log (0.6 OD600) in rich medium (YPD) shaking at 250rpm in baffled flasks.
2022-04-01 | GSE173209 | GEO
Project description:Purpose: Investigate the dynamics of cryptococcal cell and transcriptional remodeling during pulmonary infection in a murine model Methods: Dual-RNA sequencing Sample preparation - C57BL/6 mice were infected intratracheally with the H99 strain to analyze the transcriptome. After 6h or 240h of infection, BALF obtained from 6 mice of each condition were pooled together, generating two replicates of 6h and 240h (10d). BALF was centrifuged at 1200 x g and resuspended in 1mL TRIzol Reagent (Invitrogen Life Technologies) for RNA isolation, according to the manufactures' protocol. RNA from H99 yeasts grown in YPD was used as control. Results: Dual RNA-Seq analysis of C. neoformans and mice revealed molecular signatures of early and late events of infection We analyzed the up and downregulated genes after 6h and 10 days of infection, compared to the inoculated yeast (YPD x 6h and YPD x 10d) and the differentially expressed genes (DEGs) between 6h and 10 days of infection (designated BAL6h x BAL10d). These analyses revealed molecular signatures unique to early and late stages of infection. Conclusions: Our findings support a scenario in which the fungus initially deploys mechanisms aimed at survival, proliferation and tissue invasion. Later, the fungus may focus on mechanisms aimed at resistance to the immune response and colonization, that are crucial for disease development. Overall, our study provides new insights into understanding the biology of C. neoformans during infection and generating perspectives for the survey for new therapeutic and diagnostic targets for cryptococcosis.
2022-12-14 | GSE206758 | GEO