Aspergillus fumigatus whole genome transcriptomic study using AWAFUGE microarray after exposition to murine macrophages (RAW 264.7) and human lung epithelial cells (A549).
Ontology highlight
ABSTRACT:
ORGANISM(S): Aspergillus fumigatus
SUBMITTER: Xabier Guruceaga Sierra
PROVIDER: E-MTAB-13476 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Aspergillus fumigatus is a saprophytic fungus that occasionally can produce a wide range of diseases. The ubiquity and great adaptability of this fungus play a crucial role in its pathogenicity. Its adaptation begins in the germination process when it is exposed to the media. In this study pre- and post-polarization steps of the germination of RPMI cultures have been analyzed. When the conidia reach 30% of swelling (Swollen) or germination (Control), the total RNA was isolated and purified using the RNeasy Plant Mini Kit (Qiagen). The AWAFUGE (Agilent Whole A. fumigatus Genome Expression 44K v.1) hybridization was carried out following previously publish protocols (A-MEXP-2352,E-MTAB-5314 and E-MTAB-13476)
2024-04-01 | E-MTAB-13921 | biostudies-arrayexpress
Project description:Response of A549 cells treated with Aspergillus fumigatus wild type germinating conidia (WT_GC) or PrtT protease deficient mutant conidia (PrtT-GC) or inert acrylic 2-4 micron beads (Beads) for 8h Aspergillus fumigatus is the most commonly encountered mold pathogen of humans, predominantly infecting the respiratory system. Colonization and penetration of the lung alveolar epithelium is a key but poorly understood step in the infection process. This study focused on identifying the transcriptional and cell-signaling responses activated in A549 alveolar carcinoma cells incubated in the presence of A. fumigatus wild-type and ÎPrtT protease-deficient germinating conidia and culture filtrates (CF). Microarray analysis of exposed A549 cells identified distinct classes of genes whose expression is altered in the presence of germinating conidia and CF and suggested the involvement of both NFkB and MAPK signaling pathways in mediating the cellular response. Phosphoprotein analysis of A549 cells confirmed that JNK and ERK1/2 are phosphorylated in response to CF treatment in a protease-dependent manner. Inhibition of JNK or ERK1/2 kinase activity substantially decreased CF-induced cell damage, including cell peeling, actin-cytoskeleton damage, and reduction in metabolic activity and necrotic death. These results suggest that inhibition of MAPK-mediated host responses to treatment with A. fumigatus CF decreases cellular damage, a finding with possible clinical implications. 2 independent controls (uninfected A549 cells) as ctrl3_1-2, 2 independent treatments of A549 cells with wild-type A. fumigatus germinating conidia (WT_GC_1-2 ) , 2 independent treatments of A549 cells with inert acrylic beads (Beads 1-2), 3 independent treatments of A549 cells with A. fumigatus prtT mutant germinating conidia (PrtT-GC_1-3).
2010-10-29 | E-GEOD-24984 | biostudies-arrayexpress
Project description:Response of A549 cells treated with Aspergillus fumigatus germinating conidia (WT-GC) or culture filtrate (WT-CF) for 8h Aspergillus fumigatus is the most commonly encountered mold pathogen of humans, predominantly infecting the respiratory system. Colonization and penetration of the lung alveolar epithelium is a key but poorly understood step in the infection process. This study focused on identifying the transcriptional and cell-signaling responses activated in A549 alveolar carcinoma cells incubated in the presence of A. fumigatus wild-type and ÎPrtT protease-deficient germinating conidia and culture filtrates (CF). Microarray analysis of exposed A549 cells identified distinct classes of genes whose expression is altered in the presence of germinating conidia and CF and suggested the involvement of both NFkB and MAPK signaling pathways in mediating the cellular response. Phosphoprotein analysis of A549 cells confirmed that JNK and ERK1/2 are phosphorylated in response to CF treatment in a protease-dependent manner. Inhibition of JNK or ERK1/2 kinase activity substantially decreased CF-induced cell damage, including cell peeling, actin-cytoskeleton damage, and reduction in metabolic activity and necrotic death. These results suggest that inhibition of MAPK-mediated host responses to treatment with A. fumigatus CF decreases cellular damage, a finding with possible clinical implications. 3 independent controls (uninfected A549 cells) as ctrl2_1-3, 2 independent treatments of A549 cells with wild-type A. fumigatus culture filtrates (WT-CF2_1-2) and 2 independent treatments of A549 cells with wild-type A. fumigatus germinating conidia (WT-GC_2-3).
2010-10-29 | E-GEOD-24983 | biostudies-arrayexpress
Project description:Response of A549 cells treated with Aspergillus fumigatus wild type culture filtrate (WT-CF) or PrtT protease deficient mutant culture filtrate (PrtT-CF) for 8h Aspergillus fumigatus is the most commonly encountered mold pathogen of humans, predominantly infecting the respiratory system. Colonization and penetration of the lung alveolar epithelium is a key but poorly understood step in the infection process. This study focused on identifying the transcriptional and cell-signaling responses activated in A549 alveolar carcinoma cells incubated in the presence of A. fumigatus wild-type and ÎPrtT protease-deficient germinating conidia and culture filtrates (CF). Microarray analysis of exposed A549 cells identified distinct classes of genes whose expression is altered in the presence of germinating conidia and CF and suggested the involvement of both NFkB and MAPK signaling pathways in mediating the cellular response. Phosphoprotein analysis of A549 cells confirmed that JNK and ERK1/2 are phosphorylated in response to CF treatment in a protease-dependent manner. Inhibition of JNK or ERK1/2 kinase activity substantially decreased CF-induced cell damage, including cell peeling, actin-cytoskeleton damage, and reduction in metabolic activity and necrotic death. These results suggest that inhibition of MAPK-mediated host responses to treatment with A. fumigatus CF decreases cellular damage, a finding with possible clinical implications. 3 independent controls (uninfected A549 cells) as ctrl2_1-3, 3 independent treatments of A549 cells with wild-type A. fumigatus culture filtrates (WT-CF1_1-3) and 2 independent treatments of A549 cells with A. fumigatus prtT mutant culture filtrates (PrtT-CF_1-2).
2010-10-29 | E-GEOD-24985 | biostudies-arrayexpress
Project description:The mechanism of action of the new antifungal compound 089 was identified in Saccharomyces cerevisiae. The compound had antifungal effects also on pathogenic fungi. While on Candida species the treatment induced cells death, on A. fumigatus strains it inhibited the conidia transition to hyphae. We carried out RNA sequencing analysis to evaluate at the molecular level the effect of the treatment on Aspergillus.
2020-03-04 | E-MTAB-5309 | biostudies-arrayexpress
Project description:Transcriptome of A. fumigatus shifted from ammoniumtartrate to different nitrogen sources and incubated for a defined time was compared. After 16h preculture, the fungus was transferred into fresh medium containing ammonium tartrate, sodium nitrate, proline or bsa as nitrogen source. After 1h, fungus was reisolated, RNA was prepared from fungus, transcriptome was assessed and used for further analysis. Ammoniumtartrate, sodiumnitrate, BSA and proline as nitrogen sources, 2 biological replicates for each source. A. fumigatus liquid media shifts were performed according to ref. (Narendja et al.,2002) with minor modifications: 200 ml minimal medium base with 5 mM ammonium tartrate was inoculated with 10^8 conidia freshly harvested. A. fumigatus ATCC 46645 conidia were grown at 37°C and 150 rpm for 16 hours. This pre-culture was then harvested, washed liberally with sterile saline and divided into mycelial masses of equal size on a sterile surface. The portions were then added to 100 ml of minimal medium base without nitrogen source. When a defined carbon source was needed, 1% glucose was added. Flasks were incubated for 20 min at 37°C. Thereafter, one of the following sterile nitrogen sources was added: ammonium tartrate to a final concentration of 5 mM, Sodiumnitrate to a final concentration of 10 mM, 1 g proline suspended in 2 ml minimal medium base, or 0.5 g BSA (Albumin Fraktion V, Roth), suspended in 15 ml minimal medium base. The cultures were incubated for another 60 minutes, harvested by filtering through Miracloth, snap frozen in liquid nitrogen, and ground using a cooled mortar to obtain a fine powder.
2011-10-29 | E-GEOD-30384 | biostudies-arrayexpress
Project description:Experimental factor: Time after the temperature shift from 30C to 37C or 30C to 48C. Conidia (5x106 /ml) from Aspergillus fumigatus Af293 were incubated in the CM medium for germination (~ 17 hrs) at 30C. The culture was transferred to a water bath of 37C or 48C for continued growth. Samples were taken after the defined time (i.e. 0, 15, 30, 60, 120, and 180 min.).
2005-05-15 | E-MEXP-332 | biostudies-arrayexpress
Project description:Aspergillus fumigatus, a common airborne fungus, has been reported as one of the most frequent agents of human fungal infections. However, A. fumigatus conidia atmospheric resistance and longevity, and their aging mechanism are unknown. Therefore, the main purpose of this work is to clarify the main processes associated with conidial adaptation to nutrient limitation, similar to those found in their atmospheric transport. To that a time course evaluation of the changes in the proteome and in the ultrastructure of A. fumigatus’ conidia subjected to limiting nutrient conditions were performed, allowing a comprehensive characterization of conidia cells behavior and, revealing possible targets for the development of new antifungal medicines and improve infection control strategies. In the proposed work, a total of 712 proteins were identified and compared in the A. fumigatus conidia, with 387 proteins presenting significant differences among the considered conditions. These 387 proteins were then grouped into clusters according to similarities in their dynamic profile (relative levels) among the three points in time analyzed, and four completely distinct profiles can be observed. According with the proteomics changes, it was observed that the conidia go from a highly active metabolic state to a dormant state, and culminate in a cell autolysis state revealed by increased levels of hydrolytic enzymes. The proteomics alterations observed were further corroborate with the structural results, where it was observed changes in mitochondria, nucleus, and plasma membrane ultrastructure, consistent with an apoptotic process. Altogether the results indicate that the changes in protein levels anticipated those in cell morphology, clearly highlighting the need for further studies that may lead to significant improvement in infection control strategies. Additionally, a total of 28 proteins were identified with one acetylated peptide. Among them, it was possible to quantify the acetylation levels in 21 proteins with 11 presenting a statistical meaningful difference between the tested time points. Furthermore, from the proteins evaluated, all except the protein Histone H3, presented N-terminal acetylation. In the case of the Histone H3, the modification was observed at the lysine 56. In general, the proteins regulated by acetylation quantified in our study could be grouped into four distinct groups and although only some of the proteins have a statistical meaningful variation between the experimental time points, those proteins are spread along the different groups. Moreover, statistical variation if observed for all the proteins belonging to the group of proteins that have higher acetylation levels at time 15 minutes. In conclusion, this work presents a comprehensive characterization of the proteomics changes associated with the adaptive mechanism of Aspergillus fumigatus’ conidia to nutrient restriction, raveling some on the main pathways associated with such capacity. Furthermore, this proteomic characterization is associated with the conidia’s ultrastructural evaluation allowing to link the changes observed at the proteome level with the respective phenotype. Finally, it was also presented an evaluation of the levels of the protein acetylation, one of the principal regulatory PTMs in eukaryotes. Therefore, the present study may be an important dataset to be used as a tool to understand and identified potential targets associated with conidia resistance, and therefore improving infection control strategies.
2017-04-04 | PXD003355 | Pride
Project description:CRZ is a C2H2 zinc finger transcription factor activated by calcineurin, a protein phosphatase activated by calcium-calmodulin, in different stress conditions related with calcium cell accumulation. CRZ binds to a specific element on the promoter region of genes called CDRE (calcineurin-dependent response element) shown to be sufficient for calcium- and calcineurin-dependent gene expression. In order to investigate which pathways are involved under calcium stress conditions, we determined the transcriptional profile of A. fumigatus delta crzA mutant strain upon a time course 200 mM calcium chloride treatment. Conidia from the mutant and wild type strains were incubated at 37°C in complete medium for 16 hours and were challenged with 200 mM calcium chloride for 10 and 30 minutes. At each time point, the mycelia were harvested by centrifugation and used for competitive microarray hybridizations. We were able to observe a decreased mRNA expression of genes encoding inorganic ion transport proteins and lipid transport. In contrast, increased mRNA expression was observed for several genes involved in transcription, energy production and conversion, cell cycle control, cell division, chromosome partitioning, amino acid, lipid and carbohydrate transport and metabolism, nucleotide transport, cell wall and membrane biogenesis, posttranslation modifications, protein turnover, chaperones, inorganic ion transport, signal transduction mechanisms, intracellular trafficking, secretion and vesicular transport. Keywords: gene expression array-based (log2 ratio) For the time course microarray experiments, 5.0 x 108 conidia of A. fumigatus wild type [CEA17 delta akuB(KU80)] and delta crzA strains were inoculated in 300 ml of pre-warmed liquid cultures (YG) in 500-mL erlenmeyer flasks and allowed to grow for 16 hours in a reciprocal shaker (250 rpm) at 37°C. After this time, the cultures were added by calcium chloride (200 mM) and incubated for 10 and 30 more minutes before mycelia recovery and RNA extraction. Hybridization experiments were competitive using probes derived from calcium chloride shock cultures using the wild type strain exposed to calcium (10 or 30 minutes) as the reference RNA for every hybridizantion. Normalized signal intensities were used to generate relative hybridization ratios (query/reference). Following normalization, the values for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects. These final, processed data are linked below as supplementary files.
2010-06-20 | E-GEOD-15432 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE24983: Response of A549 cells treated with Aspergillus fumigatus [WT-CF_vs_WT-GC] GSE24984: Response of A549 cells treated with Aspergillus fumigatus [WT-GC_vs_PrtT-GC] GSE24985: Response of A549 cells treated with Aspergillus fumigatus [WT-CF_vs_PrtT-CF] Refer to individual Series
2010-10-29 | E-GEOD-24986 | biostudies-arrayexpress