Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome of BEAS-2B cells infected with Aspergillus fumigates in presence or not of PI3 kinase inhibitor

ABSTRACT: To identify PI3K pathway-related genes that may contribute to BECs antifungal activity, we performed a transcriptomic profiling of BECs incubated or not with LY294002, a PI3K inhibitor, and infected with A. fumigatus for 0, 2 and 4 h.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Viviane Balloy

PROVIDER: E-MTAB-16714 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: In classrooms high concentrations of particulate matter PM10 were measured. It is unknown whether the hazard of indoor particles is similar to that of the better studied outdoor particles. This study therefore analyzed adverse biological effects of classroom in comparison to outdoor PM10. Methods: Samples were taken from six schools during teaching hours. Genome-wide gene expression in human bronchial BEAS-2B epithelial cells was analyzed, and regulated genes were verified by quantitative PCR. Polycyclic aromatic hydrocarbons (PAH), endotoxin, and cat allergen Fel d 1 were analyzed with standard methods. Enhancement of allergic reactivity by PM10 was confirmed with CD63 upregulation in human primary basophils. Acceleration of human blood coagulation was determined with supernatants of PM10-exposed human peripheral blood monocytes. Results: Indoor PM10 induced SERPINB2 (involved in blood coagulation) and inflammatory genes (like CXCL6, CXCL1, IL6, IL8, all p<0.001). Outdoor PM10 induced xenobiotic metabolizing enzymes (CYP1A1, CYP1B1, TIPARP, all p<0.001). The induction of inflammatory genes by indoor PM10 could be explained by endotoxin (indoor 128.5M-BM-142.2EU/mg versus outdoor 13.4M-BM-121.5EU/mg, p<0.001), the induction of CYP by outdoor PAH (indoor 8.3M-BM-14.9ng/mg versus outdoor 16.7M-BM-115.2ng/mg, p<0.01). The induction of SERPINB2 was confirmed by a more rapid human blood coagulation (p<0.05). Indoor PM10 had no effect on the allergic reactivity from human primary basophils, except in cat allergic individuals. This was explained by varying Fel d 1 concentrations in indoor PM10 (p<0.001). Conclusions: Indoor PM10, compared to outdoor PM10, was 6 times higher, had a different composition, and on an equal weight basis induced more inflammatory and allergenic reactions, and accelerated blood coagulation. Outdoor PM10 had significantly lower effects, but induced detoxifying enzymes. Therefore, preliminary interventions for the reduction of classroom PM10 seem reasonable, perhaps by intensified ventilation. For genome-wide gene expression analysis, BEAS-2B cells (passage 41) were incubated with 10M-BM-5g/ml PM10 (school 4 indoor and outdoor) for 4, 10 or 24h, all in triplicate. experiment type : time course

Project description:This experiment is part of the FunGenES project (FunGenES - Functional Genomics in Embryonic Stem Cells partially funded by the 6th Framework Programme of the European Union, http://www.fungenes.org).The experiment was conducted at the Unyversity of Bath, Bath, UK. Aim is to identify genes regulated by PI3K-dependent signaling in undifferentiated ES cells. Materials and methods: E14tg2a cell line was used. Cells were cultured in Knock-out DMEM supplemented with 15% (v/v) Knock-out serum replacement, 1000U/ml LIF, 2mM glutamine, 50 ?M 2-mercaptothanol and 1x NEAA (as described in Handbook of work methods, 4.3.1.1). Cells were plated at 5x105 per 10cm gelatin-coated TC dish for 24h. ES cells were then starved for 24h in media lacking LIF and pre-incubated for 30 minutes with 5 <B5>M LY294002 (the concentration of this PI3K inhibitor that we have shown to perturb self-renewal in the presence of LIF and which knocks down PI3K signals) or DMSO alone. Cells were then stimulated with 103U/ml mLIF (Chemicon) for 2h (which gave maximal activation of STAT3), 24h, 48h or 72h.</p>\n<h3>Relationships between samples</h3>\n <p ALIGN="JUSTIFY">Samples were either maintained in LIF or LIF plus LY294002 (PI3K inhibitor) for the required treatment times.</p>\n<h3>Treatments</h3>\n <p ALIGN="JUSTIFY">Treatment times with PI3K inhibitor LY294002 at 5 <B5>M <96> 2h (n=5), 24h (n=3), 48h (n=3), 72h (n=3). DMSO was used as vehicle alone treatment control.</p>\n<h3>Culture conditions</h3>\n <p ALIGN="JUSTIFY">Gelatin-coated TC dishes (Nunc)</p>\n<h3>RNA isolation method</h3>\n <p ALIGN="JUSTIFY">RNA Easy with on-column DNase treatment</p>\n<h3>Experimental description</h3>\n <p ALIGN="JUSTIFY">This information is included above. Briefly, E14tg2a ES cells were either maintained in LIF or LIF plus LY294002 (5 <B5>M) for 2, 24, 48 or 72 hours, after which RNA was extracted from each sample and sent for expression profiling. During this time-course, only 72h time points plus LY294002 showed phenotypic evidence of differentiation. </p>\n

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Transcriptome of BEAS-2B cells infected with Aspergillus fumigates in presence or not of PI3 kinase inhibitor

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