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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional response of Candida parapsilosis in low oxygen (hypoxic) conditions in SD media

ABSTRACT: Whole genome microarray was used to compare the transcriptional profile of C. parapsilosis growing in normoxic (21% oxygen) and hypoxic (1% oxygen) conditions. RNA was isolated from cells grown in SD media at 37Â°C for 3 h in atmosphere oxygen of 1% oxygen, and labeled with Cy5 or Cy3. Six independent biological replicates were compared. 4 out of 6 hypoxic samples were labeled with Cy5, and 2 were labeled with Cy3.

ORGANISM(S): Candida parapsilosis

SUBMITTER: Chen Ding

PROVIDER: E-GEOD-13722 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Correlation between biofilm formation and the hypoxic response in Candida parapsilosis.

Rossignol Tristan T Ding Chen C Guida Alessandro A d'Enfert Christophe C Higgins Desmond G DG Butler Geraldine G

Eukaryotic cell 20090116 4

The ability of Candida parapsilosis to form biofilms on indwelling medical devices is correlated with virulence. To identify genes that are important for biofilm formation, we used arrays representing approximately 4,000 open reading frames (ORFs) to compare the transcriptional profile of biofilm cells growing in a microfermentor under continuous flow conditions with that of cells in planktonic culture. The expression of genes involved in fatty acid and ergosterol metabolism and in glycolysis, i ...[more]

PMID: 19151323

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Hypoxia and biofilms in Candida parapsilosis

Project description:This SuperSeries is composed of the following subset Series: GSE13717: Transcriptional profile of Candida parapsilosis in SD media GSE13722: Transcriptional response of Candida parapsilosis in low oxygen (hypoxic) conditions in SD media Refer to individual Series

2010-05-06 | E-GEOD-13832 | biostudies-arrayexpress

Conserved and divergent roles of Bcr1 and CFEM proteins in Candida parapsilosis and Candida albicans

Project description:This SuperSeries is composed of the following subset Series: GSE33460: Transcriptional profile of Candida albicans bcr1 knockout. GSE33461: Transcriptional profile of Candida parapsilosis bcr1 knockout. GSE33462: Transcriptional profile of Candida parapsilosis CLIB214 culture in low iron conditions Refer to individual Series

2011-11-05 | E-GEOD-33490 | biostudies-arrayexpress

Transcriptional profile of Candida parapsilosis CLIB214 culture in low iron conditions

Project description:Whole genome microarrays were used to generate the transcriptional profile of Candida parapsilosis in low iron conditions RNA was isolated from CLIB214 grown in SD medium and in SD medium supplemented with 200 μM BPS and labeled with Cy3 or Cy5. Seven independent biological replicates were compared. Three dye swaps were perfomed so that four out of seven samples grown in SD culture were labeled with Cy3, and 3 were labeled with Cy5.

2011-11-04 | E-GEOD-33462 | biostudies-arrayexpress

Transcriptional profile of Candida parapsilosis bcr1 knockout.

Project description:Whole genome microarrays were used to compare the transcriptional profile of Candida parapsilosis bcr1 knockout to wild type cells. RNA was isolated from CLIB214 (wild type) or bcr1 delete (CDb71 or CDUHB6) grown in SD medium supplemented with 50 mM glucose and 10% fetal calf serum and labeled with Cy3 or Cy5. 7 independent biological replicates were compared. Two dye swaps were perfomed so that five of seven CLIB214 cultures were labeled with Cy3, and two were labeled with Cy5.

2011-11-04 | E-GEOD-33461 | biostudies-arrayexpress

Differentially expressed adipocyte-associated genes in Bone-marrow Mesenchymal stem cells under normal and hypoxic conditions

Project description:To identify proteins involved in the regulation of adipogenic differentiation under hypoxic conditions, an RT2 Profiler PCR array was used to screen a panel of 84 genes associated with human adipogenesis in Bone-marrow Mesenchymal stem cells under normal and hypoxic conditions. Bone-marrow Mesenchymal stem cells were put in hypoxic chamber, set at an oxygen concentration of 0.2%. Cells under normoxia are considered as a control.

2015-02-11 | E-GEOD-65842 | biostudies-arrayexpress

Hypoxia-responsive gene expression profile of U87 MG glioblastoma cells and their exosomes.

Project description:How cancer cells adapt to hypoxia during tumor development remains an important question. The hypothesis tested in the present study was that tumor cell-derived exosome vesicles (also known as microvesicles or extracellular vesicles) are mediators of hypoxia-dependent intercellular signaling in glioblastoma (GBM), i.e. highly aggressive brain tumors characterized by hypoxia and a vascular density that is among the highest of all human malignancies. In vitro hypoxia experiments and studies with patient materials reveal the enrichment in exosomes of hypoxia-regulated mRNAs and proteins, several of which were associated with poor patient prognosis. We show that cancer cell exosomes mediate hypoxia-dependent, phenotypic modulation of stromal cells in vitro and ex vivo, resulting in accelerated GBM tumor angiogenesis and growth in mice. These data suggest that exosomes constitute potent mediators of hypoxia-driven tumor development, and circulating multiparameter biomarkers of tumor hypoxia. U87 MG glioblastoma cells were grown at normoxic (21% oxygen) or hypoxic (1% oxygen) conditions for 48 hours. Conditioned media from normoxic and hypoxic cells were then used to isolate exosomes by differential centrifugation. Both cells and exosomes were lysed in Trizol reagent, and RNA was isolated.Total RNA from all samples (four types of samples in three biological repilicates) was subjected to genome-wide transcriptional analysis with Illumina HumanHT-12 V3.0 expression beadchip. Gene expression profile obtained from hypoxic U87 MG glioblastoma cells was compared to the profile of normoxic control cells. Analogically, gene expression profile obtained from hypoxic U87 MG cells was compared to the profile of exosomes secreted by normoxic U87 MG cells.

2013-03-20 | E-GEOD-45301 | biostudies-arrayexpress

Genome-wide analysis of gene expression perturbed by reptin shRNA in MCF7 subjected to normoxic and hypoxic conditions

Project description:In order to investigate the role of reptin methylation on the expression of hypoxia-responsive genes across the whole genome, we performed a microarray analysis from RNAs isolated from MCF7 cells expressing either control shRNA (shRNA) or reptin shRNA (shreptin) in normoxic and hypoxic conditions. MCF7 cells were transiently transfected with either non-specific shRNA or reptin shRNA in replicates. Cells were grown for 24 hours before being exposed to either normoxic (21% oxygen) or hypoxic (1% oxygen) conditions for 18 hours. Cells were then lysed and RNA was isolated.

2010-07-13 | E-GEOD-15530 | biostudies-arrayexpress

The effect of skyrin in normoxia and hypoxia on HCT 116 cell line

Project description:Skyrin is a plant secondary metabolite from Hypericum genus with potential in anticancer therapy. It is structurally very similar to hypericin. The mechanism of its action in normoxia as well as in hypoxia, when cells are expressing multiple adaptive mechanisms connected to poor prognosis, could be very interesting. To achieve it, label-free comparative proteomic analysis of HCT 116 cell lines samples was performed.

2021-04-08 | PXD019995 | Pride

Autophagy is essential for tumor development and survival in hypoxia and in vivo in glioblastoma. (Provisional)

Project description:Hypoxia is negatively associated with glioblastoma patient survival and contributes strongly to tumor resistance. Unfortunately novel anti-angiogenic therapy increases hypoxia and activates survival pathways in tumor cells leading to inevitable tumor relapse. Here we demonstrate that primary glioma cultures and cell lines depend on autophagy to survive severe hypoxia but also at normal oxygen levels. Positive regulators of autophagy are expressed at higher levels in tumor cells and induction in severe hypoxia is more prominent compared to normal brain cells. We demonstrate that autophagy is an essential/critical target for novel treatment in glioblastoma. We show ATG9A is induced by severe hypoxia and could be a novel player of the autophagic response in glioma cells. ATG9A targeting inhibited tumor growth, suggesting an essential role in glioma cell survival in vivo. While autophagy induction was also observed in normal astrocytes, glioma cells displayed a higher sensitivity towards autophagy inhibitors. Importantly, patient-derived cultures exhibited varying sensitivity towards anti-autophagy treatment, where certain cultures were dependent on autophagy already in normoxic conditions. The treatment of tumor bearing mice with the autophagy inhibitor chloroquine significantly increased mice survival, but combination treatment of the agent with bevacizumab did not reveal additive or synergistic effect. The present study demonstrates that inhibition of autophagy using chloroquine as a single agent provides a novel treatment strategy against glioblastoma. It remains to be seen whether autophagy inhibition will improve current standard of care treatment of newly diagnosed glioblastoma patients and whether more specific inhibitors will lead to stronger therapeutic outcome. (Provisional)

2015-11-10 | E-MTAB-3085 | biostudies-arrayexpress

Breast cancer hypoxia secretome LC-MS/MS

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2023-06-23 | PXD027136 | Pride

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