[URE3] Prion formation by the Candida albicans Ure2p (but not by C. glabrata Ure2p)
Ontology highlight
ABSTRACT:
ORGANISM(S): Candida albicans
SUBMITTER: Huei-Fung Tsai
PROVIDER: E-GEOD-26620 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Shared Molecules
Only show the datasets with similarity scores above: 0.5
Threshold
0.5
Similar Datasets
Project description:Hepatocarcinogenesis is a multi-stage process in which precursor lesions progress into early hepatocellular carcinomas (eHCC) by sequential accumulation of multiple genetic and epigenetic alterations. To decode the molecular events during early stages of liver carcinogenesis, we performed gene expression profiling on cirrhotic (regenerative) and dysplastic nodules (DN) as well as eHCC. Although considerable heterogeneity was observed at the regenerative and dysplastic stages, clear differences were detected between DN and eHCC which included 460 differentially expressed genes. Functional analysis of the significant gene set identified the MYC oncogene as a plausible driver gene for malignant conversion of the dysplastic nodules. In addition, gene set enrichment analysis (GSEA) revealed a remarkable enrichment of MYC up-regulated gene set in eHCC versus dysplasia. Presence of the MYC signature significantly correlated with increased expression of CSN5 as well as with the higher overall transcription rate of genes located in the 8q chromosome region. Furthermore, a classifier constructed from MYC target genes could robustly discriminate eHCC from high- and low-grade dysplastic nodules. In conclusion, our study identified unique expression patterns associated with the transition of high-grade dysplastic nodules to early HCC and demonstrated that activation of the MYC transcription signature is critical for the malignant conversion of pre-neoplastic liver lesions. Samples from forty-nine nodular liver lesions including 24 regenerative (cirrhotic) nodules (CN), 3 low-grade (LGDN), 12 high-grade dysplastic nodules (HGDN) and 10 early hepatocellular carcinomas (Early HCC) were used. The Human Operon V2 oligonucleotide library containing 22K features representing expressed sequences was printed to glass arrays in the Advanced Technology Center (National Cancer Institute, Gaithersburg, MD). The aRNA probes were fragmented and hybridized to the microarray slides following the standard procedures. All samples were hybridized against a common amplified reference RNA pooled from normal liver samples. Experimental duplicates were prepared following a reverse-flour design.
2010-05-15 | E-GEOD-12443 | biostudies-arrayexpress
Project description:Administration of tamoxifen (TAM) as breast cancer adjuvant therapy is associated with a 50% reduction in breast cancer risk and an increase in endometrial cancer risk. To investigate underlying mechanisms, we documented TAM-induced gene expression changes in cultured normal human mammary epithelial cell (NHMEC) strains (numbered 5, 16 and 40) established from tissue taken at reduction mammoplasty from three different individuals. Cells exposed to 0 and 10 uM TAM for 48 hours were evaluated for survival, TAM-DNA adduct formation by TAM-DNA chemiluminescence immunoassay (CIA), and gene expression changes using DNA-oligonucleotide microarray and real time reverse transcriptase-PCR (RT-PCR). At 48 hr, cells exposed to 10 uM TAM were 78% viable, respectively, and there were no measurable TAM-DNA adducts (limit of detection [LOD] = 0.3 adducts/10^8 nucleotides). For microarray analysis, RNA was extracted from cells exposed on three occasions to 10 uM TAM and the corresponding oligonucleotide probes were labeled with fluorescent dyes and hybridized to NCI microarrays (>20,000 human genes). Expression changes of > 3-fold were considered significant, and by these criteria, thirteen genes were up-regulated and one was down-related in NHMEC strain 16, seventeen genes were up-regulated in strain 05, and eleven genes were up-regulated in strain and 40. Elements that were up-regulated in all three cell strains included several interferon-induced genes (IFITM1, IFIT1, IFNA1, MXI and GIP3), and a potassium ion channel (KCNJ1). No significant expression changes were found for genes related to estrogen or xenobiotic metabolism. RT-PCR revealed TAM-induced up-regulation of the five genes of interest, and interferon á (IFNA1), in all three NHMEC strains, with the exception of GIP3 and MX1, which were unchanged in strain 40. The magnitude of TAM-induced up-regulation ranked: strain 16 > strain 05> strain 40. The consistent induction of interferon-related genes in all three NHMEC strains suggests that, in addition to hormonal effects, TAM exposure may enhance immune response, through interferon induction, in normal breast tissue. RNA was extracted from three cell strains (NHMEC 98016, 98040 and 99005) and exposed on three separate occasions to 10 uM TAM. Comparisons were made using 16 arrays with 8 dye swaps for cell strain NHMEC 99005, 9 arrays with 4 dye swaps for NHMEC 98016, and 12 arrays with 6 dye swaps for NHMEC 98040.
2009-01-29 | E-GEOD-13476 | biostudies-arrayexpress
Project description:We determined the gene expression profiles of murine melan-a melanocytes treated with ASP or alpha-MSH over a 4 days time course using genome-wide oligonucleotide microarrays. As expected, the gene expression patterns emphasized the opposing effects of the 2 ligands, and there were significant reductions in expression of numerous melanogenic proteins elicited by ASP, which correlates with its inhibition of pigmentation. However, ASP also unexpectidly modulated the expression of genes involved in various other cellular pathways, including glutathione synthesis and redox metabolism. Many genes up-regulated by ASP are involved in morphogenesis, cell adhesion and ECM-receptor interactions. Treatment with ASP or alpha-MSH was performed for 3 hr, 1 day, 2 days, 3 days and 4 days, in triplicate. Each biological replicate was submitted to a direct hybridization (treated/untreated samples) after coupling with Cy5 or Cy3 and to a reverse dye-swap, leading to 2 replicated hybridization for each biological sample. A total of 6 hybridized arrays was used for each of the 5 time points, for each drug.
2009-02-02 | E-GEOD-14089 | biostudies-arrayexpress
Project description:[URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3]. These results suggest that the sequence is not conserved to preserve prion forming ability. Two groups (WT and ure2 mutants) consisted of 4 biological replicates in which a ure2 deleted strain sample was paired with the wild type strain sample. Each group included 1 reciprocally labeled sample.
2012-01-01 | E-GEOD-26613 | biostudies-arrayexpress
Project description:Human embryonic stem (hES) cells have unique features: self-renewal ability and pluripotency. They can be continuously cultured in undifferentiated state and give rise to cells and tissues of all three germ layers. Thus hES cells provide a resource not only for cell replacement therapy but also for studying human developmental biology. We aimed to identify the unique signature of miRNAs in human embryonic stem cells. Keywords: cell type comparison design We performed microRNA expression profiling on 3 passages from 2 different hES cell lines (WA09 (H9) and BG01v) and 4 passages from 1 hES cell line (TE06 (I6)), EBs samples derived from WA09 cells at 4 different time points with replicates, and 5 types of adult cells (HUVEC, HMVEC, UASMC NHA, and LFB).
2009-04-17 | E-GEOD-12229 | biostudies-arrayexpress
Project description:The activated B cell-like (ABC) subgroup of diffuse large B cell lymphoma (DLBCL) is characterized by constitutive activation of the NF-êB pathway. Here we show that the NF- êB pathway induces the expression of the cytokines IL-6 and IL-10 in ABC DLBCL cell lines, which also have high levels of total and phosphorylated STAT3 protein, suggesting autocrine signaling. Using RNA interference for STAT3, we defined a gene expression signature of IL-6 and IL-10 signaling through STAT3. Based on this signature, we constructed a molecular predictor of STAT3 signaling that defined a subset of ABC DLBCL tumors with high expression of STAT3, IL-6 and/or IL-10, and their downstream targets. Although the STAT3-high and STAT3-low subsets had equivalent expression of genes that distinguish ABC DLBCL from GCB DLBCL, STAT3-high ABC DLBCLs had higher expression of signatures that reflected NF-kB activity, proliferation, and glycolysis. A smallmolecule inhibitor of JAK signaling, which blocked STAT3 signature expression, was toxic only for ABC DLBCL lines, and synergized with an inhibitor of NF-kB signaling. These findings suggest that the biological interplay between the STAT3 and NF-kB pathways may be exploited for the treatments of a subset of ABC DLBCLs. Activated B cell-like (ABC) subgroup of diffuse large B cell lymphoma (DLBCL) cell lines were used as model systems to study the cytokine pathways in these cells. We expressed inducible IkB super-repressor for 1 to 24 hours to identify NF-kB target genes in OCI-Ly3 and OCI-Ly10 cells for a total of 13 arrays with replicates of each time point. We treated OCI-Ly3 cells with IL-10 for 1 to 96 hours for a total of 10 arrays with replicates of each time point. We treated OCI-Ly10 cells with IL-6 for 30 minutes to 24 hours for a total of 8 arrays with replicates of each time point. OCI-Ly10 cells transfected with no siRNA versus STAT3-siRNA for 8, 24, or 48 hours for a total of 5 arrays with replicates for 24 and 48 hours. We treated OCI-Ly10 cells with JAK inhibitor I for 3 and 6 hours for a total of 4 arrays with replicates of each time point.
2010-05-27 | E-GEOD-10009 | biostudies-arrayexpress
Project description:Human embryonic stem (hES) cells have unique features: self-renewal ability and pluripotency. They can be continuously cultured in undifferentiated state and give rise to cells and tissues of all three germ layers. Thus hES cells provide a resource not only for cell replacement therapy but also for studying human developmental biology. However, much work needs to be done to understand the molecular mechanisms responsible for the maintenance of the undifferentiatiation state and the differentiation process of human embryonic stem cells. Keywords: cell type comparison design We performed gene expression profiling on 3 separate passages from 3 different hES cell lines (WA09 (H9), TE06 (I6) and BG01v), EBs samples derived from WA09 cells at 3 different time points, and 5 types of adult cells (HUVEC, HMVEC, UASMC NHA, and LFB).
2009-04-17 | E-GEOD-12228 | biostudies-arrayexpress
Project description:Using RNA interference to identify IRF4 target genes. Keywords: time series design Gene expression was analyzed using Lymphochip cDNA spotted arrays. Myeloma cell lines were infected with control (shluc, Cy3) or shIRF4 (Cy5) constructs, and changes in gene expression were monitored over time after induction of the shRNA with doxycyclin.
2008-07-07 | E-GEOD-8958 | biostudies-arrayexpress
Project description:To understand the mechanism of action of the RelE family of toxins on metabolism of Mycobacterium tuberculosis. To this effect, toxin expression was induced under control of a tetracycline regulatable promoter and transcriptional profiles compared during overexpression of the three RelE toxin family members. Profiles were also compared to previously published profiles of drugs of known mechanism of action against this organism. For the design, RNA isolated from cells where toxin expression was induced with anhydrotetracycline was converted to Cy5-labeled cDNA whereas RNA derived from cells in which toxin expression was not induced (treated with ethanol solvent only) was converted to Cy3-labeled cDNA. Time points were taken for each overexpression condition. Treatments were performed indepedently a minimum of two times to give independent biological replicates.
2010-05-18 | E-GEOD-13998 | biostudies-arrayexpress
Project description:Superparamagnetic iron oxide nanoparticles (SPION) are increasingly used to label human bone marrow stromal cells (BMSCs, also called mesenchymal stem cells) to monitor their fate by in vivo MRI and histology after Prussian blue (PB) staining. SPION-labeling appears to be safe as assessed by in vitro differentiation of BMSCs, however, we chose to determine the effect of labeling on maintaining the “stemness” of cells within the BMSC population. Colony forming efficiency, CD146 expression, gene expression profiling, bone and myelosupportive stroma formation in vivo were evaluated. SPION-labeling did not alter these assays. Equivalent bone with host hematopoiesis was formed by SPION-labeled and unlabeled BMSCs. PB+ adipocytes were noted, definitively demonstrating their donor origin, as well as PB+ pericytes, indicative of self-renewal of the stem cell in the BMSC population. This study confirms that SPION labeling does not alter the differentiation potential of the subset of stem cells within BMSCs. We performed gene expression profiling on BMSCs labeled with FePro. For comparison, gene express profiling on human embryonic stem cells (hES) WA09 (H9) and adult cells: fibroblasts (FB), endothelial cells (EC) and smooth muscle cells (SMC) was conducted. Total RNA from PBMCs pooled from six normal donors was amplified into aRNA to serve as the reference.
2011-01-24 | E-GEOD-20431 | biostudies-arrayexpress