Comparison of gene expression profile of lymphocytes samples from prednisolone-treated and control cows.
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ABSTRACT:
ORGANISM(S): Bos taurus
PROVIDER: GSE50757 | GEO | 2016/12/22
SECONDARY ACCESSION(S): PRJNA218847
REPOSITORIES: GEO
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Project description:A bovine oligo microarray platform (GPL7053) was used to evidence differences in gene expression profiles from eight (8) thymus samples from prednisolone-treated cows and seven (7) from control animals. Significance analysis of microarray found 154 up-regulated and 234 down-regulated transcripts in the prednisolone-treated animal group respect to the controls. In this study, we analyzed fifteen (15) bovine thymus samples, eight (8) from prednisolone-treated cows and seven (7) from control animals. Gene expression profiling was performed using the Agilent-015354 Bos taurus Oligo Microarray platform (GPL7053) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
2014-09-02 | E-GEOD-40884 | biostudies-arrayexpress
Project description:Background: Glucocorticoids are important pharmaceutical agents in the treatment of acute lymphoblastic leukemia in children. Resistance or sensitivity to glucocorticoids is considered to be of crucial importance for disease prognosis. Prednisolone is a first-line chemotherapeutic agent in the treatment of acute lymphoblastic leukemia. Here, the effects of prednisolone on the resistant CCRF-CEM leukemic cell line were studied. Methods: Prednisolone’s cytotoxic and cell cycle effects were studied with flow cytometry. NF-κB translocation was studied with Western Blotting and differential gene expression was studied with cDNA microarrays. Results: Prednisolone exerted a delayed biphasic effect, necrotic at low doses and apoptotic at higher doses. At low doses, prednisolone exerted a pre-dominant mitogenic effect despite its induction on total cell death, while at higher doses, prednisolone’s mitogenic and cell death effects were counterbalanced. NF-κB was constitutively present in the nucleus. Early gene microarray analysis revealed 40 differentially expressed genes upon 4 hours of prednisolone’s exposure. Notable differences in gene regulation were observed between the lowest and the highest glucocorticoid doses. Prednisolone activated genes related to apoptosis/tumor suppression, cell cycle progression, metabolism and intra-/ extra-cellular signaling pathways. Conclusions: The mitogenic/biphasic effects of prednisolone are of clinical importance in the case of resistant leukemic cells. This approach might lead to the identification of gene candidates for future molecular drug targets in combination therapy with glucocorticoids, along with early markers for glucocorticoid resistance.
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2021-04-27 | PXD020543 | Pride
Project description:Acute Lymphoblastic Leukemia (ALL) in infants (<1 year of age) is characterized by a high incidence of MLL translocations which is associated with a poor prognosis. Contributing to this poor prognosis is cellular drug resistance, especially to glucocorticoids like prednisolone. Although in vitro prednisolone resistance mechanisms have been proposed in pediatric ALL, it has never been studied in MLL-rearranged infant ALL, which are highly resistant to glucocorticoids in vitro and in vivo. We analyzed primary MLL-rearranged infant ALL expression profiles, which were either in vitro prednisolone-resistant or prednisolone-sensitive, in order to study in vitro prednisolone resistance.
2011-10-12 | E-GEOD-32962 | biostudies-arrayexpress
Project description:Dengue is the most important arboviral infection of humans. A host pro-inflammatory immune response is widely believed to contribute to the clinical complications that occur in some patients with dengue. Here, immune correlates of early prednisolone therapy were defined in Vietnamese dengue patients enrolled in a randomized controlled trial, comparing a three day regimen of high (2mg/kg) or low (0.5mg/kg) dose prednisolone with placebo. Prednisolone conferred a small change in the whole blood gene expression profile, with 81 transcripts from 64 genes differentially abundant between high-dose prednisolone and placebo treated patients. A prominent theme in the prednisolone gene expression signature was the under-abundance of transcripts from genes associated with T and NK cell cytolytic effector functions. Surprisingly, prednisolone therapy was not associated with attenuation of early-convalescent T cell responses or plasma cytokine levels. Collectively, these findings are consistent with a remarkably benign influence of prednisolone on immune response parameters in dengue patients, and are in line with the trial evidence showing lack of impact on clinical laboratory endpoints and clinical phenotype.
2012-12-31 | GSE40165 | GEO
Project description:Background: Glucocorticoids are important pharmaceutical agents in the treatment of acute lymphoblastic leukemia in children. Resistance or sensitivity to glucocorticoids is considered to be of crucial importance for disease prognosis. Prednisolone is a first-line chemotherapeutic agent in the treatment of acute lymphoblastic leukemia. Here, the effects of prednisolone on the resistant CCRF-CEM leukemic cell line were studied. Methods: Prednisolone’s cytotoxic and cell cycle effects were studied with flow cytometry. NF-κB translocation was studied with Western Blotting and differential gene expression was studied with cDNA microarrays. Results: Prednisolone exerted a delayed biphasic effect, necrotic at low doses and apoptotic at higher doses. At low doses, prednisolone exerted a pre-dominant mitogenic effect despite its induction on total cell death, while at higher doses, prednisolone’s mitogenic and cell death effects were counterbalanced. NF-κB was constitutively present in the nucleus. Early gene microarray analysis revealed 40 differentially expressed genes upon 4 hours of prednisolone’s exposure. Notable differences in gene regulation were observed between the lowest and the highest glucocorticoid doses. Prednisolone activated genes related to apoptosis/tumor suppression, cell cycle progression, metabolism and intra-/ extra-cellular signaling pathways. Conclusions: The mitogenic/biphasic effects of prednisolone are of clinical importance in the case of resistant leukemic cells. This approach might lead to the identification of gene candidates for future molecular drug targets in combination therapy with glucocorticoids, along with early markers for glucocorticoid resistance. Elucidation of the mechanisms of GC action may lead to identification of gene targets responsible for GC resistance. Key tools in this process are high-throughput technologies such as microarray-based gene expression analysis. For this purpose, the parental CCRF-CEM cell line was chosen as the system of study for the effects of prednisolone treatment. This is a T-cell leukemia cell line characterized by a mutation (L753F) on one GR gene allele that impairs ligand binding (Thompson and Johnson 2003). It is known that both the DNA and ligand binding domains of the GR are required in order to repress NF-κB transactivation (Wissink, van Heerde et al. 1997). Interestingly, concerning the question whether this mutation would affect GC resistance, it has been reported previously that both the GC-resistant as well as the GC-sensitive CCRF-CEM subclones express heterogeneous populations of the GR (GRwt/GRL753F) (Palmer and Harmon 1991; Powers, Hillmann et al. 1993). The CCRF-CEM cell line has been reported to be resistant to GCs, presumably due to the accumulation of more resistant variants after long periods of prolonged culture (Norman and Thompson 1977). It is possible that these cells are clonally inhomogeneous, as possibly the cells obtained in vivo by patients. Moreover, the large number of the CCRF-CEM subclone studies in the literature makes it difficult to choose an appropriate resistant cell model. In addition, the utilization of an in vitro system for this study offered reproducibility, an opportunity to closely examine intracellular signals and avoid interference from other in vivo-participating systems. Thus, the cell line used for this study was considered to be useful in studying GC action and resistance in leukemic cells. The aim of this work was to determine the cytotoxic, cell cycle phase distribution and early cancer-specific gene expression effects of prednisolone in CCRF-CEM cells, as an in vitro model of ALL resistance to glucocorticoids. The early gene expression profile allowed identification of genes initiating pivotal, early onset regulatory mechanisms activated by GC and excluded ensuing feedback responses and further downstream signals. Samples tested were in the form of a loop-design i.e. control vs. 10nM prednisolone (designated 0vs1) , 10nM prednisolone vs.700uM prednisolone (designated 1vs3) and control vs. 700uM prednisolone (designated 0vs3), the sum of the logarithms of the first two should equal the third. In other words if Rj,i is the ratio of the ith gene in the jth experiment then R0vs1,i+R1vs3,i=R0vs3,i. We tested this using a statistical test. We have applied an intensity-dependent z-score where the sum of the ratios was compared to the ratio of the third experiment. If the difference was significant genes, in a standard deviation threshold of ±1.5 in relative units, were rejected from further analysis (Kerr and Churchill 2001; Kerr and Churchill 2001; Altman and Hua 2006; Kerr and Churchill 2007).
2011-03-22 | E-GEOD-27989 | biostudies-arrayexpress
Project description:Dengue is the most important arboviral infection of humans. A host pro-inflammatory immune response is widely believed to contribute to the clinical complications that occur in some patients with dengue. Here, immune correlates of early prednisolone therapy were defined in Vietnamese dengue patients enrolled in a randomized controlled trial, comparing a three day regimen of high (2mg/kg) or low (0.5mg/kg) dose prednisolone with placebo. Prednisolone conferred a small change in the whole blood gene expression profile, with 81 transcripts from 64 genes differentially abundant between high-dose prednisolone and placebo treated patients. A prominent theme in the prednisolone gene expression signature was the under-abundance of transcripts from genes associated with T and NK cell cytolytic effector functions. Surprisingly, prednisolone therapy was not associated with attenuation of early-convalescent T cell responses or plasma cytokine levels. Collectively, these findings are consistent with a remarkably benign influence of prednisolone on immune response parameters in dengue patients, and are in line with the trial evidence showing lack of impact on clinical laboratory endpoints and clinical phenotype. The gene expression microarray assay was conducted on samples from the first 123 consecutive patients (placebo, 40; 0.5mg/kg prednisolone, 42; 2.0mg/kg prednisolone, 41).
2012-12-31 | E-GEOD-40165 | biostudies-arrayexpress