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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MicroRNA expression profiles for paediatric brain tumours

ABSTRACT: In this study, we screened a cohort of 57 paediatric brain tumours, with a wide range of pathologies to identify microRNA profiles We analysed the microRNA profiles in paediatric brain tumours as compared to normal adult brain. Our cohort included 14 pilocytic astrocytomas, 3 diffuse astrocytomas, 2 anaplastic astrocytomas, 5 glioblastomas, 14 ependymomas, 9 medulloblastomas, 5 atypical teratoid/rhabdoid tumours, 4 choroid plexus papillomas, 1 papillary glioneuronal, and 7 adult brain controls.

ORGANISM(S): Homo sapiens

SUBMITTER: Denise Sheer

PROVIDER: E-GEOD-42657 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profiles for paediatric brain tumours

Project description:In this study, we screened a cohort of 57 paediatric brain tumours, with a wide range of pathologies to identify gene expression profiles We analysed gene expression in paediatric brain tumours as compared to normal adult brain in order to understand the molecular profiles. Our cohort included 15 pilocytic astrocytomas, 3 diffuse astrocytomas, 2 anaplastic astrocytomas, 5 glioblastomas, 14 ependymomas, 9 medulloblastomas, 5 atypical teratoid/rhabdoid tumours, 4 choroid plexus papillomas, 8 adult brain and 8 foetal brain controls.

2013-07-29 | E-GEOD-42656 | biostudies-arrayexpress

Expression profiles for paediatric brain tumours

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-07-29 | E-GEOD-42658 | biostudies-arrayexpress

Identification of novel candidate oncogenes in chromosomal region 17p11.2-p12 in human osteosarcoma

Project description:in 25% - 30% of all OS cases the chromosome region 17p11.2-p12 is aberrant. Using SNP array in conjunction with expression microarrays we try to identify genes which can be classified as oncogens or are in someway benificial to the survival of the tumor. To identify minimal significant amplified region(s) that is(are) aberrant in osteosarcoma tumorigenesis, with a special emphasis on but not limitied to chromosome region 17p11.2-p12

2013-04-15 | E-GEOD-32964 | biostudies-arrayexpress

miR-132 mediates renal fibrosis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-02-16 | E-GEOD-76550 | biostudies-arrayexpress

miR-132 mediates renal fibrosis: Genome-wide analysis of gene expression in foxd1-derivative interstital cells derived from fibrotic kidneys from mice treated with antagomir-132 or scramblemir

Project description:Chronic kidney disease is associated with progressive renal fibrosis, where perivascular cells give rise to the majority of Î±-SMA positive myofibroblasts. We sought to identify pericytic miRNAs that could serve as a target to decrease myofibroblast formation. We induced kidney fibrosis in FoxD1-GC;Z/Red-mice by unilateral ureteral obstruction (UUO) followed by FACS sorting of dsRed-positive FoxD1-derivative cells and miRNA profiling. MiR-132 selectively increased 21-fold during pericyte-to-myofibroblast formation whereas miR-132 was only 2.5-fold up in total kidney lysates (both in UUO and ischemia-reperfusion injury). MiR-132 silencing in UUO decreased collagen deposition (35%) and tubular apoptosis. Immunohistochemistry, western blot and qRT-PCR confirmed a similar decrease in interstitial Î±-SMA+ cells. Pathway analysis identified a rate-limiting role for miR-132 in myofibroblast proliferation that was confirmed in vitro. Indeed, antagomir-132 treated mice displayed a reduction in the number of proliferating, ki67+ interstitial myofibroblasts. Interestingly, this was selective for the interstitial compartment and did not impair the reparative proliferation of tubular epithelial cells, as evidenced by an increase in ki67+ epithelial cells, as well as increased (p-)RB1, Cyclin-A and decreased RASA1, p21 levels in kidney lysates. Taken together, silencing miR-132 counteracts the progression of renal fibrosis by selectively decreasing myofibroblast proliferation and could potentially serve as a novel antifibrotic therapy. Total RNA obtained from FACS sorted mouse renal FoxD1-derivatve interstitial cells from mice that were treated with antagomir-132 or scramblemir and underwent UUO (n=4)

2016-02-16 | E-GEOD-76548 | biostudies-arrayexpress

Genome wide gene expression array analysis in T-ALL

Project description:In short: The objective with the gene expression array (Illumina HT-12 v.4) analysis of 17 T-ALL samples was to correlate gene expression levels with DNA promoter methylation status. Manuscript Abstract: Background: Treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has improved, but there is a considerable fraction of patients experiencing a poor outcome. There is a need for better prognostic markers and aberrant DNA methylation is a candidate in other malignancies, but its potential prognostic significance in T-ALL is hitherto undecided. Design and Methods: Genome wide promoter DNA methylation analysis was performed in pediatric T-ALL samples (n=43) using arrays covering >27000 CpG sites. Clinical outcome was evaluated in relation to methylation status and compared with a contemporary T-ALL group not tested for methylation (n= 32). Results: Based on CpG island methylator phenotype (CIMP), T-ALL samples were subgrouped as CIMP+ (high methylation) and CIMP- (low methylation). CIMP- T-ALL patients had significantly worse overall and event free survival (p=0.02 and p=0.001, respectively) compared to CIMP+ cases. CIMP status was an independent factor for survival in multivariate analysis including age, gender and white blood cell count. Analysis of differently methylated genes in the CIMP subgroups showed an overrepresentation of transcription factors, ligands and polycomb target genes. Conclusions: We identified global promoter methylation profiling as being of relevance for subgrouping and prognostication of pediatric T-ALL. RNA was extracted with TRIZOL according to manufacturer instructions. Total RNA was amplified bu the Illumina TotalPrep RNA Amplification kit. Gene expression array analysis was performed on the 17/43 pediatric T-ALL samples from which RNA was availible. 2 control samples of stimulted T-cells were included and one replicate.

2013-07-01 | E-GEOD-41621 | biostudies-arrayexpress

RABL6A promotes G1-S phase progression and pancreatic neuroendocrine tumor cell proliferation in an Rb1-dependent manner

Project description:Mechanisms of neuroendocrine tumor (NET) proliferation are poorly understood and therapies that effectively control NET progression and metastatic disease are limited. We found amplification of a putative oncogene, RABL6A, in primary human pancreatic NETs (PNETs) that correlated with high level RABL6A protein expression. Consistent with those results, stable silencing of RABL6A in cultured BON-1 PNET cells revealed that it is essential for their proliferation and survival. Cells lacking RABL6A predominantly arrested in G1 phase with a moderate mitotic block. Pathway analysis of microarray data suggested activation of the p53 and retinoblastoma (Rb1) tumor suppressor pathways in the arrested cells. Specific inactivation of p53 had no effect on the RABL6A knockdown phenotype, indicating RABL6A functions independent of p53 in this setting. By comparison, Rb1 inactivation restored G1 to S phase progression in RABL6A knockdown cells although it was insufficient to override the mitotic arrest and cell death caused by RABL6A loss. Thus, RABL6A promotes G1 progression in PNET cells by inactivating Rb1, an established suppressor of PNET proliferation and development. This work identifies RABL6A as a new negative regulator of Rb1 that is essential for PNET proliferation and survival. We suggest RABL6A is a new potential biomarker and target for anticancer therapy in PNET patients. Total RNA obtained from human BON-1 PNET cells with RABL6A shRNA knockdown compared to BON-1 cells expressing control vector.

2014-07-01 | E-GEOD-53778 | biostudies-arrayexpress

Genome-wide comparative analysis of gene expression in wild type (WT3) and TRPM7-/- (K09) mouse embryonic stem cells

Project description:TRPM7 is a ubiquitous ion channel and kinase, a unique M-bM-^@M-^XchanzymeM-bM-^@M-^Y, required for proper early embryonic development. In order to assess the effects of TRPM7 activity on cellular gene expression, mouse embryonic stem cells with TRPM7 gene deletion (TRPM7-/- mESC) were established. By using microarray analysis, we identified genes with transcription significantly different in TRPM7-deficient mESC. Total RNA was extracted from cells using Qiagen RNAeasy Plus mini Kit. Triplicate samples were made for each wild type clone 3 (WT3) and and TRPM7-/- clone 9 (KO9) mESC

2014-04-15 | E-GEOD-55578 | biostudies-arrayexpress

Genome-wide analysis of FSH and LH dependent gene expression and the crosstalk between these two pathways in mice testes

Project description:Effects of the absence of a functional LH receptor and/or expression of a constitutively active FSH receptor on gene expression in the gonads of male mice were studied. The results provide insights into the roles of the hormones LH and FSH in male reproduction. The main conclusion is that constant strong FSH stimulation is able to rescue the impaired spermatogenesis and fertility of male mice in the absence of LH signalling. Total RNA was obtained from testis of 12 weeks old mice of different genotypes and extracted using Trizol followed by clean up with Qiage RNeasy MinElute Cleanup Kit

2016-01-20 | E-GEOD-76945 | biostudies-arrayexpress

Genome-wide analysis of gonadotropin-dependent gene expression and crosstalk of the regulatory pathways in the female ovaries

Project description:Effects of lack of functional LH receptor and/or a constitutively active FSH receptor on gene expression in the ovaries of female mice were studied. The results suggest that transgenic expression of the mouse Fshr in granulosa cells leads to abnormal ovarian structure/function and infertility. This finding indicates that gain-of-function mutations of the Fshr in female mice bring about distinct and clear changes in ovarian function. Total RNA was obtained from ovaries of 12 weeks old mice of different genotypes and extracted using Trizol followed by clean up with Qiage RNeasy MinElute Cleanup Kit

2016-02-03 | E-GEOD-77479 | biostudies-arrayexpress

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