Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: FLORENCE LE CALVEZ-KELM
PROVIDER: E-GEOD-41160 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Shared Molecules
Only show the datasets with similarity scores above: 0.5
Threshold
0.5
Similar Datasets
Project description:Trastuzumab, a humanized monoclonal antibody directed to the HER2 protein, is the standard-of-care treatment for patients with HER2 positive breast cancer, reducing the risk of relapse and death in patients. Nonetheless, some patients do not benefit from this treatment, underscoring the need to identify patients for whom chemotherapy + trastuzumab is adequate versus patients requiring additional drugs. The series comprised 24 incisional biopsies of breast carcinomas derived from patients that received neoadjuvant trastuzumab based therapy. Gene expression profiling was performed using RNA from frozen core biopsies from 24 patients with primary HER2-positive (HER2+) tumors treated with neoadjuvant chemotherapy and trastuzumab.
2016-03-31 | E-GEOD-62327 | biostudies-arrayexpress
Project description:Signal transducer and activator of transcription 3 (STAT3) is altered in several epithelial cancers and represents a potential therapeutic target. Here, STAT3 expression, activity and cellular functions were examined in two main histotypes of esophageal carcinomas. In situ, immunohistochemistry for STAT3 and STAT3-Tyr705 phosphorylation (P-STAT3) in esophageal squamous cell carcinomas (ESCC) and BarrettM-bM-^@M-^Ys adenocarcinomas (BAC) revealed similar STAT3 expression in ESCCs and BACs, but preferentially activated P-STAT3 in ESCCs. In vitro, strong STAT3 activation was seen by EGF-stimulation in OE21 (ESCC) cells, whilst OE33 (BAC) cells showed constitutive weak STAT3 activation. STAT3 knockdown significantly reduced cell proliferation of OE21 and OE33 cells and reduced cell migration in OE33, but not in OE21 cells. Transcriptome analysis identified STAT3-knockdown associated down-regulation of cell cycle processes and the selective down-regulation of cyclins and cyclin dependent kinaes associated genes in both OE21 and OE33 cells. Moreover, the transcriptome response showed changes in cell migration/invasion related genes that correlated with the associated phenotype measurements. This study demonstrates the importance of STAT3 expression and activation in esophageal carcinomas, whereby the extent differs between ESCCs and BACs. STAT3 knockdown significantly reduces cell proliferation in both types of esophageal cancer cells and inhibits migration in BAC cells. Thus, STAT3 may be further exploited as potential novel therapeutic target for esophageal cancers. The effect of STAT3 knock-down in OE33 and OE21 cells was calculated from three biologically independent experiments. 3x10e4 cells were seeded in triplicate in 24 well-plates and were transfected with twice 100nM STAT3 siRNA (pool of 4 STAT3 sequences, siGENOMEM-BM-.SMARTpoolM-BM-., Dharmacon RNAi Technologies, Thermo Fisher Scientific, Lafayette, USA) or SilencerM-BM-. negative siRNA control (Invitrogen/Life Technologies GmbH, Darmstadt, Germany) using 1M-BM-5l DharmaFECT (Dharmacon RNAi Technologies, Thermo Fisher Scientific, Lafayette, USA) transfection reagent for OE33 cells or siPORTTM NeoFXTM (Invitrogen/Life Technologies GmbH, Darmstadt, Germany) transfection reagent for OE21 cells. Differential gene regulation was quantified 72 hours after the first transfection by comparing separately for the OE21 and OE33 cells the STAT3 siRNA replicates and the respective cell lines containing the scrambled siRNA vector.
2013-06-16 | E-GEOD-47763 | biostudies-arrayexpress
Project description:According to the evolution of the NPC, with normal time series, we identified microRNAs (miRNAs) showing robust differential expression between nasopharyngeal carcinomas (NPCs) and normal healthy nasopharyngeal epithelial samples. This research use miRNA chip testing at different stages in 12 cases of NPC (TNM Ⅰ - II, III, IV each stage 4 cases), 4 patients matched sample and transfer lymphoma 6 samples. Analysis the difference miRNA distribution of in the NPC development, adopt modern bioinformatics methods selection differentially expressed genes. we study the miRNA dynamic expression profiles in different clinical stages of nasopharyngeal carcinoma and NPC lymphoid node metastasis. Samples were taken from a range of tumors of different stages. 6 cases of normal, 4 respective cases of stage I or II, III, IV and lymph node metastasis. The microdissection was performed with Methyl Green staining to separate tumor cells to non-tumor cells.
2012-03-01 | E-GEOD-32906 | biostudies-arrayexpress
Project description:The SNAI1 and SNAI2 embryonic genes are reactivated in numerous cancer types, including carcinomas. They promote cancer cell dissemination by inducing an epithelial-to-mesenchymal transition (EMT) and by protecting cells from anoikis. We now have demonstrated that the sequentially related SNAI3 gene is aberrantly reactivated in human breast carcinomas. To compare the functional properties of the three SNAIL family members, the transcription factors were ectopically expressed in immortalized mammary epithelial cells. Immortalized human mammary epithelial cells (HMEC-hTERT cells) or MCF10A cells were infected with SNAIL retroviral expression constructs. The gene expression profiles of the resulting cell lines, cultured in standard conditions or after plating them 24h in low-adherent (LA) conditions, were performed.
2013-09-30 | E-GEOD-40690 | biostudies-arrayexpress
Project description:Naturally occurring genetic polymorphisms influence patterns of gene expression in normal tissues, and can provide a molecular view of the component cell lineages and signaling pathways responsible for normal tissue architecture. Analysis of the coordinated changes in this architecture that take place during tumor development can help to identify the functional roles of oncogenes or tumor suppressors and provide potential new therapeutic targets. We have applied a network analysis approach to a set of 92 normal human lung samples from cancer patients and their matched adenocarcinomas. We have identified networks associated with particular cell lineages (alveolar type 2 pneumocytes and Clara cells) in normal lung and document the changes in these networks that accompany transformation to adenocarcinomas. Expression of the transcription factor NKX2-1 (TTF1) is linked to surfactant protein markers of the alveolar type 2 lineage in normal and transformed lung cells, but its network is rewired in tumors to include pathways linked to cell growth such as glutaminase (GLS2). Analysis of mitotic networks revealed the presence of novel components such as the kinase VRK1 that are preferentially linked to the mitotic cycle in tumors but not in normal lung. We show that shRNA-mediated inhibition of VRK1 cooperates with inhibition of PARP signaling to inhibit growth of lung tumor cells. Targeting of genes that are recruited into tumor mitotic networks may provide a wider therapeutic window than that seen by inhibition of integral components of the mitotic machinery such as Aurora kinases. 87 lung adenocarcinomas and 92 adjacent uninvolved lung tissue samples, 85 matched pairs
2013-04-01 | E-GEOD-32665 | biostudies-arrayexpress
Project description:Analysis of gene expression levels during Fibroblast to sphere cell conversion induced by albumax I containing medium. Murine embryonic fibroblasts (MEF) can be converted to sphere cells in the presence of arachidonic acid and pluronic - F 68. The converted cells exhibit stem cell like properties and and have the potential to differentiate into all the three embryonic germ layers. Our results provide important information on genes that are up- or down-regulated during the reprogramming/conversion process. Total RNA was isolated from murine embryonic fibroblasts, normal mouse embryonic stem (MES) cells and converted sphere cells. MES cells were taken as a control/reference population. Three replicated were included for each sample.
2011-05-13 | E-GEOD-29277 | biostudies-arrayexpress
Project description:The type II Oncostatin M receptor (OSMR) serves as the main binding site for the pleiotropic cytokine OSM. We have previously demonstrated a positive correlation between copy number driven OSMR over-expression and adverse clinical outcome in cervical tumours and have also established enhanced angiogenic, migratory and invasive potential as major consequences of OSMR over-expression using cell-line models of cervical cancer. By analysis of gene expression patterns in cell lines and tumours, this study now systematically defines cohorts of genes that are implicated for the phenotypes observed. Importantly, we have identified 15 OSM induced genes that are involved in at least one of these key functions and are up-regulated in both OSMR over-expressing cell-lines and tumours. These genes can serve as markers of OSM signalling in OSMR over-expressing SCCs and represent suitable targets for functional characterisation. Gene expression of 4 cervical SCC cell lines analysed (2 with and 2 without OSMR overexpression) at 6 different time-points, with 3 replicates at each time-point.
2011-09-29 | E-GEOD-27480 | biostudies-arrayexpress
Project description:The purpose of this study was to characterise the effects of trastuzumab and pertuzumab, either as single agents or as combination therapy on gene and protein expression in human ovarian cancer in vivo. Illumina BeadChips were used to profile the transcriptome after four days treatment of SKOV3 tumor xenografts. Although genes involved with HER2, MAP-kinase and p53 signaling pathways were commonly induced by all treatments, a greater number and variety of genes were differentially expressed by the complementary combination therapies compared to either drug on its own. The protein level of the CDK-inhibitors p21 and p27 were increased in response to both agents alone and further by the combination; pERK signaling was inhibited by all treatments; but only pertuzumab alone inhibited pAkt signaling. The expression of proliferation, apoptosis, cell division and cell cycle markers was distinct in a panel of primary ovarian cancer xenografts, suggesting heterogeneity of response in ovarian cancer and the need to establish biomarkers of response. This first comprehensive study of the molecular response to trastuzumab, pertuzumab and combination therapy in vivo highlights that there are both common and distinct downstream effects to different HER2 antibodies and that pathways may be invoked more strongly or in a different manner by a combination of agents. Some of the in vivo results for ovarian tumors differ from previous in vitro studies in breast cancer cells, emphasizing that the molecular response to anti-cancer agents involves variable and complex disease-specific interactions of signaling mechanisms. SCOV3 Ovarian cell line xenografts treated with Trastuzumab, pertuzumab or combination after 4 days
2012-05-02 | E-GEOD-31432 | biostudies-arrayexpress
Project description:This study aimed at investigating the impact of chronic ingestion of sebacic acid (SA), a 10 carbons medium-chain dicarboxylic acid, on glycemic control in a mouse model of type 2 diabetes (db/db mice). Three groups of 15 mice were fed for 6 weeks either a chow diet (Ctrl), or a chow diet supplemented with 1.5% or 15% (SA1.5% and SA15% resp.) energy from SA. Fasting glycemia was measured once a week and HbA1c before and after supplementation. An oral glucose tolerance test (OGTT) was performed at the end of the supplementation. Gene expression was determined by transcriptomic analysis on the liver of the Ctrl and SA15% groups. Results-After 42 days of supplementation, fasting glycemia and HbA1c were ~70% and ~25% lower in the SA15% group compared to other groups showing a beneficial effect of SA on hyperglycemia. During OGTT, blood glucose area under the curve (AUC) was reduced after SA15% compared to other groups. This effect was associated with a tendency for an improved insulin response. In the liver, Pck1 and FBP mRNA were statistically decreased in the SA15% compared to Ctrl suggesting a reduced hepatic glucose output induced by SA. Conclusions-Dietary supplementation of SA largely improves glycemic control in a mouse model of type 2 diabetes. This beneficial effect may be due (1) to a reduced hepatic glucose output resulting from transcriptional down regulation of key gluconeogenesis genes and (2) to an improved glucose induced-insulin secretion. Microarray analysis of 6-8 wk old male BKS.Cg-m+/+Leprdb/J 000642 db/db mice. 2 groups. n=15/group: 1) Control group. 2) Sebacic acid high dose group - 15% (77.6g/kg food, â??9g/kg body weight per day).
2010-10-29 | E-GEOD-21083 | biostudies-arrayexpress
Project description:Analysis of wig-1 pathways via suppression of Wig-1 by antisense oligonucleotides Total RNA obtained from mouse brain subjected to antisense oligonucleotide (ASO) treatement compared to PBS (control), and negative control ASO brain treatment.
2011-06-06 | E-GEOD-29751 | biostudies-arrayexpress