Comparison of the differentially expressed genes in normal vs ovarian cancer cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE109981 | GEO | 2019/02/01
REPOSITORIES: GEO
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Project description:Comparison of the differentially expressed genes in normal vs ovarian cancer cells
| PRJNA432514 | ENA
Project description:Recent studies suggest that long non-coding RNAs (lncRNAs) play crucial roles in many types of human malignant cancers. However, the function of lncRNAs in benign tumors remains poorly understood. In the present study, to explored the potential roles of lncRNAs in benign epithelial ovarian cysts (BEOCs) which commonly occur in young women and possess malignant potential, we described the expression profile of the lncRNAs between BEOC and normal ovarian tissues using lncRNA microarray techniques. The results showed that 1,325 transcripts of lncRNAs (1,014 upregulated and 311 downregulated) were differentially expressed in the BEOCs compared with the normal controls [absolute fold-change ≥2, false discovery rate (FDR) <0.05]. We also conducted quantitative real-time PCR (qPCR) to confirm the microarray data. The results of qPCR revealed that the expression trend of 6 randomly selected lncRNAs was consistent with the microarray data. Furthermore, candidate lncRNAs were characterized by pathway analysis and Gene Ontology (GO). The present study is the first to demonstrate different expression profiles of lncRNAs between BEOCs and normal ovarian tissues. These lncRNAs may play a crucial role in the pathological process of BEOCs.
| S-EPMC5562051 | biostudies-literature
Project description:The aim of the present study was to identify common microRNAs (miRNAs) in ovarian cancer (OC) cells and their exosomes using microarray data (accession number GSE76449) available from the Gene Expression Omnibus database, including exosomal samples from 3 OC cell lines, 1 normal ovarian surface epithelial cell line and their original cell samples. Differentially-expressed miRNAs (DE-miRNAs) were identified using the Linear Models for Microarray data method, and mRNA targets of DE-miRNAs were predicted using the miRWalk2 database. The potential functions of the target genes of the DE-miRNAs were analyzed using the Database for Annotation, Visualization and Integrated Discovery tool. The association between crucial miRNAs and target genes, and their clinical associations, were validated using The Cancer Genome Atlas data. As a result, 12 upregulated and 12 downregulated DE-miRNAs were shared by the 3 OC cell lines compared with normal controls in the exosomal samples, while 5 upregulated and 65 downregulated DE-miRNAs were shared between the original cells. Among them, 9 downregulated DE-miRNAs were shared between exosomal and original cells. The target genes of 4 common DE-miRNAs between exosomal and original cells (miR-127-3p, miR-339-5p, miR-409-3p and miR-654-3p) were predicted. Functional enrichment analysis indicated that these target genes may be involved in the Wnt signaling pathway (miR-409-3p-CTBP1 and miR-339-5p-CHD8) and Proteoglycans in cancer (miR-127-3p-PPP1CA). The negative associations between these 3 miRNAs and target genes were confirmed by a Pearson's correlation analysis. miR-127 was negatively associated with tumor grade. In conclusion, our results describe a set of miRNAs involved in OC development, in exosomal and non-exosomal manners, by regulating their target genes. They may be potential targets for treatment of OC.
| S-EPMC6036573 | biostudies-literature
Project description:We have compared the microsomal protein fractions from benign and malignant adrenocortical tumors. Protein extracts were trypsinized, peptides separated by HiRIEF (high resolution isoelectric focusing) and analysed by LC-MS.
2014-02-11 | PXD000604 | Pride
Project description:To investigate the role of miRNAs in the progression of colon cancer, we performed comprehensive miRMA microarray analysis on RNA derived from colon cancer tissues and normal colon tissues. We identified a novel set of colon cancer-related miRNAs.
2013-12-16 | GSE53339 | GEO
Project description:AimTo identify and analyze the differentially expressed proteins in normal and cancerous tissues of four patients suffering from colon cancer.MethodsColon tissues (normal and cancerous) were homogenized and the proteins were extracted using three protein extraction buffers. The extraction buffers were used in an orderly sequence of increasing extraction strength for proteins with hydrophobic properties. The protein extracts were separated using the SDS-PAGE method and the images were captured and analyzed using Quantity One software. The target protein bands were subjected to in-gel digestion with trypsin and finally analyzed using an ESI-ion trap mass spectrometer.ResultsA total of 50 differentially expressed proteins in colonic cancerous and normal tissues were identified.ConclusionMany of the identified proteins have been reported to be involved in the progression of similar or other types of cancers. However, some of the identified proteins have not been reported before. In addition, a number of hypothetical proteins were also identified.
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Project description:This laboratory is focusing on to clarify the biologic relevance of a virulence factor known as trans-sialidase from Trypanosoma cruzi, the agent of the Chagas disease (American trypanosomiasis).
2011-02-17 | GSE27353 | GEO
Project description:Using differential display (DD), we discovered a new member of the serine protease family of protein-cleaving enzymes, named protease M. The gene is most closely related by sequence to the kallikreins, to prostate-specific antigen (PSA), and to trypsin. The diagnostic use of PSA in prostate cancer suggested that a related molecule might be a predictor for breast or ovarian cancer. This, in turn, led to studies designed to characterize the protein and to screen for its expression in cancer.The isolation of protease M by DD, the cloning and sequencing of the cDNA, and the comparison of the predicted protein structure with related proteins are described, as are methods to produce recombinant proteins and polyclonal antibody preparations. Protease M expression was examined in mammary, prostate, and ovarian cancer, as well as normal, cells and tissues. Stable transfectants expressing the protease M gene were produced in mammary carcinoma cells.Protease M was localized by fluorescent in situ hybridization analysis to chromosome 19q13.3, in a region to which other kallikreins and PSA also map. The gene is expressed in the primary mammary carcinoma lines tested but not in the corresponding cell lines of metastatic origin. It is strongly expressed in ovarian cancer tissues and cell lines. The enzyme activity could not be established, because of difficulties in producing sufficient recombinant protein, a common problem with proteases. Transfectants were selected that overexpress the mRNA, but the protein levels remained very low.Protease M expression (mRNA) may be a useful marker in the detection of primary mammary carcinomas, as well as primary ovarian cancers. Other medical applications are also likely, based on sequence relatedness to trypsin and PSA.
| S-EPMC2230195 | biostudies-other
Project description:To investigate the role of miRNAs in the progression of colon cancer, we performed comprehensive miRMA microarray analysis on RNA derived from colon cancer tissues and normal colon tissues. We identified a novel set of colon cancer-related miRNAs. Total RNA was isolated from colon cancer tissues and normal colon tissues. Six-condition experiment: H normal tiss vs. H tumor tissue, S normal tiss vs. S tumor tissue, W1 normal tiss vs. W1 tumor tissue, M normal tiss vs. M tumor tissue, W2 normal tiss vs. W2 tumor tissue, and Y normal tiss vs. Y tumor tissue. Biological replicates: 1H normal tiss, 1H tumor tissue, 1S normal tissM-oM-<M-^L1S tumor tissue, 1W1 normal tissM-oM-<M-^L1W1 tumor tissue, 1M normal tissM-oM-<M-^L1M tumor tissue, 1W2 normal tissM-oM-<M-^L1W2 tumor tissue, 1Y normal tiss and 1Y tumor tissue, independently grown and harvested. One replicate per array.
2013-12-16 | E-GEOD-53339 | biostudies-arrayexpress
Project description:Brain metastasis (BM) can affect up to 25% of non-small cell lung cancer (NSCLC) patients during their lifetime. Efforts to characterize patients that will develop BM have been fairly disappointing. Small non-coding microRNAs (miRNAs) regulate the expression of target mRNAs by repressing their translation or regulating their sequence-specific degradation. miRNAs play a role in regulating a variety of targets and, consequently, multiple pathways, which makes them a powerful tool to be exploited for early detection of disease, risk assessment, and prognosis. In this study, we investigated miRNAs that may serve as biomarkers to differentiate between NSCLC patients with and without BM. miRNA microarray profiling was performed on samples from clinically matched NSCLC from patients with BM (BM+) and without BM (BM-). miR-328 and miR-330-3p were able to correctly classify BM+ vs. BM- patients. Gene expression analysis comparing NSCLC parental and stably transfected miR-328 cells identified several significantly differentially-expressed genes, whose expression may be directly or indirectly regulated by miR-328. NSCLC Cell Line A549 analysis: Two-condition experiment, A549 GFP Control vs. A549 miR-328 cells. Biological replicates: 2 control replicates, 2 miR-328 replicates. miRNA microarray analysis was performed on RNA extracted from formalin-fixed paraffin-embedded (FFPE) NSCLC tumor specimens from 7 BM+ patients and 5 BM- patients.
| S-ECPF-GEOD-23019 | biostudies-other