Integrated metabolite and gene expression profiles identify lipid biomarkers associated with progression of hepatocellular carcinoma and patient outcomes.
OBJECTIVE We combined gene expression and metabolic profile analysis to identify factors associated with the outcomes of patients with hepatocellular carcinoma (HCC).
METHOD We compared the pattern of metabolism and gene expression between paired tumor and nontumor tissue from 30 patients with HCC, and validated the results using a sample of 356 patients with HCC. A total of 469 metabolites were measured by using chromatography / mass spectrometry spectrometry liquid and gas chromatography / mass. Metabolism and integrated genomic data, and Kaplan-Meier and Cox proportional hazards analysis was used to a certain pattern associate with patient outcomes. related factors were evaluated for their effect on cancer cells in vitro and tumor formation in nude mice.
RESULTS We identified 28 metabolites and 169 genes associated with aggressive HCC. lipid metabolite-stearoyl-CoA desaturase (SCD) is associated with the aberrant activity of palmitate signal in aggressive HCC samples. The expression of gene products associated with these metabolites, including SCD, was independently associated with survival time and recurrence of tumors in test and validation sets.
The combined expression of SCD and α-fetoprotein associated with outcomes of patients with early-stage liver cancer. Levels of monounsaturated palmitic acid, the product of SCD activity, an increase in aggressive HCCS; monounsaturated palmitic acid increased migration and invasion of HCC cells cultured and colony formation by liver cancer cells. HCC cells expressed small interfering RNA against SCD decreased cell migration and the formation of colonies in culture and reduced tumorigenicity in mice.
CONCLUSION By using a combination of gene expression and metabolic profile analysis, we identified a network of lipogenic involving SCD and palmitic signal and associated with the development of HCC and patient outcomes. Microarray platform and data that has been submitted to the Gene Expression Omnibus at NCBI public database following the guidelines MIAME. accession numbers: GPL4700 (platform), and GSE6857 (sample).
Integrated metabolite and gene expression profiles identify lipid biomarkers associated with progression of hepatocellular carcinoma and patient outcomes.
Interferome v2.0: updated database of interferon-regulated genes described.
Interferome v2.0 is an update of an earlier version of DB Interferome NAR published in the 2009 edition of the database. Much better computing infrastructure now allows more complex and faster queries, and supports more data sets of types I, II and III interferon (IFN) -treated cells, rat or human.
Quantitative, MIAME appropriate data is collected, carried out a thorough analysis, standardized, quantitative and statistical and then significant changes in gene expression are uploaded. a comprehensive manual collection of metadata in v2.0 allows flexible, detailed searches capacity including the parameters: range double change, the type of IFN, concentration and time, and cell / tissue types.
Description: This product includes the reaction buffer and fluorescence dye H19 for 1000 assays of DNA relaxation reactions in a 96-well plate assay format or 2000 assays in a 384-well assay format.
Human topoisomerase I DNA relaxation assay HTS kit (enzyme not included)
Description: This product includes 4800 ul of 10 x Buffer HT1, 170 ul of 1500 x Dye H19 and 30 ml of 10 x H19 dilution buffer. It is for 1000 DNA relaxation assays in a 96-well plate format or 2000 assays in a 384-well assay format. Supercoiled DNA and human topo I enzyme can be purchased separately.
There is no limit to the number of genes that can be used to search the database in one query. secondary analysis such as gene ontology, regulatory factors, the location of the plot chromosome or tissue expression of IFN-regulated genes (IRGs) can be done in Interferome v2.0, or data can be downloaded in text format that is readily compatible with the common secondary analysis program. Given the importance of IFN to the innate immune response in infectious, inflammatory diseases and cancer, this upgrade of Interferome to version 2.0 will facilitate the identification of signatures of genes important in the pathogenesis of this disease.
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