Transcriptomics,Multiomics

Dataset Information

3

Transcription profiling by array of human hepatocellular carcinoma cell line HepG2 treated with tumor necrosis factor-alpha


ABSTRACT: The proinflammatory cytokine, TNFalpha is critical in maintaining liver homeostasis since it is a major determiner of hepatocyte life and death. Considering this, gene transcription profiling was examined in control and TNFalpha treated HepG2 cells. Results indicated that TNFalpha could significantly alter the expression of a significant number of genes; most of them were functionally distributed among molecular functions like catalytic activity, binding, molecular transducer activity, transporter activity, translation and transcription regulator activities or enzyme regulator activity. Also, within genes up-regulated by TNFalpha, several GO terms related to lipid and fat metabolism were significantly overrepresented indicating global dysregulation of fat metabolism within the hepatocyte and those within the down-regulated dataset included genes involved in immunoglobulin receptor activity and IgE binding thereby indicating a compromise in immune defense mechanism(s) apart from those involved the DNA binding and protein binding categories. The interacting network of “lipid metabolism, small molecule biochemistry” was derived to be significantly affected that correlated well with the top canonical pathway of “biosynthesis of steroids” and molecular and cellular function of “lipid metabolism”. All these indicate TNFalpha to be significantly altering the transcriptome profiling within HepG2 cells with genes involved in lipid and steroid metabolism being the most favoured. This study suitably addresses the genes that determine TNFalpha mediated alterations within the hepatocyte mainly the phenotypes of hepatic steatosis and fatty liver that are associated with several hepatic pathological states. HepG2 cells were maintained in DMEM supplemented with 10% fetal calf serum with 1% antibiotic-antimycotic. On attaining confluency, cells were serum starved overnight and incubated in the absence (control) and presence of TNFalpha (0.5nM, 12h). On termination of incubation, total RNA was isolated, reverse transcribed to cDNA and subjected to in vitro transcription to produce biotinylated cRNA that was hybridized to the human array chip (Human Genome U133 Plus 2.0, Affymetrix) according to the manufacturer's instructions. Images were scanned using the GeneChip 3000 7G scanner (Affymetrix) and analysed. The experiment was performed with triplicates of each set (Control and TNF alpha treated). This experiment was reloaded in November 2010 after additional curation.

OTHER RELATED OMICS DATASETS IN: PRJNA113449

DISEASE(S): Hepatocellular Carcinoma

SUBMITTER: Amit K Pandey   Neha Munjal  Malabika Datta 

PROVIDER: E-GEOD-12161 | ArrayExpress | 2010-03-04

SECONDARY ACCESSION(S): GSE12161PRJNA113449

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-12161.idf.txt Idf
E-GEOD-12161.processed.1.zip Processed
E-GEOD-12161.raw.1.zip Raw
E-GEOD-12161.sdrf.txt Txt
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Publications

Gene expression profiling and network analysis reveals lipid and steroid metabolism to be the most favored by TNFalpha in HepG2 cells.

Pandey Amit K AK   Munjal Neha N   Datta Malabika M  

PloS one 20100204 2


<h4>Background</h4>The proinflammatory cytokine, TNFalpha, is a crucial mediator of the pathogenesis of several diseases, more so in cases involving the liver wherein it is critical in maintaining liver homeostasis since it is a major determiner of hepatocyte life and death. Gene expression profiling serves as an appropriate strategy to unravel the underlying signatures to envisage such varied responses and considering this, gene transcription profiling was examined in control and TNFalpha treat  ...[more]

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