Gene Set: CHIBA_RESPONSE_TO_TSA

Standard name CHIBA_RESPONSE_TO_TSA
Systematic name M16977
Brief description Genes up-regulated in more than one of several human hepatoma cell lines by TSA [PubChem=5562].
Full description or abstract BACKGROUND/AIMS: Epigenetics is the key factor in the regulation of gene expression. We conducted cDNA microarray analysis to screen for genes induced by histone deacetylase (HDAC) inhibition and examined epigenetic alterations. METHODS: Microarray analysis was performed in six hepatoma cell lines and primary hepatocytes treated with trichostatin A (TSA). mRNA expression of several genes was examined by reverse transcription-polymerase chain reaction in TSA-treated cells and hepatoma samples. Acetylated histones and methylation status in 5'CpG islands was assessed by chromatin immunoprecipitation (ChIP) assay and bisulfite genomic sequencing, respectively. RESULTS: Fifty-seven genes showed greater than 2-fold change after TSA treatment in multiple cell lines. Among them, four genes including p21(WAF1) exhibited substantial induction (greater than 5-fold changes). Decreased mRNA levels of these genes in hepatoma tissues were observed in more than half of patients. ChIP assay, in general, demonstrated a good correlation between mRNA expression and histone acetylation, but only a limited correlation with the methylated DNA in the promoter region. CONCLUSIONS: We identified 57 up-regulated genes by TSA treatment in hepatoma cells and some of them appeared to be cancer-related genes in hepatomas. The alterations in acetylated histones are likely closely associated with gene expression.
Collection C2: curated gene sets
      CGP: chemical and genetic perturbations
Source publication Pubmed 15336447   Authors: Chiba T,Yokosuka O,Arai M,Tada M,Fukai K,Imazeki F,Kato M,Seki N,Saisho H
Exact source Table 4
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Organism Homo sapiens
Contributed by John Newman (University of Washington)
Source platform HUMAN_SEQ_ACCESSION
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Version history 3.0: Renamed from TSA_HEPATOMA_UP

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