Project description:Smad2/3 are transcription factors that engage in TGF-beta-induced transcription. We determined and analyzed HepG2 and Hep3B-specific Smad2/3 binding sites by ChIP-chip. We used expression microarrays to compare the Smad2/3 and HNF4alpha binding sites identified by ChIP-chip or ChIP-seq, respectively, to TGF-beta-induced gene expressions. HepG2 cells were transfected with control or HNF4A siRNAs and treated with 3 ng/ml TGF-beta for 0, 1.5 and 24 h (6 samples in total, no replicates). Total RNA was extracted and expression microarray analysis was performed as described in the protocols.
Project description:Smad2/3 are transcription factors that engage in TGF-beta-induced transcription. We determined and analyzed HepG2 and Hep3B-specific Smad2/3 binding sites by ChIP-chip. We used expression microarrays to compare the Smad2/3 and HNF4alpha binding sites identified by ChIP-chip or ChIP-seq, respectively, to TGF-beta-induced gene expressions.
Project description:Increased fatty acid (FA) is often observed in highly proliferative tumors, contributing to promoting proliferation of tumor cells. FA affects secreted factors from tumor cells, which can modulate tumor microenvironment in favor of tumor survival. However, the secreted factors affected by the increased FA have not been systematically explored. Here, we performed comprehensive secretome profiling of oleate-treated and untreated HepG2 cells. Comparison of the secretomes identified 349 differentially secreted proteins (DSPs; 145 up-regulated and 192 down-regulated) in oleate-treated samples, compared to untreated samples. Functional enrichment and network analyses of the DSPs revealed that the 145 up-regulated secreted proteins by oleate treatment were mainly associated with cell proliferation-related processes, such as lipid metabolism, inflammatory response, and ER stress. Based on the network models of the DSPs, we selected four up-regulated secreted proteins (MIF, THBS1, PDIA3, and APOA1) that can represent such processes related to cell proliferation. Thus, our results provided a secretome profile indicative of oleate-induced proliferation of HepG2 cells.
Project description:The TCF7L2 transcription factor is linked to a variety of human diseases, including type 2 diabetes and cancer. One mechanism by which TCF7L2 could influence expression of genes involved in diverse diseases is by binding to distinct regulatory regions in different tissues. To test this hypothesis, we performed ChIP-seq for TCF7L2 in 6 human cell lines. We identified 116,000 non-redundant TCF7L2 binding sites, with only 1,864 sites common to the 6 cell lines. Using ChIP-seq, we showed that many genomic regions that are marked by both H3K4me1 and H3K27Ac are also bound by TCF7L2, suggesting that TCF7L2 plays a critical role in enhancer activity. Bioinformatic analysis of the cell type-specific TCF7L2 binding sites revealed enrichment for multiple transcription factors, including HNF4alpha and FOXA2 motifs in HepG2 cells and the GATA3 motif in MCF7 cells. ChIP-seq analysis revealed that TCF7L2 co-localizes with HNF4alpha and FOXA2 in HepG2 cells and with GATA3 in MCF7 cells. Interestingly, in MCF7 cells the TCF7L2 motif is enriched in most TCF7L2 sites but is not enriched in the sites bound by both GATA3 and TCF7L2. This analysis suggested that GATA3 might tether TCF7L2 to the genome at these sites. To test this hypothesis, we depleted GATA3 in MCF7 cells and showed that TCF7L2 binding was lost at a subset of sites. RNA-seq analysis suggested that TCF7L2 represses transcription when tethered to the genome via GATA3. Our studies demonstrate a novel relationship between GATA3 and TCF7L2, and reveal important insights into TCF7L2-mediated gene regulation. RNAseq analysis of MCF7 cells transfected with siCONTROL, siTCF7L2 or siGATA3. ChIP-seq analysis of H3K27ac, H3K4me1, H3K27me3, H3K9me3 in MCF7 cells; H3K4me1 and H3K27ac in HCT116 cells.
Project description:Here we report a comprehensive proteomic analysis of purified human hepatocytes and a human hepatoma cell line HepG2. The complete dataset comprises 9,400 proteins and provides quantitative depiction of the proteomes of hepatocytes and HepG2 cells at the protein titer and copy number dimensions.
Project description:We used microarrays to identify a transcriptional signature of oxidative stress induced senescence in a hepatocyte cell line (HepG2) by globally assessing differential gene expression after treatment with 0.5mM of H2O2 for 60 minutes, compared to nontreated cells as a control. We performed genome-wide comparison of gene expression and identified genes that are differentially expressed in senescent HepG2 cells relative to untreated cells, 4 biological replicates per condition
Project description:Statins are cholesterol lowering drugs that inhibit cholesterol synthesis and reduce intracellular sterol levels, stimulating a transcriptional response. We sought to identify genes that were statin responsive in the HepG2 human hepatoma cell line and determine which of those genes were sterol responsive using sterol addback conditions. Though the vast majority of statin responsive genes are sterol responsive, we identified a subset of statin responsive genes whose gene expression changes are not reversed upon sterol addback.
Project description:The farnesoid X receptor (FXR) is a nuclear receptor activated by bile acids that regulates bile acid metabolism, glucose and cholesterol homeostasis. FXR is expressed as four isoforms (α1-4), and their relative abundance is tissue specific. Human livers express predominantly FXR isoforms α1 and α2. From mouse studies we know that the FXR agonist obeticholic acid (OCA) regulates expression of many genes in the liver. However, there is currently no data on the effects of OCA on FXR isoform selective gene regulation. This is particularly relevant since the relative FXR isoform amounts in the liver are regulated by general bioenergetic cues (Correia JC et al. 2015). In this study we investigate the effect of variations in FXR isoforms α1 or α2 expression on HepG2 cell lines response to treatment with OCA.