Project description:Cholestatic liver diseases, such as primary sclerosing cholangitis (PSC), are characterized by biliary fibroinflammation. Transforming growth factor-β (TGFβ) activated cholangiocytes release signals that recruit immune cells to drive inflammation and activate myofibroblasts to deposit the extracellular matrix (ECM). TGFβ signaling interacts with RUNX1 transcription factor. However, the role of RUNX1 has not been investigated in biliary fibroinflammation. Here we used mouse large biliary epithelial (MLE) cells that were treated with TGFβ (10ng/mL). ChIP-seq was performed followed by pathway analysis of genes associated with regions of RUNX1 binding.
Project description:Cholestatic liver diseases, such as primary sclerosing cholangitis (PSC), are characterized by biliary fibroinflammation. Transforming growth factor-β (TGFβ) activated cholangiocytes release signals that recruit immune cells to drive inflammation and activate myofibroblasts to deposit the extracellular matrix (ECM). TGFβ regulates stearoyl-CoA desaturase (SCD) in stimulating lipid signaling. However, the role of SCD or its inhibitor, Aramchol, has not been investigated in biliary fibroinflammation. Here we used human transformed H69 cholangiocytes that were treated with TGFβ (10ng/mL) with and without Aramchol acid (30µM) overnight. RNA-seq analysis showed significant inhibition of TGFβ-induced hepatic fibrosis pathways while upregulating peroxisome proliferator-activated receptor (PPAR) signaling by Aramchol.
Project description:We performed SMAD2/3 ChIP-seq analysis in MCF10A MII cells. To validate whether the changes in SMAD2/3 binding to the genome indeed resulted in changes in target gene expression, we performed RNA-seq transcriptome analysis after short and long periods of TGFβ stimulation (0, 1.5h and 16h) in MII cells. In addition, we revealed that JUNB is a critical AP1 component for SMAD2/3 binding after TGFβ stimulation. To assess the significance of JUNB for TGFβ-SMAD-target genes on a genome-wide scale, we also performed RNA-seq transcriptome analysis in JUNB-knock-downed MII cells.
Project description:TGF beta has profound effects on global gene expression changes. To understand the epigenetic changes associated with TGF beta stimulation, we performed ATAC-seq of cholangiocytes to understand the changes in chromatin accessibility associated with TGF beta. We also wanted to determine if H3K9ac played a role in TGF beta induced changes in chromatin accessibility. Therefore, H3K9ac inhibitor CPTH6 was used to treat cells.
Project description:TGF beta has profound effects on global gene expression changes. To understand the epigenetic mechanisms associated with TGF beta stimulation, we performed ChIP-seq of cholangiocytes to understand the changes in histone modifications associated with TGF beta. We choose H3K27ac and H3K9ac, histone modification associated with gene expression. These histone modifications were correlated with SMAD3 occupancy, which is a canonical downstream mediator of TGF beta signaling.