Project description:a RNA transcriptome sequencing analysis was performed in SNU-668 erastin-resistant cells that were transfected with shRNA-SOX13 or control shRNA
Project description:Deubiquitinating enzymes (DUBs) are divided into seven subgroups based on sequence and structure and perform the roles of mediating the deubiquitination of substrate proteins, regulating protein function, and participating in various cellular life activities. Among them, the ubiquitin-specific protease family (USP) is the DUB subtype with the most members and structural diversity discovered so far. USP48 is a member of the USP family of ubiquitin-specific proteases and has been found to promote glioblastoma by deubiquitinating the Gli1 transcription factor and to promote the progression of non-small-cell lung cancer through inhibition of the Wnt/β-catenin signaling pathway. We used microarrays to detail changes in gene expression regulated by USP48 overexpression in HCC cells.
Project description:RNA transcriptome sequencing analysis was performed in SNU-668 Erastin-resistant cells and SNU-668 parental cells, SNU-484 RSL3-resistant cells and SNU-484 parental cells
Project description:Human SNU cell lines derived from hepatocellular carcinomas associated with chronic hepatitis B virus (HBV) infection were examined. The analysis of intracellular RNA and DNA markers of HBV replication and examination of HBV RNA reads coverage of selected regions on HBV-related RNAs and polyadenylation positions within HBV sequence using RNA-sequencing suggested absence of HBV replication in SNU-423, SNU-368 SNU-398, SNU-182, SNU-449, SNU-475, SNU-354, SNU-739 and SNU-387 cells, while SNU-761 and SNU-886 still could maintain residual HBV replication. The undetectable intracellular HBV core antigen (HBcAg) and absence of significant levels of secreted core-associated and virion-associated HBV DNA confirmed the absence or profound suppression of HBV replication in parental SNU cell lines. Various 5'-human-HBV-3' and 5'-HBV-human-3' RNAs transcribed from integrated HBV DNA were found in most of SNU cell lines. The 5'-HBV-human-3' junctions suggested that several SNU cell lines could generate 5'-HBV-human-3' RNAs encoding HBV envelope proteins. The known and novel spliced HBV RNAs were detected in SNU-886, SNU-739, SNU-387, SNU-761, and SNU-354 cells. At least some of them were generated independently of HBV replication. All SNU cell lines could not support efficient HBV replication after transfection with the vector initiating efficient HBV replication in Huh7 cells. This was reflected by three distinct accumulation patterns of HBV replication markers, undetectable intracellular HBcAg, and by the lack of considerable levels of secreted core-bound and virion-associated HBV DNA. Overall, SNU cell lines represent valuable model systems for detailed analysis of integrant-transcribed HBV RNAs, spliced HBV RNAs, and mechanisms of suppression of HBV genome replication.
Project description:Transforming Growth Factor beta (TGF-beta) is a pleiotropic cytokine playing a key role in liver carcinogenesis. The goal of this study was to identify genes differentially expressed in hepatocellular carcinoma cell lines PRC/PRF/5 and SNU-449 after a treatment with TGF-beta and/or Galunisertib, an inhibitor of the type I TGF-beta receptor (TGFBRI). Thus, cells were treated for 16 hours with 1 ng/mL recombinant human TGF-β1 (R&D Systems, Minneapolis, MN) and/or 10 μM LY2157299 (Sigma-Aldrich, St. Louis, MO) after overnight serum starvation. Gene expression profiling was performed using Agilent SurePrint G3 Human GE 8x60K microarrays.
Project description:Transcriptional profiling of human hepatocarcinoma comparing Huh-7 and SNU-739. Two-condition experiment, normalized ratio represented by Huh-7/SNU-739. Biological replicates: 2 Huh-7 replicates, 2 SNU-739 replicates.
Project description:a microarray analysis of long noncoding RNAs was performed in exosomes from SNU-668 Erastin-resistant cells and parental SNU-668 cells