Genome wide mapping of long noncoding (lnc) RNAs in hepatic stellate cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE68108 | GEO | 2016/03/23
SECONDARY ACCESSION(S): PRJNA281757
REPOSITORIES: GEO
Similar Datasets
Project description:Hepatic stellate cells are the primary cell type responsible for development of fibrosis in chronic liver disease. We used directional RNA sequencing (RNA-seq) and chromatin immunoprecipitation and sequencing (ChIP-seq) to identify the lncRNAs expressed in human HSCs. We also identified the lncRNAs that change in expression with differentiation of nonfibrotic quiescent HSCs into fibrotic HSC myofibroblasts and those that are regulated by TGF-beta signaling. ChIP-seq was also performed to identify DNA regions occupied by H3K27ac to define super-enhancers in HSC myofibroblasts. This study identified lncRNAs expressed HSCs that may regulate fibrosis. Analysis of genome-wide lncRNA expression using RNA-seq and ChiP-seq in human HSCs under four different conditions
2016-03-23 | E-GEOD-68108 | biostudies-arrayexpress
Project description:Activation and migration of hepatic stellate cells (HSCs) followed by matrix deposition are characteristics of liver fibrosis. Several studies have shown the importance of hepatocyte and endothelial cell-derived extracellular vesicles (EVs) in liver pathobiology. However, less is known about the role of HSC-derived EVs in liver diseases. In this study, we investigated the molecules released through HSC-derived EVs and whether these can promote fibrosis.
2018-10-18 | PXD007258 | Pride
Project description:Development of liver fibrosis is associated with activation of quiescent Hepatic Stellate Cells (qHSCs) into Collagen Type I-producing myofibroblasts (aHSCs). Cessation of liver injury often results in fibrosis resolution and inactivation of aHSCs/myofibroblasts into a quiescent-like state (iHSCs). To identify the molecular drivers of these HSC phenotypes, we investigated the global gene expression and epigenetic changes in H3K4me2 and H3K27ac marks of primary murine and human HSCs. Motif enrichment identified ETS1/2, GATA4/6, and IRF1/2 transcription factors (TFs) as putative regulators of the HSC lineage identity in murine and human HSCs. shRNA-knockdown of these TFs resulted in marked upregulation of fibrogenic and inflammatory genes and a loss of HSC-specific phenotype in targeted murine HSCs. In support, in vivo HSC-specific ablation of GATA4, GATA6, and ETS1, and ETS1 target genes NF1 (neurofibromin 1) and PPARγ exacerbated development of carbon tetrachloride (CCl4)-induced liver fibrosis in LratΔGATA6, LratETS1+/-, LratΔNF1, and LratΔPPARγ mice (vs wt littermates), but only LratΔGATA6, and LratΔPPARγ mice exhibited a defect in fibrosis resolution due to the lack of HSC inactivation. Therapeutic administration of a PPARγ agonist accelerated regression of liver fibrosis in CCl4-induced wt, but not in LratΔPPARγ mice, suggesting that PPARγ signaling in HSCs is critical for HSC inactivation and regression of liver fibrosis. Common transcription factors determine the phenotype of mouse and human HSCs. Similar to murine HSCs, human aHSCs can revert into a quiescent-like, inactivated phenotype. GATA4, GATA6, and PPARγwere identified as an important driver of human HSC inactivation.
2020-01-27 | GSE140641 | GEO
Project description:Activated hepatic stellate cells (HSC) that transdifferentiate to myofibroblasts in the injured liver are responsible for scar formation that leads to fibrosis and eventually cirrhosis. To investigate the gene expression profile during different stages of this process, we performed serial analysis of gene expression (SAGE), representing a quantitative and qualitative description of all expressed genes. Stellate cells were isolated from human livers and cultured. SAGE was performed on RNA isolated from quiescent, activated and transdifferentiated HSC. Comparison of the three resulting transcriptomes showed that less than 5% of all genes changed significantly in expression. Established markers of liver fibrosis showed enhanced expression in accordance with the transdifferentiation process. In addition, induction was seen for several genes not yet recognized to be involved in liver fibrosis, such as insulin-like growth factor binding proteins (IGFBP) and antagonists of bone morphogenic proteins: follistatin and gremlin. The induction of these genes was validated in vivo in mice developing liver fibrosis. The expression of IGFBPs and gremlin was measurable in the livers of these mice while it was low or undetectable in control mice without liver fibrosis. Since gremlin modulates the activity of bone morphogenic growth factors, it may represent a novel pathway and a target for therapeutic intervention and together with IGFBPs as a specific marker of liver fibrosis. In conclusion, the comparison of the three transcriptomes of (activated) stellate cells reveals novel genes involved in fibrogenesis and provides an appreciation of the sequence and timing of the fibrotic process in liver. Keywords: cell type comparison Human hepatic stellate cells (HSC) were isolated from wedge sections of normal human liver unsuitable for transplantation or from tumor-free human liver after partial hepatectomy as previously reported. Briefly, after a combined digestion with collagenase/pronase, HSC were separated from other liver nonparenchymal cells by ultracentrifugation over gradients of Larcoll (Sigma). The percentage of HSC in these isolates was > 90% as assessed by transmission microscopy, autofluorescence of vitamin A and immunofluorescence of vimentin. Immediately after isolation RNA was extracted for the construction of the SAGE library of quiescent HSC. To obtain activated stellate cells, these cells were cultured for 15 days on plastic culture dishes in modified Dulbecco's medium supplemented with 0.6 U/ml insulin, 2.0 mmol/L glutamine, 0.1 mmol/L nonessential amino acids, 1.0 mmol/L sodium pyruvate, antibiotic antifungal solution (Gibco) and 20% fetal bovine serum. To obtain fully transdifferentiated hepatic stellate cells, or myofibroblasts, the cells were cultured until they had reached passage 6 to 7. Myofibroblast phenotype was confirmed by detection of vimentin and ?-smooth muscle actin using immunofluorescence with monoclonal antibodies from Dako and Sigma, respectively. Medium was refreshed twice a week and at the indicated period RNA was extracted using Trizol (Quiagen)
2006-07-01 | E-GEOD-5022 | biostudies-arrayexpress
Project description:Hepatic stellate cells (HSCs) are the major driving factor in liver fibrosis. Upon liver inflammation caused by alcohol abuse and/or a fatty liver, HSCs transform from a quiescent- into a proliferating, fibrotic phenotype. We study this transformation termed “activation”, using state of the art TIMS-TOF mass spectrometry proteomics, as well as phenotype analysis of the immortalized LX-2 HSC cell line. In our work we employ a simple, yet reliable model of HSC activation via an in-crease in growth media serum concentration (serum activation). Protein network analysis of ac-tivated LX 2 cells reveals an increase in the production of ribosomal proteins and proteins related to migration. Interestingly, we could also observe a decrease in the expression of lipogenic pro-teins and a loss of cytosolic lipid droplets during activation. Especially the downregulation of proteins associated with cholesterol biosynthesis might be a promising target for further study. This work provides an update on HSC activation characteristics using contemporary proteomic and bioinformatic analysis and presents an accessible model for HSC activation.
2022-02-14 | PXD029121 | Pride
Project description:Hepatic stellate cells (HSCs) are considered to be the main source of extracellular matrix in liver fibrosis. During chronic liver injury HSCs become activated and transdifferentiate into pro-fibrotic myofibroblasts. This process is associated with major changes in gene expression as well as intracellular signaling and can potentially be regulated by microRNAs (miRNA). In a recent study we found miRNA-25-3p (miR-25) to be upregulated in serum of children with Cystic Fibrosis (CF) who have no evidence of liver disease, compared to children with CF liver disease and healthy individuals. In this study we investigated the role of miR-25 in HSC biology and on the development of liver disease.
2018-08-28 | GSE119019 | GEO
Project description:Unveiling the regulatory pathways maintaining hepatic stellate cells (HSC) in a quiescent (q) phenotype is essential to develop new therapeutic strategies to treat fibrogenic diseases. To uncover the miRNA-mRNAs regulatory interactions in qHSCs, HSCs were FACS-sorted from healthy livers and activated HSCs were generated in vitro. MiRNA Taqman array analysis showed HSCs expressed a low number of miRNA, from which 46 were down-regulated and 212 up-regulated upon activation. Computational integration of miRNA and gene expression profiles revealed that 66% of qHSCs miRNAs correlated with more than 6 altered targeted mRNAs (17,28±10,7 targets/miRNA), whereas aHSC-associated miRNAs had an average of 1,49 targeted genes. Interestingly, interaction networks generated by miRNA-targeted genes in qHSCs were associated with key HSCs activation processes. Next, selected miRNAs were validated in healthy and cirrhotic human livers and miR-192 was chosen for functional analysis. Down-regulation of miR-192 in HSC was found to be an early event during fibrosis progression in mouse models of liver injury. Moreover, mimic assays for miR-192 in HSCs revealed its role in HSC activation, proliferation and migration. Together, these results uncover the importance of miRNAs in the maintenance of qHSC phenotype and form the basis for understanding the regulatory networks in HSCs. Transcriptomic profile derived from four quiescent hepatic stellate (QHSC), four activated hepatic stellate (AHSC), three liver sinusoidal endothelial (LSEC) and two hepatocytes cells (HEP).
2015-11-23 | E-GEOD-67664 | biostudies-arrayexpress
Project description:Liver fibrosis is characterized by the excessive formation and accumulation of matrix proteins as a result of wound healing in the liver. A main event during fibrogenesis is the activation of the liver resident quiescent hepatic stellate cell (qHSC). Recent studies suggest that reversion of the activated HSC (aHSC) phenotype into a quiescent-like phenotype could be a major cellular mechanism underlying fibrosis regression in the liver, thereby offering new therapeutic perspectives for the treatment of liver fibrosis. The goal of the present study is to identify experimental conditions that can revert the activated status of human HSCs and to map the molecular events associated with this phenotype reversion by gene expression profiling Transcriptomic profiling of primary human quiescent HSCs (qHSCs), in vitro activated HSCs (aHSCs) and in vitro reverted HSCs (rHSCs). The cell types come from different donors (This is detailed in the original manuscript.).
2015-08-12 | E-GEOD-68001 | biostudies-arrayexpress
Project description:We report the RNA sequencing results of human primary hepatic stellate cells (HSCs) treated with DMSO or 1 µM nanchangmycin (NCMC) for 48 hours. We find that multiple HSC activity and liver fibrosis related gene signatures, including ECM-related gene signatures, are negatively enriched in nanchangmycin treated HSCs.
2022-05-18 | GSE180980 | GEO
Project description:Activated hepatic stellate cell (HSC) is the main myofibroblast cell in the liver fibrosis(LF). An important characteristic of the recovery of LF is not only the apoptosis of activated HSCs but also reversal of myofibroblast-like phenotype to a quiescent-like phenotype. Understanding the changes of secreted proteins in the reversion of activated HSCs may provide the broader view of cellular regulatory networks and discover candidate markers or targets for therapeutic strategies of LF. In this study, stable isotope labeling with amino acids (SILAC) combining with LTQ-FT mass spectrometer were performed on in vitro activated HSCs and reverted HSCs to obtain a proteomic view of secretory proteins. In total, 330 proteins showed significant differences in reverted HSCs. Among these, 109 up-regulated proteins were mainly involved in amino acid metabolism pathway and glucose metabolism pathway using GeneGO/MetaCore software, while 221 down-regulated proteins are closely associated with HSCs activation, such as cytoskeleton remodeling, chemokines and cell adhesion. Additionally, a set of novel proteins associated with HSCs activation and reversion were validated by Western blotting in the cell secretion and in the sera of LF, including Vitronectin, laminin beta 1(LAMB1) and Ubiquitin conjugation factor E4B(UBE4B). Our study provided the valuable insight into the mechanisms in the reversion of activated HSCs and identified some potential biomarkers of LF in clinical studies.
2014-08-11 | PXD000773 | Pride