MicroRNA Expression profiles of mature hepatocytes and foetal liver progenitor cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Iain Gallagher
PROVIDER: E-GEOD-57833 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Human liver progenitor cells (LPCs) show therapeutic potential, however, their in vitro culture results in inadequate function and phenotypic instability reflecting incomplete understanding of in vivo processes. Foetal LPCs capable of differentiation to a hepatocyte phenotype were isolated and mRNA expression profiling carried out using Affymetrix HGU133plus2 microarrays. This was compared to profiles from mature human hepatocytes and human embryonic stem cells undergoing hepatocytic differentiation. Foetal LPCs exhibit a distinct molecular profile consistent with a stem cell signature, cell division, and some liver-specific functions. 9 independent samples of second trimester liver progenitor cells were profiled along with 3 independent mature hepatocyte samples and 3 each of embryonic stem cells at day 9 and day 17 of differentiation to hepatocyte like cells.
2015-05-01 | E-GEOD-57812 | biostudies-arrayexpress
Project description:Human liver progenitor cells (LPCs) show therapeutic potential, however, their in vitro culture results in inadequate function and phenotypic instability reflecting incomplete understanding of in vivo processes. Foetal LPCs capable of differentiation to a hepatocyte phenotype were isolated and mRNA expression profiling carried out using Exiqon miRCURY microarrays. This was compared to profiles from mature human hepatocytes. Foetal LPCs exhibit a distinct miRNA profile consistent with a stem cell signature, cell division, and some liver-specific functions.
2015-05-01 | GSE57833 | GEO
Project description:Human liver progenitor cells (LPCs) show therapeutic potential, however, their in vitro culture results in inadequate function and phenotypic instability reflecting incomplete understanding of in vivo processes. Foetal LPCs capable of differentiation to a hepatocyte phenotype were isolated and mRNA expression profiling carried out using Affymetrix HGU133plus2 microarrays. This was compared to profiles from mature human hepatocytes and human embryonic stem cells undergoing hepatocytic differentiation. Foetal LPCs exhibit a distinct molecular profile consistent with a stem cell signature, cell division, and some liver-specific functions.
2015-05-01 | GSE57812 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-05-01 | E-GEOD-57878 | biostudies-arrayexpress
Project description:T cells were collected from four healthy donors using heparin anti-coagulant, diluted with equal amounts of PBS EDTA, then layered over Lymphoprep and spun to collect PBMCs. CD4+ T cells were purifed using the Miltenyi positive selection magnetic labeling kit. Cells were resuspended in RPMI (Invitrogen) with 10% FCS amd 50 U/ml IL-2 (Immunotools), and 3.5x105 plated out per well in 48 well plates, coated overnight with 2 µg/ml anti-CD3 and either anti-CD28 or anti-CD46. Purity was assessed by flow cytometry and was in all cases ⥠95%. RNA was purified from a set of unactivated cells before plating, to represent the resting, 0 hr time point samples. For early activation samples, CD28 or CD46 co-stimulated cells were harvested 2 hrs after plating. Then, 36 hours after plating, the remaining CD46-stimulated cells were harvested and labeled for IL-10 or IFN-g secretion using the Miltenyi cytokine detection kits, according to manufacturerâs instructions. Cells were then sorted into separate cytokine-secreting populations (IFN-g+/IL-10â, IFN-g+/IL-10+, and IFN-gâ/IL-10+) using a BD biosciences FACS machine.RNA from separate populations was labeled using the Hy3 microRNA (miRNA) Power labeling kit (Exiqon) and hybridised to an LNA (locked nucleic acid)-based miRCURY miRNA microarray slides (Exiqon, version 11) using a Maui hybridisation chamber (BioMicrosystems). Spot signals were acquired with an Agilent array scanner and GenePix Pro 4.1 was used for annotation (mirBase 14.0), signal processing and quantification using default background subtraction.
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Project description:The cellular source for hepatocyte transplantation and liver regeneration in chronically hepatic diseases is a fundamental topic in liver biology. A successful therapeutic approach based on a benificial stem/progenitor cells would involve replacing damaged cells or restoring homeostasis to the areas that underlie the fibrotic response. This study aims to isolate and culture hepatocyte and non-parenchymal cells derived liver progenitor-like cells (HepLPCs and NPC-LPCs) to identify a beneficial cell sources for cell-based therapy against chronic liver injury. Two types of lineage tracing models including tdTomato mice with AAV8-TBG-Cre and AlbCreERT/R26GFP were purified for hepatocytes and non-parenchymal cells respectively, and cultured for transition to progenitor-like cells (LPCs) in TEM. The differences between them were clarified by RNA sequencing, suggesting that HepLPCs retaining basal levels of hepatic function and transcription factors (TFs), including Foxa3. Organoids and 3D hepatic spheroids culturing systems were used for further analysis of bile duct and hepatic functioning diversity. When transplanting in mice with CCL4 treatment, HepLPCs displayed the characteristics of TFs regulatory reactivation and physiological balance restoration, resulting in a significant improvement in liver fibrosis compared with NPC-LPCs, which are crucial for liver regeneration in the treatment of patients with a broad range of hepatic fibrosis.
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Project description:Background - Hepatocellular carcinomas (HCCs) are heterogeneous tumors with respect to etiology, cell of origin and biology. The course of the disease is unpredictable and is in part dependent on the tumor microenvironment. One of the microenvironmental factors is hypoxia, which is known to promote aggressiveness in other malignant tumors. We hypothesized that certain regions in HCC exist with chronic hypoxia and a characteristic gene expression pattern. Moreover, during the development of HCC there is an important contribution of this chronic hypoxia on prognosis via this gene expression. Until now, most research has been performed in acute hypoxic models (< 24 hours). Methods – Human hepatoblastoma cells HepG2 were cultured in either normoxic (20% O2) or hypoxic (2% O2) conditions for 72 hrs, the time it takes to adapt to chronic hypoxia. After 3 days the cells were harvested and analyzed by microarray technology. The highly significant differentially expressed genes were selected and used to assess the clinical value of our in vitro chronic hypoxia gene signature in four published patient studies. Three of these independent microarray studies on HCC patients were used as training sets to determine a minimal prognostic gene set and one study was used for validation. Gene expression analysis and correlation with clinical outcome was assessed with the bioinfomatic method of Goeman et al (). Results – In the HepG2 cells, 3592 genes were differentially expressed in cells cultured at 2% oxygen for 72 hrs. Out of these, 265 showed a high significant change (2-fold change and p=0.0001). The level of gene expression after 72 hrs was different from the acute hypoxic response (during the first 24 hours) and represented chronicity. Using computational methods we identified 7 out of the 265 highly significant genes that showed correlation with prognosis in all three different training sets and this was independently validated in a 4th dataset. With our approach we could include the largest number of HCC patients in one single study. Conclusion – We identified a 7-gene signature, which is associated with chronic hypoxia and predicts prognosis in patients with HCC. In the future this signature could be used as a diagnostic tool. In addition, chronic hypoxia gene expression information can be used in the search for new therapeutic targets. Two conditions were compared and each sample has a biological replicate. Samples are hybridized in dye-swap, resulting in 4 hybridizations.
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Project description:Analyze the gene expression profile of BMDC before and after nkt cell modulation. Total RNA was extracted from CD11c cells with TRIzol Reagent, purified with RNeasy Kit (Qiagen) and subsequently amplificated using the one cycle target labeling kit according to the AffymetrixGeneChip® Expression Analysis Technical Manual (Affimetrix). Fragmented cRNAs were probed to AffymetrixGeneChip® Mouse Genome 430 2.0 arrays for 16 hours at 45°C in the AffymetrixHybridization Oven 640. The arrays were then washed and stained with streptavidin-phycoerythrin using the AffymetrixFluidic Station 450/250 and scanned using the AffymetrixGeneChip® Scanner 3000. The images were analyzed using GCOC® Software and comparison analyses carried out according to the instructions provided by Affymetrix. Each experiment was performed in triplicates and repeated two times. Data handling was mainly done using Bioconductor Software. The probe set-based summary data were log transformed and normalized for probe set intensity-dependent biases. The identification of differentially expressed genes was addressed using linear modeling approach and empirical Bayer methods together with false discovery rate correction of the p-value. We considered a gene to be differentially increased in nkt-DCs only if its expression intensity was significantly changed (p<0.001) compared to Untr-DCs.
2010-03-03 | E-GEOD-18547 | biostudies-arrayexpress
Project description:The ability to purify to homogeneity a population of hepatic progenitor cells from adult liver is critical for their characterization prior to any therapeutic application. As a step in this direction, we have utilized gene profiling of a bipotential liver cell line from dpc 14 mouse embryonic liver to catalog genes expressed by liver progenitor cells. These cells, known as Bipotential Mouse Embryonic Liver (BMEL) cells, proliferate in an undifferentiated state and are capable of differentiating into hepatocyte-like and cholangiocyte-like cells in vitro. Upon transplantation, BMEL cells are capable of differentiating into hepatocytes and cholangiocytes in vivo. Microarray analysis of gene expression in the 9A1 and 14B3 BMEL cell lines grown under proliferating and differentiating conditions was used to identify cell surface markers preferentially expressed in the bipotential undifferentiated state. This analysis revealed that proliferating BMEL cells express many genes involved in cell cycle regulation whereas differentiation of BMEL cells by cell aggregation causes a switch in gene expression to functions characteristic of mature hepatocytes. In addition, microarray data and protein analysis indicated that the Notch signaling pathway could be involved in maintaining BMEL cells in an undifferentiated stem cell state. Using GO annotation, a list of cell surface markers preferentially expressed on undifferentiated BMEL cells was generated. One marker, Cd24a, is specifically expressed on progenitor oval cells in livers of DDC treated animals. We therefore consider Cd24a expression a candidate molecule for purification of hepatic progenitor cells. Experiment Overall Design: RNA was extracted from two independently isolated BMEL cell lines (9A1 and 14B3) after culture under three conditions (basal, aggregate 1 day, and aggregate 5 days). Duplicate biological replicates were collected for each cell line:culture condition combination for a total of 12 samples. Samples were biotin-labeled, hybridized to mouse 430 2.0 chips, and scanned according to established Affymetrix protocols.
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