Sequencing of HepaRG cells with functional knockout of PXR
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA627103 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11579200_1.fastq.gz | Fastqsanger.gz | |||
| SRR11579200_2.fastq.gz | Fastqsanger.gz | |||
| SRR11579192_1.fastq.gz | Fastqsanger.gz | |||
| SRR11579192_2.fastq.gz | Fastqsanger.gz | |||
| SRR11579193_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: To assess effect of PXR functional knockout
2022-02-10 | GSE149001 | GEO
Project description:The nuclear pregnane X receptor (PXR) regulates the expression of genes involved in the metabolism, hepatobiliary disposition, and toxicity of drugs and endogenous compounds. PXR is a promiscuous nuclear hormone receptor (NHR) with significant ligand and DNA-binding crosstalk with the constitutive androstane receptor (CAR); hence, defining the precise role of PXR in gene regulation is challenging. Here, utilising a novel PXR-knockout (KO) HepaRG cell line, real-time PCR analysis was conducted to determine PXR involvement for a range of inducers. The selective PXR agonist rifampicin, a selective CAR activator, 6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime (CITCO), and dual activators of CAR and PXR including phenobarbital (PB) were analyzed. HepaRG control cells (5F clone) were responsive to prototypical inducers of CYP2B6 and CYP3A4. No response was observed in the PXR-KO cells treated with rifampicin. Induction of CYP3A4 by PB, artemisinin, and phenytoin was also much reduced in PXR-KO cells, while the response to CITCO was maintained. This finding is in agreement with the abolition of functional PXR expression. The apparent EC50 values for PB were in agreement between the cell lines; however, CITCO was ~threefold (0.3 μmol/L vs. 1 μmol/L) lower in the PXR-KO cells compared with the 5F cells for CYP2B6 induction. Results presented support the application of the novel PXR-KO cells in the definitive assignment of PXR-mediated CYP2B6 and CYP3A4 induction. Utilization of such cell lines will allow advancement in composing structure activity relationships rather than relying predominantly on pharmacological manipulations and provide in-depth mechanistic evaluation.
| S-EPMC5045942 | biostudies-literature
Project description:The constitutive androstane receptor (CAR, NR1I3) modulates the transcription of numerous genes involving drug metabolism, energy homeostasis, and cell proliferation. Most functions of CAR however were defined from animal studies. Given the known species difference of CAR and the significant cross-talk between CAR and the pregnane X receptor (PXR), it is extremely difficult to decipher the exact role of human CAR (hCAR) in gene regulation, relying predominantly on pharmacological manipulations. Here, utilizing a newly generated hCAR-knockout (KO) HepaRG cell line, we carried out RNA-seq analysis of the global transcriptomes in wild-type (WT) and hCAR-KO HepaRG cells treated with CITCO, a selective hCAR agonist, phenobarbital (PB), a dual activator of hCAR and hPXR, or vehicle control. Real-time PCR assays in separate experiments were used to validate RNA-seq findings. Our results indicate that genes encoding drug-metabolizing enzymes are among the main clusters altered by both CITCO and PB. Specifically, CITCO significantly changed the expression of 135 genes in an hCAR-dependent manner, while PB altered the expression of 227 genes in WT cells of which 94 were simultaneously modulated in both cell lines reflecting the dual effects of PB on hCAR/PXR. Notably, we found that many genes promoting cell proliferation and tumorigenesis were up-regulated in hCAR-KO cells, suggesting that hCAR may play an important role in cell growth that differs from mouse CAR. Together, our results reveal both novel and known targets of hCAR and support the role of hCAR in maintaining the homeostasis of metabolism and cell proliferation in the liver.
2015-09-30 | GSE71446 | GEO
Project description:Gene expression profile analysis allowed to identify a panel of genes and pathways characteristic of hESC-and HepaRG-derived cholangiocytes. Microarrays were conducted at day 23 and day 10 of differentiation for hESC-Chol and HepaRG-Chol respectively and compared to hESC-HB and HepaRG-HB. Five, four or three independent experiments were performed depending the experimental sample
2013-10-28 | E-GEOD-51791 | biostudies-arrayexpress
Project description:Purpose: To explore the role of PXR signaling in regulating macrophage transcriptome related to atherogenesis Methods: Peritoneal macrophages were isolated from LDLR knockout mice with myeloid specific PXR deficiency (PXRΔMyeLDLR-/-) and their littermates (PXRF/FLDLR-/-). Then the macrophages were treated with a PXR ligand PCN or DMSO control for 12 hr. Total RNA was extracted for RNAseq Results: PCN-mediated PXR activation induced 439 differentially expressed genes (DEGs) with false discovery rate (FDR) < 5% and fold change >1.5 in control macrophages. By contrast, PCN only induced 38 DEFs in PXR-deficient macrophages. Conclusions: These results indicate that PXR signaling may affect many genes in macrophages related atherosclerosis development.
2020-02-22 | GSE145719 | GEO
Project description:Propiconazole is a triazole fungicide previously shown to induce triglyceride accumulation in human liver HepaRG cells, potentially via activation of the Pregnane X Receptor (PXR). However, whether propiconazole can disrupt hepatic and whole-body metabolism in vivo is currently unknown. Therefore, we aimed to examine the metabolic effects of propiconazole in the context of metabolic dysfunction-associated steatotic liver disease (MASLD), obesity, and insulin resistance. To this end, male C57BL/6J mice were fed a high-fat diet for 20 weeks. During the last 10 weeks, mice additionally received vehicle, 0.04, 30, or 100 mg/kg body weight (bw)/day propiconazole via oral gavage. High-dose propiconazole, but not low or intermediate dose, reduced body weight gain and adipose tissue weight in obese mice. Mice receiving high-dose propiconazole displayed improved glucose tolerance and reduced levels of plasma triglycerides and cholesterol. Propiconazole dose-dependently increased liver weight and triglyceride levels and at high dose caused signs of hepatic inflammation. RNA sequencing on the liver revealed that propiconazole mainly induced PXR target genes. At intermediate and high-dose, propiconazole induced pathways related to cell-cell interactions and inflammation, while oxidative phosphorylation was repressed by propiconazole. Comparison of gene regulation in wildtype and PXR knockout primary hepatocytes as well as gene reporter assays confirmed the activation of PXR by propiconazole. All in all, our data underscore the capacity of propiconazole to activate PXR in the liver and thereby promote the development of hepatic steatosis in vivo.
2025-01-07 | GSE285121 | GEO
Project description:Gene expression profile analysis allowed to identify a panel of genes and pathways characteristic of hESC-and HepaRG-derived cholangiocytes.
2013-10-28 | GSE51791 | GEO
Project description:To investigate the role of the nuclear receptors CAR (constitutive androstane receptor) and PXR (Pregnane X receptor) in mediating the effects of non-genotoxic carcinogens, groups of mice humanised or deleted for CAR and PXR were treated with 1,4-Dichlorobenzene or cyproterone acetate for 3d and liver tissue harvested for expression profiling. Control groups were treated with appropriate vehicles.
2018-04-27 | GSE68365 | GEO
Project description:Primary human hepatocytes, the gold standard for in vitro studies of liver-related functions, suffer from uncertain availability and high variability in cell activity. Over years, a number of alternative hepatic cell lines have lost major liver-like functions, but not HepaRG cells. Therefore, their increasing use worldwide today arouses the need for establishing a reference functional status of differentiated HepaRG cells known as HPR116, which originate from the initial cell bank. Deep proteome and secretome analyses enabled us to show that they nicely express, at levels generally close to those in primary hepatocytes, master regulators of the hepatic phenotype, structural elements that ensure liver-like polarisation and factors supporting their transdifferentiation properties. Their highly differentiated status, mitochondrial functionality, hepatokine secretion ability and response to insulin was verified. Overall, the HepaRG cell system appears as robust surrogate cell system to primary hepatocytes, versatile enough to study not only xenobiotic detoxification but also the control of hepatic energy metabolism, secretory function and disease-related signalling pathways.
2019-02-27 | PXD010304 | Pride
Project description:Purpose: to investigate transcriptomal differences between wild-type and SXR/PXR knockout mice and the impact of PCB-153 exposure to both strains to help reveal the mechanism behind the phenotype of hemolytic anemia observed in SXR knockout mice exposed to PCB-153
2019-08-17 | GSE135916 | GEO