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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Relationship between Differential Hepatic microRNA Expression and Decreased Hepatic Cytochrome P450 3A Activity in Cirrhosis

ABSTRACT: Background and Aim: Liver cirrhosis is associated with decreased hepatic cytochrome P4503A (CYP3A) activity but the pathogenesis of this phenomenon is not well elucidated. In this study, we examined if certain microRNAs (miRNA) are associated with decreased hepatic CYP3A activity in cirrhosis. Hepatic CYP3A activity and miRNA microarray expression profiles were measured in cirrhotic (n=22) and normal (n=12) liver tissue. Hepatic CYP3A activity was measured via midazolam hydroxylation in human liver microsomes. Additionally, hepatic CYP3A4 protein concentration and the expression of CYP3A4 mRNA were measured. Analyses were conducted to identify miRNAs which were differentially expressed between two groups but also were significantly associated with lower hepatic CYP3A activity. Liver tissue was collected from individuals with established cirrhosis who were awaiting liver transplantation (n=22) at the time of their liver transplantation procedure in the operating room. Normal liver tissue (n=12) was obtained from patients undergoing liver resection for metastatic/benign liver lesions with no underlying chronic liver disease

ORGANISM(S): Homo sapiens

SUBMITTER: Chirayu Goswami

PROVIDER: E-GEOD-49012 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Relationship between Differential Hepatic microRNA Expression and Decreased Hepatic Cytochrome P450 3A Activity in Cirrhosis

Project description:Background and Aim: Liver cirrhosis is associated with decreased hepatic cytochrome P4503A (CYP3A) activity but the pathogenesis of this phenomenon is not well elucidated. In this study, we examined if certain microRNAs (miRNA) are associated with decreased hepatic CYP3A activity in cirrhosis. Hepatic CYP3A activity and miRNA microarray expression profiles were measured in cirrhotic (n=22) and normal (n=12) liver tissue. Hepatic CYP3A activity was measured via midazolam hydroxylation in human liver microsomes. Additionally, hepatic CYP3A4 protein concentration and the expression of CYP3A4 mRNA were measured. Analyses were conducted to identify miRNAs which were differentially expressed between two groups but also were significantly associated with lower hepatic CYP3A activity.

2013-08-15 | GSE49012 | GEO

Identification of microRNAs specifically expressed in HCV-associated hepatocellular carcinoma

Project description:Background: Several studies have investigated the association of miRNAs with hepatocellular carcinoma (HCC) but the data are not univocal. Methods: We performed a microarray study of miRNAs in hepatitis C virus (HCV)-associated HCC and other liver diseases and healthy conditions. Results and Conclusions: The simultaneous comparison of different liver diseases and normal livers allowed the identification of 18 miRNAs exclusively expressed in HCV-associated HCC, with sensitivity and specificity values of diagnostic-grade. A total number of 76 liver specimens obtained from 43 patients were analyzed: 26 liver specimens obtained from 10 patients with HCV-associated HCC, including 9 specimens from the tumor area (HCC) and 17 specimens from the surrounding non-tumorous tissue affected by cirrhosis (HCC-CIR); 18 specimens from 10 patients with HCV-associated cirrhosis without HCC (CIR); 13 specimens from 4 patients with HBV-associated acute liver failure (ALF); 12 specimens from 12 liver donors (LD); and 7 from normal liver of 7 subjects who underwent hepatic resection for liver angioma (NL).

2013-02-20 | E-GEOD-40744 | biostudies-arrayexpress

Mouse Liver LC-MS/MS LNA miR-676 treated dbdb mice

Project description:Over 40 % of microRNAs are located in introns of coding genes, and many intronic microRNAs are co-regulated with their host genes. In such cases of co-regulation, the products of host genes and their intronic microRNAs can cooperate to coordinately regulate biologically important pathways. Therefore, we screened intronic microRNAs dysregulated in liver of obese mouse models to identify previously uncharacterized coding host genes that may contribute to the pathogenesis of obesity-associated insulin resistance and type 2 diabetes mellitus. Our approach identified that expression of both Ectodysplasin A (Eda), the causal gene of X-linked hypohidrotic ectodermal dysplasia (XLHED; MIM 305100) and its intronic microRNA, miR-676, was strongly increased in liver of obese mouse models. Moreover, hepatic EDA expression is increased in obese human subjects, reduced upon weight loss, and its hepatic expression correlates with systemic insulin resistance. Eda expression in murine liver is controlled via PPARg activation, increases in circulation and promotes JNK activation and inhibitory serine phosphorylation of IRS1 in skeletal muscle. Consistently, bi-directional modulation of hepatic Eda expression in mouse models affects systemic glucose metabolism with alterations of muscle insulin signaling, revealing a novel role of EDA as an obesity-associated hepatokine, which impairs insulin sensitivity in skeletal muscle.

2017-11-14 | PXD006573 | Pride

RNA-seq of human liver biopsies from patients with NAFLD, patient with cirrhosis, and healthy controls under both fasting and postprandial conditions.

Project description:The data provides a unique opportunity for investigating the differences in the hepatic transcriptome in health and liver disease through studying gene expression in a cohort of patients with NAFLD, cirrhosis, and healthy controls. The randomization of patients and healthy controls between the fasting and fed state further enables exploration of differences in the liver transcriptome.

2023-08-27 | E-MTAB-12807 | biostudies-arrayexpress

Impact of Microbiome on Hepatic Drug Processing Genes in Mice during Pregnancy

Project description:While microbiome and pregnancy are known to alter drug disposition, the interplay of the two physiological factors to impact expression and/or activity of drug processing genes (DPGs) has yet to be elucidated. This study aimed to investigate the effects of microbiome on host hepatic DPGs during pregnancy using conventional (CV) and germ-free (GF) mice. Four groups of female mice were used, namely CV non-pregnant (CVNP), GF non-pregnant (GFNP), CV pregnant (CVP), and GF pregnant (GFP) mice. Pregnant mice examined were on gestation day 15. Transcriptomic and targeted proteomics of hepatic DPGs were profiled using a multi-omics approach. Plasma bile acid and steroid hormone levels were quantified using LC-MS/MS. Cyp3a activities were measured by mouse liver microsome incubations. While the overall trend in pregnancy-induced changes in the expression or activity of hepatic DPGs in CV and GF mice was similar, significant differences in the magnitude of changes were observed. For certain genes, we noticed opposite effects of pregnancy on mRNA and protein expression of DPGs in both CV and GF mice. For instance, the mRNA levels of Cyp3a11, the murine homolog of human CYP3A4, were decreased by 1.7-fold and 3.3-fold by pregnancy in CV and GF mice, respectively. However, the protein levels of Cyp3a11 were increased similarly ~2-fold by pregnancy in both CV and GF mice. Yet, microsome incubations revealed a marked induction of Cyp3a activity by pregnancy that was >5-fold greater in CV mice than that in GF mice. Plasma bile acid and steroid hormone levels were also significantly altered by microbiome and pregnancy, respectively, which may contribute to the differential effects of pregnancy in CV and GF mice. This is the first study to show that microbiome can alter hepatic DPGs in pregnancy.

2020-08-26 | GSE143391 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of miRNAs in hepatic fibrosis and normal tissues.

Project description:Aim: Hepatic fibrosis is a major worldwide medical problem and can develop into liver cirrhosis and hepatocellular carcinoma(HCC). Until now, there are no effective drugs for liver ?brosis because the molecular mechanism of progression of liver fibrosis is not fully understood. MicroRNAs (miRNAs) are an important class of small non-coding functional RNAs that play a key role in many biological processes. The purpose of this study was to clarify how the aberrant expression of miRNAs participates in development of the liver fibrosis in rat liver fibrosis model. Methods: Fibrotic and paired normal liver tissues were collected and assesssed by deep sequencing technology. MiRNA pro?ling results were validated by quantitative real-time polymerase chain reaction (qRT-PCR) and bioinformatics was used to predict miRNA targets. Results: Nine deregulated miRNAs were induced in porcine serum (PS)-induced hepatic fibrosis versus normal liver. Further analysis revealed several signaling pathways (e.g., gap junction and neuroactive ligand-receptor interaction) may be associated with hepatic fibrogenesis. Conclusion: Several miRNAs are dysregulated in PS-induced hepatic fibrosis and seem to be closely associated with hepatic fibrogenesis. These results provide an experimental basis for understanding the mechanism of hepatic fibrosis. We sequenced two samples, including case and control. Each sample has two replicates.

2015-06-04 | E-GEOD-54028 | biostudies-arrayexpress

TGF-beta-mediated microRNA expression in breast cancer cells

Project description:We utilized 3D-organotypic cultures whose physical properties were altered by inclusiong of type I collagen to create biomechanically rigid microenvironments that approximated those typically observed in primary mammary tumors. Compliant 3D-organotypic cultures were also generated to recapitulate the biomechanical properties of pulmonary microenvironments typically encountered by disseminated breast carcioma cells. The murine 4T1 progression series represents an established model of triple negative breast cancer development and metastasis and consists of isogenically-derived nonmetastatic 67NR, systemically invasive 4TO7, and highly metastatic 4T1 cells that were propagated for 6 days in the absense or presense of TGF-beta in either rigid or compliant 3D-cultures. Afterward, total RNA was extracted and subjected to miRNA profiling. two replicates of each growth and treatment condition for each cell line.

2012-10-31 | E-GEOD-41274 | biostudies-arrayexpress

Transcription profiling of rat cirrhotic liver treated with angiogenesis inhibitors

Project description:Background and aims: There are considerable evidences demonstrating that angiogenesis and chronic inflammation are mutually dependent. However, although cirrhosis progression is characterized with a chronic hepatic inflammatory process, this connection is not sufficiently explored as a therapeutic strategy. Therefore, this study was aimed to assess the potential benefits of targeting angiogenesis in cirrhotic livers to modulate inflammation and fibrosis. For this purpose, we evaluate the therapeutic utility of angiogenesis inhibitors. Methods: The in vivo effects of angiogenesis inhibitors were monitored in liver of cirrhotic rats by measuring angiogenesis, inflammatory infiltrate, fibrosis, a-smooth muscle actin (a-SMA) accumulation, differential gene expression (by microarrays), and portal pressure. Results: Cirrhosis progression was associated with a significant enhancement of vascular density and expression of vascular endothelial growth factor-A (VEGF-A), angiopoietin-1, angiopoietin-2 and placental growth factor (PlGF) in cirrhotic livers. The newly formed hepatic vasculature expressed vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1). Interestingly, the expression of these adhesion molecules correlated well with local inflammatory infiltrate. Livers of cirrhotic rats treated with angiogenesis inhibitors presented a significant decrease in hepatic vascular density, inflammatory infiltrate, a-SMA abundance, collagen expression and portal pressure. Conclusion: Angiogenesis inhibitors may offer a potential novel therapy for cirrhosis due to its multiple mechanisms of action against angiogenesis, inflammation and fibrosis in cirrhotic livers. Experiment Overall Design: RNA from liver of 4 non-treated cirrhotic rats or 4 rats treated with angiogenesis inhibitors was hybridized to 8 high-density oligonucleotide microarray (Rat2302, Affymetrix, Santa Clara, CA)

2008-06-15 | E-GEOD-6929 | biostudies-arrayexpress

Regulatory variants in a novel distal enhancer regulate the expression of CYP3A4 and CYP3A5: ATAC-Seq and 4C data from human hepatocytes [ATAC-seq]

Project description:The cytochrome P450 3As (CYP3As) are abundantly expressed in the liver and metabolize many commonly prescribed medications. Their expression is highly variable between individuals with little known genetic cause. Despite extensive investigation, cis-acting genetic elements that control the expression of CYP3As remain uncharacterized. Using chromatin conformation capture (4C assays), we detected reciprocal interaction between a distal regulatory region (DDR) and the CYP3A4 promoter. The DRR colocalizes with a variety of enhancer marks and was found to promote transcription in reporter assays. CRISPR-mediated knockout of the DRR decreased expression of CYP3A4, CYP3A5, and CYP3A7, supporting its role as a shared enhancer regulating the expression of three CYP3A genes. Here we provided data generated from ATAC-Seq analysis of human primary hepatocytes originating from both black and white donors.

2023-06-26 | GSE207590 | GEO

ALD miRNA expression

Project description:Alcoholic liver diseases (ALDs) encompass a broad spectrum of clinical features of alcoholic fatty liver, alcoholic steatohepatitis and cirrhosis, and increased risk of hepatocellular carcinoma. While the toxic effects of alcohol likely result from complex interactions between genes and the environment, the molecular mechanisms of alcohol-induced liver damage remains undefined. Thus, a better understanding of the mechanisms regulating hepatic cell injury may lead to more effective therapeutic approaches for ALD. Here we compared the miRNA expression profile from tissues from control mice and mice receiving intragastric ethanol feeding. Four microarray hybridization studies were performed on three different pairs of liver-derived RNA from intragastric ethanol feeding and normal mice. The miRNAs differentially overexpressed in livers from ethanol fed mice.

2014-10-07 | E-MTAB-2311 | biostudies-arrayexpress

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