Ena-DATASET-UMCU-02-05-2018-11:13:59:140-20 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001004105 | EGA |
REPOSITORIES: EGA
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Project description:Intrahepatic cholangiocyte organoid clone from patients with chronic alcohol consumption, NASH (nonalcoholic steatohepatitis), and PSC (primary sclerosing cholangitis)
| EGAD00001007775 | EGA
Project description:Non‑alcoholic steatohepatitis (NASH) is a pathological condition of the liver in which hepatocyte steatosis, invasion of inflammatory cells and hepatic injury occur without alcohol abuse. Despite the known risk of liver cancer and liver fibrosis that may progress to liver cirrhosis that exists with NASH, an understanding of related gene expression and associated functional changes remains insufficient. The present study used a mouse model of NASH induced by a high‑fat diet to examine gene expression in the liver and to search for transcripts that could predict early liver fibrosis in the future. Mice fed a high‑fat diet for 2 weeks showed typical NASH liver histology by hematoxylin and eosin staining, and increased fibrosis was confirmed by Sirius red staining after 6 weeks. Functional changes associated with liver damage, liver inflammation, liver steatosis and liver fibrosis were predicted by toxicological ontology analysis using Ingenuity Pathways Analysis. Downregulated microRNA (miR)‑21 and upregulated collagen type III α1 mRNA in the liver and upregulated exosomal miR‑21 in serum of mice fed a high‑fat diet for 1 and/or 2 weeks were confirmed by reverse transcription‑quantitative PCR, suggesting that these changes occur prior to histological confirmation of fibrosis. Therefore, it may be possible to predict future liver fibrosis by analyzing fibrosis‑related genes that shift prior to pathological findings.
2022-06-01 | GSE200409 | GEO
Project description:Background & Aims: Little is known about the molecular pathophysiology of non-alcoholic steatohepatitis (NASH). Methods: Total RNA from NASH livers and normal healthy livers were analyzed on a whole genome DNA oligo microarray. The microarray data were validated by real-time quantitative PCR analysis for many of the genes of interest. Results: Genes related to liver inflammation and fibrosis were found to be elevated in NASH livers compared to normal livers. The most striking finding is the increased gene transcription of alcohol dehydrogenase (ADH) genes, genes for catalase and cytochrome P450 2E1, and aldehyde dehydrogenase genes. Transcription of genes TLR4, LBP, CD14 and MD-2 were not significantly elevated in NASH livers. Conclusions: The augmented activity of all the available genes of the pathways for alcohol catabolism suggest that 1) there is a significant increase of alcohol in the circulation of NASH patients; 2) there is a high priority for the NASH livers to scavenge alcohol from the circulation. It was reported that gastrointestinal bacteria are the major cause of elevated alcohol in the circulation of obese animals. Mechanisms for alcohol to induce steatosis and oxidative stress were established decades ago. Our data is the first human evidence to support Diehl et al’s hypothesis that alcohol is an important factor in the development of non-alcoholic fatty liver diseases.
2009-08-06 | GSE17470 | GEO
Project description:Inflammatory liver disease increases risk of developing liver cancer. The mechanism through which liver disease induces tumorigenesis remains unclear, but is thought to occur via increased mutagenesis. Here, we performed whole-genome sequencing on clonal stem cell organoid lines derived from explanted diseased liver cells from patients with chronic alcohol consumption, non-alcoholic steatohepatitis NASH, and primary sclerosing cholangitis PSC. Surprisingly, we find that these precancerous liver disease conditions do not result in a detectable increased accumulation of mutations, nor altered mutation types in normal stem cells in the liver, which contrasts with typical mutational signatures found in liver tumors. Our findings argue against the idea that liver disease drives tumorigenesis via a direct mechanism of induced mutagenesis, and suggests that the transition from healthy to cancerous liver cells likely occurs through other mechanisms, such as changes to the microenvironment that facilitate the outgrowth of precancerous cells that would normally be suppressed. Increased proliferation of such cells would result in an increase in mutations associated with endogenous mutational processes, which we indeed observed when examining the early stage mutations in a hepatocellular carcinoma.
| EGAS00001005384 | EGA
Project description:Chronic alcohol abuse has a detrimental effect on the brain and liver. There is no effective treatment for these patients and the mechanism underlying alcohol addiction and consequent alcohol-induced damage of the liver/brain axis remains unresolved. We compared experimental models of alcoholic liver disease (ALD) and alcohol dependence in mice and demonstrated that genetic ablation of IL17 Receptor A (IL17ra-/-), or pharmacological blockade of IL17 signaling effectively suppressed the increased voluntary alcohol drinking in alcohol-dependent mice, and blocked alcohol-induced hepatocellular and neurological damage. The level of circulating IL17A positively correlated with the alcohol use in excessive drinkers, and was further increased in patients with ALD as compared to healthy individuals. Our data suggest that IL17A is a common mediator of excessive alcohol consumption and alcohol-induced liver/brain injury, and targeting IL17A may provide a novel strategy for treatment of alcohol-induced pathology.
2020-04-07 | GSE137228 | GEO
Project description:Drugs of abuse including nicotine and alcohol elicit their effect by stimulating the mesocorticolimbic dopaminergic system. There is a high incidence of nicotine dependence in alcoholics. To date only limited data is available on the molecular mechanism underlying the action of alcohol and nicotine in the human brain. This study utilised gene expression screening to identify genes sensitive to chronic alcohol abuse within the ventral tegmental area of the human brain. Keywords: gene expression, brain, alcohol abuse, human, ventral tegmental area
2007-09-21 | GSE9058 | GEO
Project description:Non-alcoholic steatohepatitis (NASH)-related hepatocellular carcinoma (HCC) is increasing globally, but its molecular features are not well defined. We aimed to identify unique molecular traits characterizing NASH-HCC compared to other HCC aetiologies. We collected 80 NASH-HCC and 125 NASH samples from 5 institutions. Expression array (n=53 NASH-HCC; n=74 NASH) and whole exome sequencing (n=50 NASH-HCC) data were compared to HCCs of other aetiologies (n=184). Three NASH-HCC mouse models were analysed with RNAseq/expression-array (n=20). ACVR2A was silenced in HCC cells and proliferation assessed by MTT and colony formation assays. Mutational profiling of NASH-HCC tumours revealed TERT-promoter (56%), CTNNB1 (28%), TP53 (18%) and ACVR2A (10%) as the most-frequently mutated genes. ACVR2A mutation rates were higher in NASH-HCC than in other HCC aetiologies (10% versus 3%, p<0.05). In vitro, ACVR2A silencing prompted a significant increase in cell proliferation in HCC cells. We identified a novel mutational signature (MutSig-NASH-HCC) significantly associated with NASH-HCC (16% vs 2% in viral/alcohol-HCC, p=0.03). Tumour mutational burden (TMB) was higher in non-cirrhotic than in cirrhotic NASH-HCCs (1.45 versus 0.94 mutations/Mb; p<0.0017). Compared to other aetiologies of HCC, NASH-HCCs were enriched in bile and fatty acid signalling, oxidative stress and inflammation, and presented a higher fraction of Wnt/TGF-β proliferation subclass tumours (42% versus 26%, p=0.01) and a lower prevalence of the CTNNB1 subclass. Compared to other aetiologies, NASH-HCC showed a significantly higher prevalence of immunosuppressive cancer field. In three murine models of NASH-HCC key features of human NASH-HCC were preserved. NASH-HCCs display unique molecular features including higher rates of ACVR2A mutations and the presence of a newly identified mutational signature.
2021-06-29 | GSE164760 | GEO
Project description:Based on the identification of a transcriptomic signature, including Slit2, characterizing portal mesenchymal stem cells (PMSC) and derived myofibroblast (MF), we examined the gene expression profile of in liver tissue derived from multiple human liver disorders, including primary sclerosing cholangitis (PSC) (n=12), non-alcoholic steatohepatitis (NASH) (n=7) and other liver diseases (i.e., primary biliary cholangitis, autoimmune hepatitis, alcoholic liver disease and haemochromatosis) (n=8) and compared them to healthy controls (tumor free tissue from livers with metastasis from colorectal cancer) (n=5). We found that SLIT2 was overexpressed in the liver of patients with NASH, PSC and other chronic liver diseases. We also examined the microarray data of the human liver tissue samples for the transcriptomic signatures and found that in the different types of liver diseases the gene signature of PMSCs/PMSC-MFs was increased compared to normal liver, and correlated with the expression of ACTA2, COL1A1 and vWF.
2020-10-21 | GSE159676 | GEO
Project description:Alcohol abuse can induce brain injury and neurodegeneration, and recent evidence shows the participation of immune receptors toll-like in the neuroinflammation and brain damage. We evaluated the role of miRNAs as potential modulators of the neuroinflammation associated with alcohol abuse and the influence of the TLR4 response. Using mice cerebral cortex and next-generation sequencing (NGS), we identified miRNAs that were differentially expressed in the chronic alcohol-treated versus untreated WT or TLR4-KO mice. We observed a differentially expression of miR-183 Cluster (C) (miR-96/-182/-183), miR-200a and miR-200b, which were down-regulated, while mirR-125b was up-regulated in alcohol-treated WT versus (vs.) untreated mice. These miRNAs modulate targets genes related to the voltage-gated sodium channel, neuron hyperexcitability (Nav1.3, Trpv1, Smad3 and PP1-γ), as well as genes associated with innate immune TLR4 signaling response (Il1r1, Mapk14, Sirt1, Lrp6 and Bdnf). Functional enrichment of the miR-183C and miR-200a/b family target genes, revealed neuroinflammatory pathways networks involved in TLR4 signaling and alcohol abuse. The changes in the neuroinflammatory targets genes associated with alcohol abuse were mostly abolished in the TLR4-KO mice. Our results show the relationship between alcohol intake and miRNAs expression and open up new therapeutically targets to prevent deleterious effects of alcohol on the brain.
2018-09-25 | GSE120373 | GEO
Project description:To investigate the function of read-through circRNAs in liver, we obtained human NASH liver tissues and normal liver tissues patients without NAFLD undergoing surgery for hepatic hemangioma.Patients with positive hepatitis B surface antigen or anti-hepatitis C virus (HCV) antibody with detectable HCV RNA, excessive alcohol consumption (20 g/day in men or 10 g/day in women), secondary fatty liver (e.g., use of systemic steroids or tamoxifen), or malignancies before baseline were excluded. We then performed exome capture mRNA sequencing using livers from three NASH patients and three patients with hepatic hemangioma.
2022-09-08 | GSE212741 | GEO