Acute and chronic liver injury change the small RNA cargoes carried by serum small extracellular vesicles in mice
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Mus musculus
SUBMITTER: Juling Ji
PROVIDER: E-MTAB-9462 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Since xenobiotics enter the organism via the liver, hepatocytes must cope with numerous perturbations. In particular, exposure to hepatotoxic agents resulting in liver injury triggers a strong alteration in gene expression. The contribution of these transcriptional regulatory networks to the propagation of injury (i.e. by modulation of metabolic pathways, inflammation, proliferation) are not fully understood. Therefore, we conducted a time-resolved gene array study on mouse liver after exposure to a single intraperitoneal injection of the hepatotoxic compound carbon tetrachloride (CCl4). This model induces a transient injury which reaches its maximum between 2 to 3 days after injection, followed by a precise regenerative response. The experiment included early time points (i.e. 2 and 8h) and late time points (1 to 16 days) to cover the initial events induced by CCl4 metabolization and cell stress, and the regenerative phase between 2-6 days after intoxicaiton. C57BL/6N male mice (8-12 weeks old) were obtained from Charles Rivers (Sulzfeld, Germany). The local Ethics committee approved the experiments. 4-5 mice were used for each time point. Mice received a single intraperitoneal injection of CCl4 (1.6 g/kg body weight) dissolved in 0.5 ml olive oil. The liver tissue was collected after 2h, 8h, and 1, 2, 4, 6, 8 and 16 days following CCl4 administration. As control, mice received 0.5 ml of olive oil intraperitonealy for 1 or 8 days. Healthy liver was collected from untreated mice. At the indicated time points, mice were anesthetized and blood was collected from the heart with a 25 gauge needle, using EDTA as anticoagulant, for analysis of the liver transaminases GOT and GPT in serum. Afterwards, the liver was resected, washed in ice cold PBS and sectioned for further analysis. Liver tissue sections of about 0.5 cm2 were snap frozen in liquid nitrogen and stored at -80ﾰC for subsequent isolation of proteins or RNA. RNA was isolated from mouse liver tissue using the Phenol/Chloroform method (Trizolﾮ, Qiagen, Hilden, Germany) according to the manufacturerﾒs instructions. RNA concentration and integrity were determined spectrophotometrically in a Nanodropﾮ2000 (ThermoScientific, Waltham MA, USA) and in a Bioanalyzerﾮ (Agilent, Waldbronn, Germany), respectively.
2014-08-31 | E-MTAB-2445 | biostudies-arrayexpress
Project description:Persistent liver injury triggers a fibrogenic program that causes pathologic remodelling of the hepatic microenvironment (i.e., liver fibrosis) and portal hypertension. The dynamics of gene regulation during liver disease progression and regression remain understudied. Here, we generated hepatic transcriptome profiles in two well-established liver disease models at peak fibrosis and during spontaneous regression after the removal of the inducing agents. We linked the dynamics of key liver disease readouts, such as portal pressure, collagen proportionate area, and transaminase serum levels, to most differentially expressed genes, enabling the identification of transcriptomic signatures of progressive vs. regressive liver fibrosis and portal hypertension. These candidate biomarkers (e.g., Scube1, Tcf4, Src, Hmga1, Trem2, Mafk, Mmp7) were also validated in RNA-seq datasets of patients with cirrhosis and portal hypertension. Finally, deconvolution analysis identified major cell types and suggested an association of macrophage and portal hepatocyte signatures with portal hypertension and fibrosis area in both models.
2024-02-13 | E-MTAB-13804 | biostudies-arrayexpress
Project description:The experiment was to identify gene expression changes in mouse liver macrophages upon resolution from inflammation.<br>Macrophages were isolated from mouse livers 24 hours (inflammation) and 72 hours (resolution) following injury (hepatic fibrosis).<br>RNAs were prepared and hybrised on Affymetrix Mouse Genome 1.0 ST arrays.
2011-07-01 | E-MEXP-3177 | biostudies-arrayexpress
Project description:Hepatocellular carcinoma (HCC) is a prevalent human cancer with rising incidence worldwide. Human HCC is frequently associated with chronic liver inflammation and cirrhosis, pathophysiological processes that are a consequence of chronic viral infection, disturbances in metabolism, or exposure to chemical toxicants. To better characterize the pathogenesis of HCC, we used a human disease-relevant mouse model of fibrosis-associated hepatocarcinogenesis. In this model, marked liver tumor response caused by a pro-mutagenic chemical N-nitrosodiethylamine in presence of liver fibrosis was associated with epigenetic events indicative of genomic instability. Therefore, we hypothesized that DNA copy number alterations (CNAs), a feature of genomic instability and a common characteristic of cancer, are concordant between human HCC and mouse models of fibrosis-associated hepatocarcinogenesis. We evaluated DNA CNAs and changes in gene expression in the mouse liver (normal, tumor and non-tumor cirrhotic tissues). In addition, we compared our findings to those in human HCC (tumor and non-tumor cirrhotic/fibrotic tissues). We observed that while fibrotic liver tissue is largely devoid of DNA CNAs, highly frequently occurring DNA CNAs are found in mouse tumors, which is indicative of a profound increase in chromosomal instability in HCC. When compared to CNAs in human HCC, we found that 33% of genes in these segments are similarly affected in the mouse tumors. Our results suggest that CNAs most commonly arise in neoplastic tissue rather than in fibrotic liver, and demonstrate the utility of this mouse model in replicating the molecular features of human HCC. Genomic DNA was extracted from frozen liver samples from vehicle-control and DEN+CCl4-treated mice using a DNEasy kit (Qiagen, Valencia, CA). Eighteen mouse tumor samples were included in the study, as well as 18 matched non-tumor samples taken from fibrotic, non-tumorous, surrounding liver tissue from the same mice. Liver DNA from 6 vehicle control-mice was pooled and used as the reference genome in the aCGH experiments. Copy number alterations were identified using the normalized data.
2015-11-01 | E-GEOD-71849 | biostudies-arrayexpress
Project description:Gene-expression profiles of liver tissue of cabon tetrachloride (CCl4)-treated mouse and the effect of erlotinib Hepatocellular carcinoma (HCC) is the sixth most common solid tumor worldwide and the third leading cause of cancer-related death. Given the lack of successful treatment options, chemoprevention in high-risk patients has been proposed as an alternative strategy. Mounting evidence supports a role for epidermal growth factor (EGF) during chronic liver disease and hepatocellular transformation. We address the hypothesis that blocking the EGF-EGF receptor (EGFR) pathway may be an effective strategy for inhibiting fibrogenesis and hepatocarcinogenesis. A rat model of diethylnitrosamine (DEN)-induced cirrhosis was used to examine the effects of erlotinib on underlying chronic liver disease and HCC formation. The DEN-induced rat model closely resembles disease progression in humans both pathologically and molecularly. Erlotinib significantly prevented the development of HCC tumor nodules in a dose-dependent fashion. Further, erlotinib inhibited the activation of hepatic stellate cells and prevented fibrogenesis. Erlotinib also reduced hepatotoxicity and improved liver function. Finally, a gene expression signature predictive of poor survival in human cirrhosis patients was reversed in response to erlotinib. Our data demonstrate for the first time that EGFR inhibition prevents liver fibrogenesis. Further, our results suggest that erlotinib is a potentially effective HCC chemoprevention strategy through inhibition of cirrhosis progression which can be monitored at the molecular level. Animals received humane care according to the criteria outlined in the M-bM-^@M-^\Guide for the Care and Use of Laboratory AnimalsM-bM-^@M-^] of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Strain A/J male mice (Jackson Laboratory, Bar Harbor, ME) were treated three times a week for 18 weeks with either 0.1cc of a 40 percent solution of CCl4 (Sigma) in olive oil or with vehicle control by oral gavage. Mice were sacrificed at 19 weeks after a one-week washout to eliminate acute effects of CCl4. The liver was sectioned and fixed in phosphate-buffered 10% formaldehyde for histological analysis. The remaining portions of the liver were collected in RNase-free tubes and snap-frozen in liquid nitrogen. Frozen tissues were stored at -80M-BM-0C until use.
2014-02-28 | E-GEOD-27640 | biostudies-arrayexpress
Project description:Background: HGF/c-Met signaling plays a pivotal role in hepatocyte survival and tissue remodeling during liver regeneration. Treatment with HGF has been shown to accelerate resolution of fibrotic liver lesions in experimental animal models. To formally address the importance of c-Met signaling in hepatocytes in the context of chronic liver injury, we have used hepatocyte-specific Metfl/fl;Alb-Cre+/- conditional knockout mice (KO) and a model of liver fibrosis. Methods: CCl4 was administrated biweekly over a period of 4 weeks (injury phase), and the animals were followed over the next 4 weeks (healing phase). Macroscopic and microscopic changes during the injury and healing phases were monitored by IHC. Deposition of ECM was assessed by Sirius red staining and hydroxiproline content. Activation of hepatic stellate cells (HSC) was estimated by a-SMA using WB and IHC. Expression levels of the selected key fibrotic molecules were evaluated by RT-qPCR and WB. Time-dependent global transcriptomic changes from whole livers and isolated hepatocytes were examined using gene expression microarrays. Results: Loss of HGF/c-Met signaling in hepatocytes altered the hepatic microenvironment and dramatically aggravated hepatic fibrogenesis. Increased liver damage was associated with decreased hepatocyte proliferation, progressive accumulation of HSCs, and delayed fibrinolysis causing increased collagen deposit. Dystrophic calcification of necrotic areas impaired phagocytosis, resulting in sustained inflammatory and fibrogenic signaling further augmenting severity of fibrogenesis. Global gene-expression analysis demonstrated upregulation of key fibrogenic molecules, such as Tgf-â and Pdgf-â, paralleled by a decreased expression of genes important for cell cycle, stress response and regeneration, which could be attributed to the c-Met deficiency in hepatocytes. Additionally, key chemotactic and inflammatory cytokines, including Ccl2, SDF1/Cxcr4 and Spp1, were upregulated in Metfl/fl;Alb-Cre+/- hepatocytes. However, the major pro-fibrotic signaling originated from the non-parenchymal cell compartments, as revealed by cell type-specific gene expression signatures. Conclusion: These results indicate that lack of c-Met signaling in hepatocytes disrupts the balance between extracellular matrix production and degradation and establish a protective role for c-Met against adverse microenvironment leading to the development of fibrotic liver disease. In the present study, we reported a detailed and comprehensive dynamic characterization of the cellular and molecular alterations involved in fibrosis in the liver of c-Met transgenic mice. Liver samples from female animals were collected at various time-points after fibrosis induction using CCL4 ranging from 0 weeks to 3 weeks. Tissue samples were divided into two parts; one was fixed in 10% formalin for histological evaluation and the other was used for RNA analysis.
2011-11-09 | E-GEOD-25583 | biostudies-arrayexpress
Project description:To investigate the differences in microRNA expression profiles between fibrotic and normal livers, we performed microRNA microarrays for total RNA extracts isolated from mouse livers treated with carbontetrachloride (CCl4) or corn-oil for 10 weeks (n=3/group). MicroRNAs were considered to have significant differences in expression level when the expression difference showed more than two-fold change between the experimental and control groups at p<0.05. We found that 12 miRNAs were differentially expressed in CCl4-induced fibrotic liver. To induce chronic liver fibrosis, seven-week-old mice received 0.6 ml/kg body weight of carbon-tetrachloride (CCl4) dissolved in corn-oil by intraperitoneal (i.p.) injection, twice a week for 10 weeks (n=3). As a control, same number of mice was injected with equal volume of corn-oil for 10 weeks.
2016-03-22 | E-GEOD-77271 | biostudies-arrayexpress
Project description:Establish the miRNA expression profile between advanced liver fibrosis and liver without fibrosis in mice Administrate CCL4 or olive oil in mouse twice a week first 4 weeks per peritoneum and then administrated once a week next four weeks. Mice were sacrificed on 4, 6, and 8 weeks.
2011-01-12 | E-GEOD-19865 | biostudies-arrayexpress
Project description:Although epigenetic mechanisms, such as specific histone modifications, control common and cell-specific genetic programs, a role for histone modifying enzymes in liver metabolism and disease has not been investigated. This report demonstrates that the combined loss of the histone methyltransferases EZH1 and EZH2 in mouse hepatocytes led to the disruption of H3K27me3 homeostasis by age three months, simple fatty liver by age six months and fatal fibrosis by age 15 months. Global and gene-specific reduction of H3K27me3 marks paralleled a concomitant increase of H3K4me3 marks at genes associated with chronic liver disease. Advanced disease was accompanied by widespread infiltration of immune cells, an increase of activated hepatic stellate cells and collagen deposition. Expression of genes from the cytochrome P450 family that control drug metabolism was already deregulated by age two months and mice were fatally hypersensitive to carbon tetrachloride (CCl4). These genetic experiments, for the first time, illustrate that the simple loss of EZH1/EZH2, which results in the disruption of epigenetic modifications, is sufficient for the progression of fatal liver disease. RNA-seq and ChIP-seq were performed in liver tissues.
2013-12-24 | E-GEOD-53627 | biostudies-arrayexpress
Project description:We investigated the biological function of INSIG1 in acute (CCl4) and chronic (NASH) liver damage. Male whole-body Insig1 wild-type (WT), Heterozygous (HET) and Knock-out (KO) mice were: 1) challenged with Olive Oil or CCl4 single IP injection and sacrificed 4 days after the treatment; 2) fed Low Fat Diet (LFD) or Western Diet plus Sugar Water (WDSW) and sacrificed after 12 weeks of the challenge. Hepatic RNA was extracted and studied by Next Generation Sequencing to highlight changes in the transcriptome driven by the challenges and genotype-associated differences.
2021-04-14 | E-MTAB-9864 | biostudies-arrayexpress