Impact of high fat diet and hepatocyte nuclear factor four alpha loss on hepatic gene expression in mice.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA564330 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The transcription factor hepatocyte nuclear factor four alpha (Hnf4a) has various isoforms, one of which (P1-Hnf4a) is expressed in adult liver, where it functions as a tumor suppressor by providing circadian restrains at genes promoting cell proliferation and epithelial to mesenchymal transition. High fat diet feeding promotes the loss of nuclear P1-Hnf4a activity and a gain in the pro-proliferative P2-Hnf4a isoform, which does not function as a tumor suppressor, nor provide similar circadian restraint at cell cycle-promoting genes. P2-Hnf4a is found in all Hnf4a-positive hepatocellular carcinoma. Purpose: To determine whether inducible loss of hepatic Hnf4a followed by high fat feeding predisposes a liver to hepatocellular carcinoma. Methods: Hepatic Hnf4a was inducibly knocked out in mice at six weeks of age ("H4LivKO") followed by vivarium chow ("H4LivKOVC") or high fat feeding ("H4LivKOHF")at 8 weeks of age. Control, littermate wild-type mice (WT) were also treated with tamoxifen at six weeks of age, but since they lacked the Cre transgene, Hnf4a expression remained intact. Control mice were divided into the same feeding groups as H4LivKO mice ("WTVC" and "WTHF"). Livers were harvested at 38 weeks of age and liver tissue was flash frozen in liquid nitrogen. RNA was extracted from frozen liver tissue using Trizol, and purified RNA was submitted to Novogene for quality control and RNA-seq analysis using a 250-300 bp insert cDNA library and Illumina Platform sequencing.
2019-09-07 | GSE137051 | GEO
Project description:AIM:To uncover the role of hepatocyte nuclear factor 4 alpha (HNF4?) in regulating hepatic expression of microRNAs. METHODS:Microarray and real-time PCR were used to determine hepatic expression of microRNAs in young-adult mice lacking Hnf4? expression in liver (Hnf4?-LivKO). Integrative genomics viewer software was used to analyze the public chromatin immunoprecipitation-sequencing datasets for DNA-binding of HNF4?, RNA polymerase-II, and histone modifications to loci of microRNAs in mouse liver and human hepatoma cells. Dual-luciferase reporter assay was conducted to determine effects of HNF4? on the promoters of mouse and human microRNAs as well as effects of microRNAs on the untranslated regions (3'UTR) of two genes in human hepatoma cells. RESULTS:Microarray data indicated that most microRNAs remained unaltered by Hnf4? deficiency in Hnf4?-LivKO mice. However, certain liver-predominant microRNAs were down-regulated similarly in young-adult male and female Hnf4?-LivKO mice. The down-regulation of miR-101, miR-192, miR-193a, miR-194, miR-215, miR-802, and miR-122 as well as induction of miR-34 and miR-29 in male Hnf4?-LivKO mice were confirmed by real-time PCR. Analysis of public chromatin immunoprecipitation-sequencing data indicates that HNF4? directly binds to the promoters of miR-101, miR-122, miR-194-2/miR-192 and miR-193, which is associated with histone marks of active transcription. Luciferase reporter assay showed that HNF4? markedly activated the promoters of mouse and human miR-101b/miR-101-2 and the miR-194/miR-192 cluster. Additionally, miR-192 and miR-194 significantly decreased activities of luciferase reporters for the 3'UTR of histone H3F3 and chromodomain helicase DNA binding protein 1 (CHD1), respectively, suggesting that miR-192 and miR-194 might be important in chromosome remodeling through directly targeting H3F3 and CHD1. CONCLUSION:HNF4? is essential for hepatic basal expression of a group of liver-enriched microRNAs, including miR-101, miR-192, miR-193a, miR-194 and miR-802, through which HNF4? may play a major role in the post-transcriptional regulation of gene expression and maintenance of the epigenome in liver.
| S-EPMC5295159 | biostudies-literature
Project description:ObjectiveNonalcoholic hepatic steatosis, also known as fatty liver, is a uniform response of the liver to hyperlipidic-hypercaloric diet intake. However, the post-ingestive signals and mechanistic processes driving hepatic steatosis are not well understood. Emerging data demonstrate that protein kinase C beta (PKCβ), a lipid-sensitive kinase, plays a critical role in energy metabolism and adaptation to environmental and nutritional stimuli. Despite its powerful effect on glucose and lipid metabolism, knowledge of the physiological roles of hepatic PKCβ in energy homeostasis is limited.MethodsThe floxed-PKCβ and hepatocyte-specific PKCβ-deficient mouse models were generated to study the in vivo role of hepatocyte PKCβ on diet-induced hepatic steatosis, lipid metabolism, and mitochondrial function.ResultsWe report that hepatocyte-specific PKCβ deficiency protects mice from development of hepatic steatosis induced by high-fat diet, without affecting body weight gain. This protection is associated with attenuation of SREBP-1c transactivation and improved hepatic mitochondrial respiratory chain. Lipidomic analysis identified significant increases in the critical mitochondrial inner membrane lipid, cardiolipin, in PKCβ-deficient livers compared to control. Moreover, hepatocyte PKCβ deficiency had no significant effect on either hepatic or whole-body insulin sensitivity supporting dissociation between hepatic steatosis and insulin resistance.ConclusionsThe above data indicate that hepatocyte PKCβ is a key focus of dietary lipid perception and is essential for efficient storage of dietary lipids in liver largely through coordinating energy utilization and lipogenesis during post-prandial period. These results highlight the importance of hepatic PKCβ as a drug target for obesity-associated nonalcoholic hepatic steatosis.
| S-EPMC7785956 | biostudies-literature
Project description:The purpose of this experiment was to obtain samples for microRNA analysis in IHH cells infected with human interferon alpha. Immortalized human hepatocyte (IHH) cells were seeded at 1 x 10^6 cells per well on 6 well plates 3 days before infection. Treatments were initiated by replacing culture medium (containing 10% FBS) with fresh medium containing 500 U/ml of human interferon α (PBL Biosciences). Mock-treated cells were given normal culture medium only. Mock and treated cells were incubated at 37°C until sample collection time points. Infected samples were collected in triplet; time-matched mocks were collected in triplet in parallel with infected samples. Time points: 6, 12, and 18 h post-infection
2015-08-06 | E-GEOD-71733 | biostudies-arrayexpress
Project description:The purpose of this experiment was to obtain samples for mRNA analysis in IHH cells infected with human interferon alpha. Immortalized human hepatocyte (IHH) cells were seeded at 1 x 10^6 cells per well on 6 well plates 3 days before infection. Treatments were initiated by replacing culture medium (containing 10% FBS) with fresh medium containing 500 U/ml of human interferon α (PBL Biosciences). Mock-treated cells were given normal culture medium only. Mock and treated cells were incubated at 37°C until sample collection time points. Infected samples were collected in triplet; time-matched mocks were collected in triplet in parallel with infected samples. Time points: 6, 12, and 18 h post-infection
2015-08-06 | E-GEOD-71732 | biostudies-arrayexpress
Project description:Hepatocyte nuclear factor-4α (HNF4α, NR2A1) is a nuclear receptor which has a critical role in hepatocyte differentiation and the maintenance of homeostasis in the adult liver. However, a detailed understanding of native HNF4α in the steady state remains to be elucidated. Here we report the native HNF4α isoforms, phosphorylation status and complexes in the steady state, as shown by shotgun proteomics in HepG2 hepatocarcinoma cells. Shotgun proteomic analysis revealed the complexity of native HNF4α, including multiple phosphorylation sites and inter-isoform heterodimerization. The associating complexes identified by label-free semi-quantitative proteomic analysis include the following: the DNA-dependent protein kinase catalytic subunit, histone acetyltransferase complexes, mRNA splicing complex, other nuclear receptor coactivator complexes, the chromatin remodeling complex, and the nucleosome remodeling and histone deacetylation complex. Among the associating proteins, GRB10 interacting GYF protein 2 (GIGYF2, PERQ2) is a new candidate cofactor in metabolic regulation. Moreover, an unexpected heterodimerization of HNF4α and Hepatocyte nuclear factor-4γ was found. A biochemical and genome-wide analysis of transcriptional regulation showed that this heterodimerization activates gene transcription. The genes thus transcribed include the cell death-inducing DEF45-like effector b (CIDEB) gene, which is an important regulator of lipid metabolism in the liver. This suggests that the analysis of the distinctive stoichiometric balance of native HNF4α and its cofactor complexes described here is important for an accurate understanding of transcriptional regulation. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series.
2010-12-22 | E-GEOD-18990 | biostudies-arrayexpress
Project description:Dysregulated glucose homeostasis and lipid accumulation characterize non-alcoholic fatty liver disease (NAFLD), but underlying mechanisms are obscure. We report here that Krüppel-like factor 6 (KLF6), a ubiquitous transcription factor that promotes adipocyte differentiation, also provokes the metabolic abnormalities of NAFLD. Mice with either hepatocyte-specific knockdown of KLF6 (DeltaHepKlf6) or global KLF6 heterozygosity (Klf6 +/-) have reduced body fat content and improved glucose and insulin tolerance. Mice with KLF6 depletion, compared to wild type mice, are protected from high fat diet-induced steatosis. Three mice with a hepatocyte-specific knockdown of KLF6 (DeltaHepKlf6) on high fat diet and 3 littermate controls on the same diet were sacrificed after 8 weeks of diet. Liver tissue was preserved in RNAlater® (Ambion, Austin, TX). RNA was isolated from liver tissue and homogenized in TRIzol® reagent (Invitrogen, Carlsbad, CA). In order to identify potential KLF6 targets that contributed to changes in glucose- and lipid-metabolism, we performed an Affymetrix Exon1 S.T. Genearray® (Affymetrix, Santa Clara, CA).
2012-03-23 | E-GEOD-36724 | biostudies-arrayexpress
Project description:Genomic analysis of human hepatocellular carcinoma (HCC) is potentially confounded by the differentiation state of the hepatic cell-of-origin. Here we integrated genomic analysis of mouse HCC (with defined cell-of-origin) along with normal liver development. We found a major shift in expression of Wnt and RXR-α pathway genes (up and down, respectively) coincident with the transition from hepatoblasts to hepatocytes. A combined Wnt and RXR-α gene signature categorized HCCs into two subtypes (high Wnt, low RXR-α and low Wnt, high RXR-α), which matched cell-of-origin in mouse models and the differentiation state of human HCC. Suppression of RXR-α levels in hepatocytes increased Wnt signaling and enhanced tumorigenicity, whereas ligand activation of RXR-α achieved the opposite. These results corroborate that there are two main HCC subtypes that correspond to the degree of hepatocyte differentation and that RXR-α, in part via Wnt signaling, plays a key functional role in the hepatocyte-like subtype and potentially could serve as a selective therapeutic target.
2015-01-17 | GSE65063 | GEO
Project description:Non-alcoholic fatty liver disease (NAFLD) is an emerging global disease with increasing prevalence. However, the mechanism of NAFLD development is not fully understood. To elucidate the cell-specific role of nuclear factor erythroid-derived 2-like 2 (NRF2) in the pathogenesis of NAFLD, we utilized hepatocyte- and macrophage-specific Nrf2-knockout [Nrf2(L)-KO and Nrf2(Mϕ)-KO] mice to examine the progress of NAFLD induced by high-fat diet (HFD). Compared to Nrf2-LoxP littermates, Nrf2(L)-KO mice showed less liver enlargement, milder inflammation and less hepatic steatosis after HFD feeding. In contrast, Nrf2(Mϕ)-KO mice displayed no significant difference in HFD-induced hepatic steatosis from Nrf2-LoxP control mice. Mechanistic investigations revealed that Nrf2 deficiency in hepatocytes dampens the expression of peroxisome proliferator-activated receptor γ (PPARγ) and its downstream lipogenic genes in the liver and/or primary hepatocytes induced by HFD and palmitate exposure, respectively. While PPARγ agonists augmented PPARγ expression and its transcriptional activity in primary hepatocytes in a NRF2-dependent manner, forced overexpression of PPARγ1 or γ2 distinctively reversed the decreased expression of their downstream genes fatty acid binding protein 4, lipoprotein lipase and/or fatty acid synthase caused by Nrf2 deficiency. We conclude that NRF2-dependent expression of PPARγ in hepatocytes is a critical initiating process in the development of NAFLD, suggesting that inhibition of NRF2 specifically in hepatocytes may be a valuable approach to prevent the disease.
| S-EPMC6940621 | biostudies-literature
Project description:Aims/introductionType 2 diabetes mellitus is frequently accompanied by fatty liver disease. Lipid accumulation within the liver is considered as one of the risk factors for insulin resistance. Hepatocyte growth factor (HGF) is used to treat liver dysfunction; however, the effect and mechanism of HGF on hepatic lipid metabolism are still not fully understood.Materials and methodsMale C57BL/6 mice were induced with a high-fat diet for 12 weeks, followed by a 4-week treatment of HGF or vehicle saline. The levels of fasting blood glucose, fasting insulin and homeostatic model assessment of insulin resistance were calculated for insulin sensitivity. Biochemical plasma parameters were also measured to assess the effect of HGF on lipid accumulation. Additionally, genes in the lipid metabolism pathway were evaluated in palmitic acid-treated HepG2 cells and high-fat diet mice.ResultsHGF treatment significantly decreased the levels of fasting blood glucose, hepatic triglyceride and cholesterol contents. Additionally, HGF-regulated expression levels of sterol regulatory element-binding protein-1c/fatty acid synthase, peroxidase proliferator-activated receptor-α, and upstream nuclear receptors, such as farnesoid X receptor and small heterodimer partner. Furthermore, c-Met inhibitor could partially reverse the effects of HGF.ConclusionsHGF treatment can ameliorate hepatic insulin resistance and steatosis through regulation of lipid metabolism. These effects might occur through farnesoid X receptor-small heterodimer partner axis-dependent transcriptional activity.
| S-EPMC6400203 | biostudies-literature