DNA binding sites of KLF6 in murine HCC
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Brian Lewis
PROVIDER: E-GEOD-54763 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2016-01-27 | E-GEOD-54764 | biostudies-arrayexpress
Project description:Gene-expression profiles of liver and hepatocellular carcinoma induced by diethylnitrosamine (DEN) in KLF6 +/- and wild type KLF6 mice. Inactivation of the KLF6 tumor suppressor is common in HCC due to hepatitis C virus (HCV), consistent with its anti-proliferative activity in HCC-derived cell lines and in hepatocytes of transgenic mice. We have evaluated the impact of KLF6 depletion on human HCC and experimental hepatocarcinogenesis. In patients with surgically resected HCC, those with significantly reduced tumor expression of KLF6 had a significantly decreased survival. We modeled this event in KLF6 +/- mice, which displayed significantly more tumorigenicity than KLF6 +/+ animals in response to the hepatic carcinogen DEN, associated with recapitulation of gene signatures in both surrounding tissue and tumors that are associated with aggressive human HCCs. In DNA microarrays, mdm2 mRNA expression was increased in tumors from KLF6 +/- compared to KLF6 +/+ mice, which was validated by realtime qPCR and Western blot in both human HCC and DEN-induced murine tumors. Moreover, chromosomal immunoprecipitation and co-transfection assays established the P2 intronic promoter of mdm2 as a bona fide transcriptional target repressed by KLF6. Whereas KLF6 over-expression in HCC cell lines led to reduced MDM2 levels and increased p53 protein and transcriptional activity, reduction in KLF6 by siRNA led to increased MDM2 and reduced p53. Our findings indicate that KLF6 deficiency contributes significantly to the carcinogenic milieu in human and murine HCC, and uncover a novel tumor suppressor activity of KLF6 in HCC, by linking its transcriptional repression of MDM2 to stabilization of p53. Keywords: Liver, Hepatocellular carcinoma, Expression array, Exon array, Affymetrix KLF6 +/- mice were previously generated by homologous recombination in which exon 2 was targeted using an 11-kb targeting construct, and replaced with neomycin/lacZ cassette. After selection with neomycin, the ES clones were injected into C57BL/6 mouse blastocysts and implanted into pseudo pregnant females; two lines of KLF6 +/- mice were generated from the resulting chimeric animals (Blood 107;1357, Oncogene 26;4428). Whereas KLF6 -/- mice are embryonic lethal, KLF6 +/- animals had no demonstrable abnormalities in the absence of any stressor. Male KLF6 +/- mice were bred with wild type C57BL/6 to generate mixed litters of KLF6 +/- and KLF6 +/+ animals. Progeny were genotyped using PCR-amplified tail DNA, using primers as previously described (Oncogene 26;4428). Amplified fragments were separated on a 2.5% agarose gel, revealing bands of ~200 bp (wild type KLF6) and ~100 bp (Neo), as expected. At 2 weeks of age, KLF6 +/+ and KLF6 +/- mice were injected intraperitoneally with either a single dose of diethyl nitrosamine (DEN), 5 µg/g body weight in 100 µl of saline, or vehicle alone. Vehicle and DEN-treated mice were maintained on standard chow, and then sacrificed 3, 6 or 9 months later. At the time of sacrifice the animals were weighed, and blood and liver samples were harvested for analysis and tumor quantification.
2011-07-31 | E-GEOD-23375 | biostudies-arrayexpress
Project description:We sequenced DNA isolated from performing ChIP of full-length KLF6 and an Input sample in an HCC cell line. The goal is to determine KLF6 binding sites in a mouse-derived HCC cell line.
2016-01-27 | GSE54763 | GEO
Project description:We performed whole genome expression profiling using a murine HCC cell line that was either infected with a virus containing shRNA targeting KLF6 or GFP. 3 sets of infections were performed for both shGFP and shKLF6 samples. RNA was isolated from these samples and subsequently analyzed. Determination of gene expression changes in a murine HCC cell line was performed with 3 sets of infections performed for both shGFP and shKLF6. RNA was isolated from these samples and subsequently analyzed using the Affymetrix Mouse Genome 430 2.0 chip.
2016-01-27 | E-GEOD-54762 | biostudies-arrayexpress
Project description:We examine the role of Klf6 in oligodendrocyte progenitor cells and determine that Klf6 acts in part through direct regulation of gp130 signaling and nuclear import via importin-α5 (Impα5), a key controller of nuclear trafficking. Examination of Klf6 DNA binding in two different stages of differentiation
2016-04-01 | E-GEOD-79243 | 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:KLF6 was overexpressed using an adenoviral delivery system. Overexpression was confirmed at 12, 24, 48 and 72 hours post infection by RT-PCR and Western Blot analysis. Codelink Whole genome microarrays were used to analyse changes in expression resulting from KLF6 overexpression. RNA Samples were taken at 48 and 72 hours from samples oeverexpressing KLF6 and the empty vector control pBabe
2014-08-22 | E-GEOD-60602 | biostudies-arrayexpress
Project description:We examine the role of Klf6 in oligodendrocyte progenitor cells and determine that Klf6 acts as a gp130-sensitive transactivator of the nuclear import factor importin-α5 (Impα5), a key controller of nuclear trafficking in oligodendrocytes. Examination of expression profiles of 2 different cell stages exposed to siRNA vs. control
2016-04-01 | E-GEOD-79244 | biostudies-arrayexpress
Project description:Gene-expression profiles of liver and hepatocellular carcinoma induced by diethylnitrosamine (DEN) in KLF6 +/- and wild type KLF6 mice. Inactivation of the KLF6 tumor suppressor is common in HCC due to hepatitis C virus (HCV), consistent with its anti-proliferative activity in HCC-derived cell lines and in hepatocytes of transgenic mice. We have evaluated the impact of KLF6 depletion on human HCC and experimental hepatocarcinogenesis. In patients with surgically resected HCC, those with significantly reduced tumor expression of KLF6 had a significantly decreased survival. We modeled this event in KLF6 +/- mice, which displayed significantly more tumorigenicity than KLF6 +/+ animals in response to the hepatic carcinogen DEN, associated with recapitulation of gene signatures in both surrounding tissue and tumors that are associated with aggressive human HCCs. In DNA microarrays, mdm2 mRNA expression was increased in tumors from KLF6 +/- compared to KLF6 +/+ mice, which was validated by realtime qPCR and Western blot in both human HCC and DEN-induced murine tumors. Moreover, chromosomal immunoprecipitation and co-transfection assays established the P2 intronic promoter of mdm2 as a bona fide transcriptional target repressed by KLF6. Whereas KLF6 over-expression in HCC cell lines led to reduced MDM2 levels and increased p53 protein and transcriptional activity, reduction in KLF6 by siRNA led to increased MDM2 and reduced p53. Our findings indicate that KLF6 deficiency contributes significantly to the carcinogenic milieu in human and murine HCC, and uncover a novel tumor suppressor activity of KLF6 in HCC, by linking its transcriptional repression of MDM2 to stabilization of p53. Keywords: Liver, Hepatocellular carcinoma, Expression array, Exon array, Affymetrix
2011-08-01 | GSE23375 | GEO
Project description:Polycomb group (PcG) proteins are major determinants of gene silencing and epigenetic memory in higher eukaryotes. Acting in multimeric protein complexes, these factors control structure and function of chromatin. We used a robust affinity purification mass spectrometry (AP-MS) approach to systematically map the PcG protein interactome in a single human cell line. Importantly, we uncovered the topology map of the human PR-DUB de-ubiquitination complexes, which comprise the O-linked N-acetylglucosamine transferase OGT1 and a number of transcription factors. Here we provide genome-wide chromatin maps of identified PR-DUB1 subunits ASXL1, FOXK1 and the OGT1 catalyzed modification O-GlcNAc based on ChIP-seq. Our data set comprises 3 ChIP-seq samples plus 2 input control samples using chromatin from Flp-In HEK293 T-REx cells cells which was immunoprecipitated using antibodies against ASXL1, FOXK1 and O-GlcNAc.
2016-09-08 | E-GEOD-51673 | biostudies-arrayexpress