Transcription profiling of tumorous and non tumorous live from Parkin-/- mice suggestsa role for Parkin as a tumor suppressor gene for hepatocellular carcinoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: mikio fujiwra
PROVIDER: E-GEOD-9651 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:To provide an insight into the molecular mechanism by which parkin deficiency contributes to hepatocarcinogenesis, we analyzed gene expression profiles of nontumorous and tumorous liver tissues from parkin–/– mice using cDNA microarray analyses. Keywords: genetic alteration
2007-11-30 | GSE9651 | GEO
Project description:KrasG12D mutation and Mdm2 loss in the liver (LiKM) accelerated liver carcinogenesis in mice, compared with LiK (KrasG12D mutation in the liver) mice. Acyclic retinoid (ACR) diet suppressed tumor development in LiKM mice. The goal of RNA-seq of non-tumorous liver tissues is to identifiy the effect of ACR diet on the transcriptomic profile of the liver and clarify the mechamism of ACR-mediated tumor suppression in LiKM mice.
2022-08-24 | GSE201067 | GEO
Project description:These paired HCC and non-tumorous liver tissues were used to determine highly differentially expressed genes in HCC and non-tumorous liver tissue. Hepatocellular carcinoma (HCC) is a malignancy with poor survival outcome. Genes showing extreme differential expression between paired human HCC and adjacent non-tumorous liver tissue were investigated. PLVAP was identified as a gene specifically expressed in vascular endothelial cells of HCC but not in non-tumorous liver tissues. This finding was confirmed by RT-PCR analysis of micro-dissected cells and immunohistochemical staining of tissue sections. A recombinant monoclonal anti-PLVAP Fab fragment co-expressing extracellular domain of human tissue factor (TF) was developed. The potential therapeutic effect and toxicity to treat HCC were studied using a Hep3B HCC xenograft model in SCID mice. Infusion of recombinant monoclonal anti-PLVAP Fab-TF into the tumor feeding artery induced tumor vascular thrombosis and extensive tumor necrosis at doses between 2.5 µg and 12 µg. Tumor growth was suppressed for 40 days after a single treatment. Systemic administration did not induce tumor necrosis. Little systemic toxicity was noted for this therapeutic agent. The results of this study suggest that anti-PLVAP Fab-TF may be used to treat HCC cases for which transcatheter arterial chemoembolization (TACE) is currently used, but without major drawbacks of TACE. Anti-PLVAP Fab-TF may improve therapeutic outcome and be a viable therapeutic agent in patients with more advanced disease and compromised liver function. Frozen hepatocellular carcinoma and adjacent non-tumorous liver tissues were used for gnee expression profiling study. Affymetrix U133A genechips were used for gene expression profiling. This dataset is part of the TransQST collection.
2015-01-01 | E-GEOD-60502 | biostudies-arrayexpress
Project description:These paired HCC and non-tumorous liver tissues were used to determine highly dfferentially expressed genes in HCC and non-tumorous liver tissue. Hepatocellular carcinoma (HCC) is a malignancy with poor survival outcome. Genes showing extreme differential expression between paired human HCC and adjacent non-tumorous liver tissue were investigated. PLVAP was identified as a gene specifically expressed in vascular endothelial cells of HCC but not in non-tumorous liver tissues. This finding was confirmed by RT-PCR analysis of micro-dissected cells and immunohistochemical staining of tissue sections. A recombinant monoclonal anti-PLVAP Fab fragment co-expressing extracellular domain of human tissue factor (TF) was developed. The potential therapeutic effect and toxicity to treat HCC were studied using a Hep3B HCC xenograft model in SCID mice. Infusion of recombinant monoclonal anti-PLVAP Fab-TF into the tumor feeding artery induced tumor vascular thrombosis and extensive tumor necrosis at doses between 2.5 µg and 12 µg. Tumor growth was suppressed for 40 days after a single treatment. Systemic administration did not induce tumor necrosis. Little systemic toxicity was noted for this therapeutic agent. The results of this study suggest that anti-PLVAP Fab-TF may be used to treat HCC cases for which transcatheter arterial chemoembolization (TACE) is currently used, but without major drawbacks of TACE. Anti-PLVAP Fab-TF may improve therapeutic outcome and be a viable therapeutic agent in patients with more advanced disease and compromised liver function.
2015-01-01 | GSE60502 | GEO
Project description:Adult mice bearing homozygous floxed Parkin alleles (PMIDs 15249681, 21376232; T M Dawson), with or without the Myh6-driven MERCreMER transgene, were administered tamoxifen at 6-10 wks of age. Tissues were obtained from euthanized mice 9-10 weeks after tamoxifen induction. 6 floxed, non-Cre (noninduced) mouse hearts; 6 floxed, MERCreMer, adult-induced, Parkin knockout mouse hearts
2015-10-31 | E-GEOD-74518 | biostudies-arrayexpress
Project description:Loss-of-function variants in the PRKN gene encoding the ubiquitin E3 ligase PARKIN cause autosomal recessive early-onset Parkinson’s disease (PD). Extensive in vitro and in vivo studies have reported that PARKIN is involved in multiple pathways of mitochondrial quality control, including mitochondrial degradation and biogenesis. However, these findings are surrounded by substantial controversy due to conflicting experimental data. In addition, the existing PARKIN-deficient mouse models have failed to faithfully recapitulate PD phenotypes. Therefore, we have investigated the mitochondrial role of PARKIN during ageing and in response to stress by employing a series of conditional Parkin knockout mice. We report that PARKIN loss does not affect oxidative phosphorylation (OXPHOS) capacity and mitochondrial DNA (mtDNA) levels in the brain, heart, and skeletal muscle of aged mice. We also demonstrate that PARKIN deficiency does not exacerbate the brain defects and the pro-inflammatory phenotype observed in mice carrying high levels of mtDNA mutations. To rule out compensatory mechanisms activated during embryonic development of Parkin-deficient mice, we generated a mouse model where loss of PARKIN was induced in adult dopaminergic (DA) neurons. Surprisingly, also these mice did not show motor impairment or neurodegeneration, and no major transcriptional changes were found in isolated midbrain DA neurons. Finally, we report a patient with compound heterozygous PRKN pathogenic variants that lacks PARKIN and has developed PD. The PARKIN deficiency did not impair OXPHOS activities or induce mitochondrial pathology in skeletal muscle from the patient. Altogether, our results argue that PARKIN is dispensable for OXPHOS function in adult mammalian tissues.
2024-04-03 | GSE263057 | GEO
Project description:Purpose: The E3 ubiquitin ligase Parkin is a well-characterized regulator of mitochondrial autophagy (mitophagy); however, it is becoming increasingly appreciated to perform additional roles in various compartments of the cell. Our laboratory confirmed the presence of Parkin in the nucleus of various tissues (biochemical fractionations) and cell types (immunofluorescent imaging). Hypoxia-induced nuclear translocation of Parkin occured independent of the mitophagy regulator PINK1, and Parkinson's disease-associated mutants were restricted from the nuclueus. Accordingly, we inserted a nuclear localization sequence (NLS) at the n-terminus of Parkin and overexpressed both NLS Parkin and the wild-type protein in HeLa cells cultured at normoxia and hypoxia. Next-generation RNA-sequencing (RNA-seq) was used to determine the effect of nuclear Parkin on cellular transcription. Methods: mCherry-tagged NLS and wild-type Parkin were overexpressed in HeLa cells. Differential expression analyses were performed on Parkin vs. mCherry control cells and NLS Parkin vs. mCherry control cells at normoxia and following 12hr of hypoxia (n=3/group/condition). Paired-end sequencing was performed using the HiSeq4000. FastQC v0.11.3 was used for quality control, Trimmomatic v0.36 was used to trim reads which were aligned to the human genome (GRCh37.p13) using the STAR aligner v2.5.3a. Read quantification was performed with RSEM v 1.3.0 and the Gencode release 19. The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis. Results: During normoxia, Parkin had no effect on basal transcription; however, overexpression of NLS Parkin was associated with 168 differentially expressed genes (DEGs: fold-change </= 1.5, FDR < 0.05) relative to mCherry control cells. Following hypoxia, the transcriptome associated with the overexpression of wild-type Parkin more closely resembled that of NLS Parkin. Along these lines, Parkin overexpression during hypoxia coincided with a total of 158 DEGs, 37% of which were shared with NLS Parkin. Overlapping and shared DEGs among Parkin and NLS Parkin were implicated in cellular metabolism, HIF1 signaling and survival. Our follow up co-immunoprecipitation and real-time quantitative PCR studies demonstrated that Parkin interacts with the Estrogen Related Receptor Alpha (ERRa) to promote the induction of its downstream target genes. Conclusions: Nuclear translocation of Parkin is a novel means by which this cytoprotective protein contributes to cellular homeostasis and especially critical during hypoxia.
2019-11-06 | GSE139989 | GEO
Project description:Adult mice bearing homozygous floxed Parkin alleles (PMIDs 15249681, 21376232; T M Dawson), with or without the Myh6-driven MERCreMER transgene, were administered tamoxifen at 6-10 wks of age. Tissues were obtained from euthanized mice 9-10 weeks after tamoxifen induction.
2015-10-31 | GSE74518 | GEO
Project description:Comparison of aged wt, krt18+/- and krt18-/- non-tumorous liver tissues
| PRJNA320385 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE23352: Whole-genome gene expression profiles of non-tumorous human lung tissues: Laval set GSE23529: Whole-genome gene expression profiles of non-tumorous human lung tissues: UBC set GSE23545: Whole-genome gene expression profiles of non-tumorous human lung tissues: GRNG set Refer to individual Series
2012-06-10 | E-GEOD-23546 | biostudies-arrayexpress