Two human HCC cells (MHCC97H and MHCC97L): PML-siRNA transfected vs. control
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE67574 | GEO | 2015/04/04
SECONDARY ACCESSION(S): PRJNA280284
REPOSITORIES: GEO
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2015-04-04 | E-GEOD-67574 | biostudies-arrayexpress
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2012-05-31 | GSE29238 | GEO
Project description:To study the potential target genes regulated by PML in endothelial cells, we carried out siRNA-mediated knockdown of PML in HUVEC cells. To eliminate the off-target effects of siRNAs, we utilized two different siRNAs. Only the genes changed in the same pattern following both siRNAs transfection are considered as potential PML-knockdown responsive genes. The experiment is one-factor (siRNA) with three ranks (siCtrl, siPML-1, siPML-2). We included technical duplicates for each sample. To minimize systemic errors assoicated with technique, we distributed the duplicates on two different microarray chips.
2012-05-30 | E-GEOD-29238 | biostudies-arrayexpress
Project description:To study the interaction effects between promyelocytic leukemia (PML) gene knockdown and tumor necrosis factor-alpha (TNFalpha) signaling in human umbilical vein endothelial cells (HUVECs), we transfected control or two independent PML siRNAs into HUVEC cells without or with 20 ng/mL TNFalpha treatment for 20 h. The total RNA was extracted for gene expression microarray analyses. The experiment is a 3x2 two-factor design. One factor is siRNA and it has three levels (siCtrl, siPML1, siPML2). siCtrl is RISC-inducing non-targeting control siRNA. siPML1 and siPML2 designate two independent siRNAs against the PML gene. Two independent siRNAs were used to eliminate the off-target effects of siRNA. The other factor is TNFalpha treatment (20 ng/mL for 20 h) and it has two levels: Untreated (U) or Treated (T). Each sample has technical duplicates.
2013-01-10 | E-GEOD-35000 | biostudies-arrayexpress
Project description:The Sp100 component of ND10/PML bodies is a potent tumor suppressor: accelerated senescence and rapid malignant transformation of human fibroblasts through modulation of an embryonic stem cell program. Identifying the functions of proteins, which define specific subnuclear structures and territories, is important for understanding eukaryotic nuclear dynamics. Sp100 is a prototypical protein of ND10/PML bodies and colocalizes with the proto-oncogenic protein PML and Daxx, proteins with critical roles in oncogenic transformation, interferon-mediated viral resistance and response to PML-directed cancer therapeutics. Sp100 isoforms contain PHD, Bromo and HMG domains and are highly sumoylated at ND10/PML bodies, all characteristics suggestive of a role in chromatin mediated gene regulation. However, a clear role for Sp100 in oncogenesis has not been defined. Using isoform-specific knockdown techniques, we show that most human diploid fibroblasts, which lack Sp100, rapidly senesce. microarray analysis of mRNAs expression in BJV (collected at passage 47) and BJ-S (collected at passage 35). In addition, samples were treated for 24 h with 1000 U/ml IFNB. All RNAs were collected in triplicates of biological samples.
2012-12-04 | E-GEOD-20613 | biostudies-arrayexpress
Project description:Identifying the functions of proteins, which define specific subnuclear structures and territories, is important for understanding eukaryotic nuclear dynamics. Sp100 is a prototypical protein of ND10/PML bodies and co-localizes with the proto-oncogenic protein PML and Daxx, proteins with critical roles in oncogenic transformation, interferon-mediated viral resistance and response to PML-directed cancer therapeutics. Sp100 isoforms contain PHD, Bromo and HMG domains and are highly sumoylated at ND10/PML bodies, all characteristics suggestive of a role in chromatin mediated gene regulation. However, no clear role for the Sp100 component of PML bodies in oncogenesis has been defined. Using isoform-specific knockdown techniques, we show that most human diploid fibroblasts, which lack Sp100, rapidly senesce and discuss gene expression changes associated with this rapid senescence.
2012-12-04 | GSE20613 | GEO
Project description:ATO is a therapeutic agents used to treat APL, a disease caused by a chromosomal translocation of the RARα gene that can occur reciprocally with the PML gene. The mechanisms through which ATO function and how increased levels of ATO adversely affect the cell are not fully characterized though they involve the SUMOylation, the ubiquitylation and the degradation of the PML/RARα oncoprotein through the PML moiety. Changes in protein SUMOylation, phosphorylation and ubiquitylation were profiled using large-scale proteomic workflows on HEK293 cells following exposure to typical (1 μM) or elevated (10 μM) ATO for 4h to understand the mechanism that underlies the cytotoxicity induced with important ATO levels. Our analyses revealed that 88 proteins displayed divergent SUMOylation with elevated ATO compared to the lower dose, where the latter caused changes in SUMOylation of 4 proteins, including PML. Some of these differing SUMOylation events occurred on known substrates of caspase-3. A similar phenomenon was observed in the phosphoproteomic studies, where 48 proteins were specifically regulated with elevated ATO levels, while low ATO doses barely altered the phosphoproteome. Elevated levels of ATO cause the erroneous SUMOylation and phosphorylation of a vast amount of substrates, which may be responsible for its cytotoxic effects.
2020-04-06 | PXD016166 | Pride
Project description:We found that HOXB7 promotes HCC cell proliferation, migration, and invasion. To further explore the mechanism, we performed a cDNA microarray assay to compare the differential gene expression profiles of HOXB7 depletion (HOXB7-siRNA-treated) and negative control siRNA-treated in MHCCLM3 cells.
2019-04-02 | GSE80104 | GEO
Project description:Human papillomaviruses (HPVs) target PML nuclear bodies during infectious entry and PML protein is important for efficient transcription of incoming viral genome.We used shRNA to knockdown PML protein in HaCaT keratinocytes to further investigate the role of PML protein in HPV entry. We used microarrays to compare the transcriptome of PML protein-deficient with vector control-transduced HaCaT cells.
2016-11-17 | GSE89937 | GEO
Project description:BACKGROUND & AIMS: Hepatocellular carcinoma (HCC) has a high mortality rate due to the lack of effective treatments and drugs. Arsenic trioxide (As2O3, ATO, arsenious acid), which has been proved to successfully treat acute promyelocytic leukemia (APL), was recently reported to show therapeutic potential in solid tumors including liver cancer. Although the mechanistic effects of ATO in APL are established, its anticancer mechanism of action in HCC is still unclear. METHODS: We established an HCC subcutaneous xenograft and intrahepatic metastasis mouse model. In CSC models, tumorspheres and the flow cytometry analysis of CSC markers together with limiting dilution and serial transplantation were used. We compared mRNA expression profiles of the ATO-treated and control cells with mRNA microarray. The expression of target molecule or a clinical correlation was analyzed by immunohistochemistry staining in tissues from ATO-treated mouse and 76 HCC patients. We generated five stable minichromosome maintenance protein 7 (MCM7)-knockdown and two stable MCM7-overexpression HCC cell lines. The chromatin immunoprecipitation (ChIP) assays, immunoprecipitation (IP) assays, the dual luciferase reporter assays, a green biarsenical labeling reagent (FlAsH-EDT2) and a “competing endogenous RNA” (ceRNA) analysis were used. RESULTS: ATO could inhibit the liver tumor-initiating capacity and distant metastasis and prolongs survival in mice. We then screened and found that ATO downregulates the overexpression of MCM7 which is correlated with the progression and prognosis in HCC patients. Knockdown of MCM7 expression recapitulates the inhibition function of ATO on self-renewal of cancer stem cells (CSCs), while overexpression of MCM7 abolishes the inhibition function of ATO on tumorsphere formation. Most importantly, we revealed that ATO directly binds to the MCM7 protein and disturbs the interaction between serum response factor (SRF) and MCM7, resulting in downregulation of MCM7 transcription. A ceRNA analysis also indicated the alterations of endogenous MCM7-associated gene networks involved in stemness-related signaling pathways and cell differentiation. CONCLUSIONS: Here, for the first time, we report that ATO inhibits liver CSCs through blocking the interaction between SRF/MCM7 and suppressing MCM7 autoregulation activity.
2019-07-02 | GSE111935 | GEO