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Next Generation Sequencing of Gene expression changes in U2OS osteosarcoma cells with PML silencing

ABSTRACT: We used next generation sequencing to analyze the gene expression changes in U2OS osteosarcoma cells expressing shRNA targeting the promyelocytic leukemia (PML) gene transcripts

ORGANISM(S): Homo sapiens

PROVIDER: GSE94126 | GEO | 2017/06/13

SECONDARY ACCESSION(S): PRJNA369001

REPOSITORIES: GEO

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U2OS osteosarcoma cells LC-MSMS

Project description:In order to identify the targets of miR-193a-5p in osteosarcoma U2OS cell line, we used a lentivirus-mediated expression system to overexpressing miR-193a precusor, miR-193a-5p target sequence and non-target sequence, respectively, in osteosarcoma cell line U2OS. A tandem mass tag (TMT)-based quantitative proteomic strategy was employed to identify the global profile of miR-193a-5p-regulated proteins. order to identify the targets of miR-193a-5p, we used a lentivirus-mediated expression system to overexpressing miR-193a precusor, miR-193a-5p target sequence and non-target sequence, respectively, in osteosarcoma cell line U2OS. A tandem mass tag (TMT)-based quantitative proteomic strategy was employed to identify the global profile of miR-193a-5p-regulated proteins.

2021-09-08 | PXD013987 | Pride

Gene regulation by m6A demethylase ALKBH5 in U2OS osteosarcoma

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Gene expression analysis of mesenchymal stem cells (MSC), osteoblasts and the U2OS (osteosarcoma) cell line

Project description:Transcriptional profiling of MSC, Osteoblasts and U2OS cells. The aim was to quantitate relative gene expression in MSC, osteoblasts and U2OS. MSC and osteoblasts were used as normal cells in this study because osteosarcoma most likely originates from MSC or osteoblasts.

2012-03-02 | GSE27900 | GEO

Spontaneous cell competition in U2OS human osteosarcoma cells.

Project description:The study compares the transcriptional profiles of U2OS human osteosarcoma cells and those of two single-cell derived sub-lines carrying a stably integrated H2BmCherry (U2OS-R1) or H2B-YFP (U2OS-YFP) expression cassette. U2OS-R1 and U2OS-YFP cell spontaneously undergo apoptosis upon co-culture with the parental (Wt) U2OS cell population. Furthermore, YFP cells also undergo apoptosis upon co-culture with R1 cells. This behavior is similar to the \cell competition\ phenomenon described in the Drosophila imaginal disc and the mouse epiblast (for review, see , where fast-growing \fit\ cells induce apoptosis in slow-growing, less \fit\ neighbors. The mRNA expression profiles of Wt, R1 and YFP cells cultured alone or in pairwise combinations for 48h were analyzed after cell sorting by RNA microarray hybridization using Affymetrix Human Gene ST 1.0 chips.

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PML regulates NF-ÎºB phosphorylation and transcriptional activity

Project description:The transcription factor NF-ÎºB is considered the master regulator of the immune response but also acts broadly to regulate gene expression that influences cell survival, proliferation and differentiation. Post-translational modification of NF-ÎºB, phosphorylation in particular, is essential for the transactivation activity of NF-ÎºB. Emerging evidence suggests that the regulation of NF-ÎºB in the nucleus is critical in controlling gene expression. Promyelocytic Leukemia (PML) is a nuclear protein that forms nuclear bodies (PML NBs), sub-nuclear structures that are associated with transcriptionally active genomic regions that have been implicated in multiple processes such as apoptosis, senescence and anti-viral responses. Chromosomal translocations leading to the expression of a PML-retinoic acid receptor-Î± (PML-RARÎ±) fusion protein are causative for acute promyelocytic leukemia (APL) characterised by a differentiation block at the promyelocytic state of myeloid development. Here we demonstrate that PML is required for phosphorylation of NF-ÎºB p65 and that PML is essential for NF-ÎºB- induced transcriptional responses. Our analysis of available transcriptional profiles of all-trans retinoic acid treated acute promyelocytic leukemia (APL) cells identifies a NF-ÎºB transcriptional programme suppressed by PML-RARÎ±. We further demonstrate that PML-RARÎ± inhibits NF-ÎºB phosphorylation and transcriptional activity. Our findings demonstrate a critical role for PML in promoting NF-ÎºB transcriptional activity which may contribute to APL initiation and maintenance. WT and PML-/- MEFs were analysed for gene expression analysis. Total of 12 samples, inlcluding triplicates were utilized. WT MEFs and PML-/- were stimulated with TNFÎ± for three hours and analysed for gene expresison using unstimulated WT MEFs as control.

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Profiling of PML-body associated regions

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Gene expression and ChIP-seq analyses of mesenchymal stem cells, osteoblasts and the U2OS osteosarcoma cell line

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2012-03-02 | E-GEOD-35576 | biostudies-arrayexpress

PML Nuclear Bodies are stress-responsive sumoylation/degradation compartments regulating KAP1 silencing function in embryonic stem cells

Project description:PML drives the assembly of PML Nuclear Bodies (NBs), where it recruits many serendipitously-identified proteins, including the SUMO-E2 enzyme UBC9. Interferons, arsenic or oxidative stress, all enhance NB-formation. Here demonstrate that PML is required for efficient basal sumoylation in mouse embryonic stem cells (mESCs) and immediate stress-responsive sumoylation in mouse liver or Acute Promyelocytic Leukemia (APL). Biochemically, PML NBs confer an oxidation-protective environment for the redox-sensitive UBC9 activity, which, together with enzyme/target concentration/immobilization, favors processive SUMO2/3 conjugation. Accordingly, PML-facilitated sumoylation is accompanied by ubiquitination and degradation of some targets. In vivo proteomic analysis of SUMO2 conjugates in APL identified therapy-responsive targets, among which the prominent KAP1 complex of epigenetic regulators. In mESCs, PML is required for SUMO-dependent KAP1 repressive activity and for the resulting silencing of transposable elements and 2-cell-like genes. The ES status is further regulated by a PML-facilitated repressive sumoylation of the Dppa2 zygote genome activation driver. These findings establish the biochemical function of PML NBs in vivo and unveiling an unsuspected epigenetic control of key ESC targets by PML.

2022-09-14 | PXD019609 | Pride

Gene expression profiles of U2OS human osteosarcoma cell lines with ablation of NR1D1 or NR1D2 gene

Project description:We have recently established a panel of mutant U2OS human osteosarcoma cells lacking either REV-ERBα or REV-ERBβ (encoded by NR1D1 and NR1D2 genes, respectively) expression by a CRISPR/Cas9 and dual sgRNA-mediated gene deletion strategy. We then intended to dissect redundant and isoform-specific roles of these circadian nuclear receptors in controlling their target genes by comparing transcriptome profiles among wild-type and mutant U2OS cells.

2024-01-01 | GSE248721 | GEO

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