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Interaction effects of knockdown of PML and TNFalpha treatment in HUVEC cells

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE35000 | GEO | 2013/01/10

SECONDARY ACCESSION(S): PRJNA151067

REPOSITORIES: GEO

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Interaction effects of knockdown of PML and TNFalpha treatment in HUVEC cells

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

The effects of knockdown of PML by different individual siRNAs in HUVEC cells

2012-05-31 | GSE29238 | GEO

RNA sequencing of HECTD3 knockdown during TNFalpha stimulation in primary HUVEC cells

Project description:We isolated and validated primary HUVECs from the neonatal umbilical cord vein, and performed genome-wide expression analysis to profile differentially expressed genes in control and HECTD3-KD HUVECs treated with or without TNFα for 2 hours. Compared with control HUVECs, 59 genes showed lower expression in HECTD3-KD HUVECs in response to TNFα. Most of them are NF-κB target genes, including adhesion molecules SELE (E-selectin), ICAM-1, and VCAM-1.

2022-06-29 | GSE201759 | GEO

The effects of knockdown of PML by different individual siRNAs in HUVEC cells

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

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.

2016-06-01 | E-GEOD-47828 | biostudies-arrayexpress

Profiling of PML-body associated regions

Project description:The promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin. To address functional roles of the PML-chromatin association, we conducted genome-wide profiling of PML body-associated regions.

2019-08-14 | GSE135560 | GEO

Genome-wide studies identify genes directly regulated by PML/RARα fusion protein

Project description:Acute promyelocytic leukemia (APL) is characterized by a specific t(15;17) chromosome translocation that generates the promyelocytic leukemia/retinoic acid receptor-α (PML/RARα) fusion gene. However, the global association between PML/RARα and transcriptional co-regulators, and the rules of their association in governing the key processes during the leukemogenesis remain obscure. Here, we performed the genome-wide binding profiling of PML/RARα, HDAC1 and P300, in NB4, an APL patient-derived cell line. We found that PML/RARα targets could be classified into two classes. Moreover, we also performed ChIP-seq of H3K27ac to determine super-enhancers in NB4. We identified a novel function of PML/RARα in super-enhancer regulation during the leukemogenesis of APL.

2020-08-26 | GSE126720 | GEO

Expression profiling in Human Umbilical Vein Endothelial Cells (HUVEC)

Project description:Whole transcriptome gene expression profiling of Normal -(HUVEC) Human Umbilical Vein Endothelial Cells The HUVEC gene expression results analyzed in this study are further described in Kustermann S. et al. (2014) A real-time impedance based screening assay for drug induced vascular leakage. A NimbleGen Homo sapiens Expression Array [100718_HG18_opt_expr] study using total RNA recovered from HUVECs grown until 80% confluency. Each microarray measures the expression level of 23,611 genes using 45,033 probe sets with three 60-mer probes (PM) per probe set. Each probe set is represented once on the array.

2014-01-07 | E-GEOD-52044 | biostudies-arrayexpress

ATAC-seq analyses with wild-type and PML KO mESCs

Project description:Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin, implying its crucial roles for particular genome functions. To investigate functional roles of PML bodies in chromatin organization, we conducted ATAC-seq with wild-type and PML KO mESCs.

2019-08-14 | GSE135561 | GEO

Genome-wide recognition of PML/RARa binding sites

Project description:PML/RARa is of crucial importance in acute promyelocytic leukemia (APL) both pathologically and therapeutically. Using a genome-wide approach, we identified in vivo PML/RARa binding sites in ZnSO4 treated PR9 cells. A total of 2,979 high quality binding sites were identified, representing 1,981 unique RefSeq genes. The supplementary bed file contains all 2,979 high quality PML-RARa binding sites reported in the paper.

2009-11-26 | GSE19202 | GEO

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