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RNA sequencing in the Kasumi-1 cell line transfected with PHF19 shRNA or scrambled control shRNA

ABSTRACT: To investigate the fuctional role of PHF19 in the regulation of cell cycle progression in t(8;21) AML, we established Kasumi-1 cell line in which PHF19 gene has been knocked down by shRNA. We then performed bulk RNA sequencing to analyze the changes of gene expression profiling in the PHF19 knockdown cells as compared with the scrambled control cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE254526 | GEO | 2024/02/05

REPOSITORIES: GEO

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Detect accessible chromatin using ATAC sequencing in the Kasumi-1 cell line transfected with PHF19 shRNA or scrambled control shRNA

Project description:To investigate the function of PHF19 in the regulation of chromatin accessibility in t(8;21) AML, we established Kasumi-1 cell line in which PHF19 gene has been knocked down by shRNA. We then performed chromatin accessibility analysis using data obtained from ATAC-seq of the PHF19 knockdown cells and the scrambled control cells.

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Methylated RNA immunoprecipitation sequencing in the Kasumi-1 cell line transfected with WTAP shRNA or scramble control shRNA

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Expression analysis of Kasumi-1 cells treated with or without FTY720

Project description:The clinical outcomes of M2 subtype Acute Myeloid Leukemia (AML-M2) with t(8;21) are poor. Here we report that FTY720 (Fingolimod), a sphingosine analogue and an FDA approved drug for treatment of multiple sclerosis, showed great antitumorigenic activity against Kasumi-1 cell line, xenograft mouse model and leukemic blasts isolated from AML-M2 with t(8;21) patients. Primary investigation indicated that FTY720 caused cell apoptosis through caspase and protein phosphatase 2A (PP2A) activation. Transcriptomic profiling further revealed that FTY720 treatment could upregulate AML1 target genes and interfere with genes involved in ceramide synthesis. FTY720 treatment led to the elimination of AML1-ETO oncoprotein and caused cell cycle arrest. More importantly, FTY720 treatment resulted in rapid and significant increment of pro-apoptotic ceramide levels, determined by HPLC-ESI-MS/MS (high-performance liquid chromatography-electrospray ionization tandem mass spectrometry) based lipidomic approaches. Additionally, structural simulation model indicated that the directly binding of ceramide to inhibitor 2 of PP2A (I2PP2A) could reactivate PP2A and cause cell death. This study demonstrates, for the first time, that accumulation of ceramide plays a central role in FTY720 induced cell death of AML-M2 with t(8;21). Targeting sphingolipid metabolism by using FTY720 may provide novel insight into drug development for AML-M2 treatment. A six chip study using total RNA recovered from three separate cultures of DMSO-treated Kasumi-1 cells and three separate cultures of FTY720-treated Kasumi-1 cells.Each chip measures the expression level of genes from DMSO-/FTY720-treated Kasumi-1 cells.

2014-04-30 | E-GEOD-55772 | biostudies-arrayexpress

Paired ChIP-Seq studies of Kasumi-1 t(8;21) AML cells

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miRNA profiling of human acute myeloid leukaemia Kasumi-1 cell line CD34+38- compartment.

Project description:The t(8;21) Acute Myeloid Leukaemia (AML) Kasumi-1cell line with N822K KIT mutation, is a model system for leukemogenesis. As AML initiating cells reside in the CD34+CD38- fraction, we addressed the refined cytogenomic characterization and miRNA expression of Kasumi-1 cell line and its FACS-sorted subpopulations focussing on this compartment. By conventional cytogenetics, Spectral Karyotyping and array-CGH the cytogenomic profile of Kasumi-1 cells evidenced only subtle regions differentially represented in CD34+CD38- cells. Expression profiling by a miRNA platform showed a set of miRNA differentially expressed in paired subpopulations and the signature of miR-584 and miR-182 upregulation in the CD34+CD38- fraction.

2010-02-19 | E-TABM-909 | biostudies-arrayexpress

Effect of cabozantinib on transcriptome and signaling pathways in leukemic cell line Kasumi-1

Project description:To identify molecular effects of the tyrosine kinase inhibitor cabozantinib (XL184), we applied gene expression profiling on human acute leukemic cell lines Kasumi-1, which harbors t(8;21) coupled with KIT mutation, by Whole Transcriptome Shotgun Sequencing (RNA-seq). After Kasumi-1 cells were treated with 100nM cabozantinib for 4h or 24h, differentially expressed genes (DEGs) of 124 genes upregulated and 416 were downregulated in 4h, and 184 genes upregulated and 69 genes were downregulated in 24h treatment, compared with vehicle group.

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The global transcriptome analysis of HCT116 cells transfected with scrambled or CBX4 shRNA

Project description:To investigate the molecular mechanism of CBX4 in CRC, the global transcriptomes were analyzed in HCT116 cells in which CBX4 was knocked down with shRNA, and these transcriptomes were compared to those of HCT116 cells transfected with scrambled shRNA.

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Phf19 knockdown effect on F9 embryonal carcinoma cells

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