Transcriptomic Profile of OCI-AML-20 Cell Line
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE120834 | GEO | 2018/10/05
REPOSITORIES: GEO
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Project description:Transcriptomic Profile of OCI-AML-20 Cell Line
| PRJNA494672 | ENA
Project description:Purpose: Treatment of acute promyelocytic leukemia (APL) with the retinoid, all trans retinoic acid (ATRA), along with standard chemotherapy has significantly improved survival compared to chemotherapy alone1. ATRA mediates its benefit in APL by overcoming the transcriptional block mediated by PML-RAR-alpha fusion oncoprotein, thereby, restoring expression of retinoid response genes2. The therapeutic benefits observed with ATRA treatment in APL have not been achieved in the other more common sub-types of acute myeloblastic leukemia (AML)3. This likely reflects the recruitment of histone deacetylase complexes by other recurrent chromosomal translocations in AML cells4. In this experiment, we evaluated if treatment of the AML cell line, OCI/AML-2, with the histone deacetylase inhibitor, valproic acid (VPA), would alter the expression of sub-sets of genes by itself or in conjunction with ATRA that have been shown to be modulated by ATRA in APL2. Keywords: other
2005-05-17 | GSE2668 | GEO
Project description:Nucleostemin (NS; product of the GNL3 gene) is a nucleolar/nucleoplasm shuttling GTPase whose levels are high in stem cells while rapidly decreasing upon differentiation. NS levels are also high in several solid and hematological neoplasms, including acute myeloid leukemia (AML). While a role in telomere maintenance, response to stress stimuli and in favoring DNA repair has been proposed in solid cancers, little or no information is available as to the role of nucleostemin in AML. Here we investigate this issue with a proteomics approach. We use as a model system the OCI-AML 3 cell line harboring a heterozygous mutation at the NPM1 gene, which is the most frequent driver mutation in AML (approximately 30% of total AML cases). We show that NS is highly expressed in this cell line but, contrary to what previously shown in other cancers, its presence is dispensable for cell growth and viability. However, proteomics analysis of OCI-AML 3 cell line before and after nu-cleostemin (NS) silencing showed several effects in different biological functions as highlighted by ingenuity pathway analysis (IPA). In particular, we report an effect in down-regulating DNA repair through homologous recombination and we confirmed higher DNA damage rate in OCI-AML 3 cells when NS is depleted, which considerably increases upon stress induced by the topoisomerase II inhibitor etoposide.
2022-08-11 | PXD034012 | Pride
Project description:Purpose: Treatment of acute promyelocytic leukemia (APL) with the retinoid, all trans retinoic acid (ATRA), along with standard chemotherapy has significantly improved survival compared to chemotherapy alone1. ATRA mediates its benefit in APL by overcoming the transcriptional block mediated by PML-RARï¡ fusion oncoprotein, thereby, restoring expression of retinoid response genes2. The therapeutic benefits observed with ATRA treatment in APL have not been achieved in the other more common sub-types of acute myeloblastic leukemia (AML)3. This likely reflects the recruitment of histone deacetylase complexes by other recurrent chromosomal translocations in AML cells4. In this experiment, we evaluated if treatment of the AML cell line, OCI/AML-2, with the histone deacetylase inhibitor, valproic acid (VPA), would alter the expression of sub-sets of genes by itself or in conjunction with ATRA that have been shown to be modulated by ATRA in APL2. Experiment Overall Design: Methods: OCI/AML-2 cells were cultured at 37°C and 5% CO2 in ï¡MEM growth media supplemented with antibiotics and 10% fetal calf serum (HyClone, UT, USA). The drugs, ATRA and VPA, were obtained from Sigma-Aldrich Canada Ltd. (ON, CAN) and were re-suspended in 100% ethanol. OCI/AML-2 cells were treated with ATRA as a single 10-6 M dose and VPA was dosed at 0.6mM every 8 hours over 24 hours. The following four treatment combinations were evaluated: i) controls (solvent only) ii) ATRA iii) VPA iv) ATRA + VPA. Experiment Overall Design: Suspension cells were pelleted at 300 g 24 h after initial drug exposure. Total RNA was isolated using an RNeasy kit (Qiagen Inc., Canada) and stored at â70°C in DEPC-H2O. Total RNA was then further concentrated to 2.5µg/ïL by ethanol precipitation overnight at â20°C in 0.3M sodium acetate pH 5.2 (Sigma-Aldrich Canada Ltd.). Experiment Overall Design: GeneChip experiments were carried out by the Microarray Facility, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON. A total of 20µg of total RNA was used to generate biotin labeled cRNA probes according to Affymetrixâs recommended protocol using a labeling kit from EnzoBiochem, Inc. (NY, USA). A total of 15µg of the biotin labeled cRNA was hybridized onto the human U133A Affymetrix GeneChip. The GeneChip was washed as per the Affymetrix EukGE-ws2v4 protocol available at (https://www.affymetrix.com/site/login/login.affx). The GeneChip was scanned using a GeneArray 2500 scanner (Agilent, CA, USA) and hybridization intensity was obtained and detection p value and signal were calculated using MAS 5.0 software. Target signal was set to 150 for scaling for all of the experiments. The output chp file was exported to text file and used for further analysis with the Multiple experiment viewer (MeV) version 2.2 available from the Institute for Genomic Research at http://www.tigr.org/. Signal intensities obtained from the OCI/AML-2 cells treated with ATRA, VPA, or ATRA + VPA were compared to untreated OCI/AML-2 controls. Only genes that were identified as present (P) and displayed more than two fold change in signal intensity compared to untreated cells (controls) were carried forward for further analysis. Gene expression experiments were normalized using total intensity, median centered and log(2) transformed to give equal weight to expression values relative to the median for analysis. Unsupervised hierarchical clustering was performed using average linkage and Pearson correlation as a measure of distance. Experiment Overall Design: Results: Relatively few genes were regulated by ATRA treatment in OCI/AML-2 cells. However, treatment of OCI/AML-2 cells with VPA altered the expression of genes that encode for proteins involved with regulation of cell cycle, interferon response, apoptosis and differentiation. Examples of genes depressed by VPA, but not ATRA, involved regulators of cell cycle, cyclin A2 and MYC. The combination of ATRA + VPA further suppressed expression of these genes. Genes such as IRF1, neutrophilic cytosolic factor, ICAM3 and C/EBPï¢ increased in response to ATRA in OCI/AML-2 cells whereas VPA did not alter their expression over untreated OCI/AML-2 cells. However the combination of ATRA + VPA further enhanced the expression of these genes. Examples of genes induced by VPA that were not affected by ATRA in OCI/AML-2 cells include cell surface markers CD9, and MHC class II, promoters/enhancers of apoptosis such as MAPK kinase, interferon responsive genes, and caspase 7, and negative regulators of cell cycle like p21 and p19. The addition of ATRA to VPA increased the expression of some, but not all of these genes. It would appear that VPA dramatically affects the gene expression pattern of OCI/AML-2 cells, and modulates the expression of a set of genes, similar to those modulated by ATRA in APL cells2. Experiment Overall Design: References Experiment Overall Design: 1. Tallman MS, Andersen JW, Schiffer CA, Appelbaum FR, Feusner JH, Ogden A, Shepherd L, Experiment Overall Design: Willman C, Bloomfield CD, Rowe JM, Wiernik PH. All-trans-retinoic acid in acute Experiment Overall Design: promyelocytic leukemia. N Engl J Med 1997; 337(15):1021-1028. Experiment Overall Design: 2. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Experiment Overall Design: Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods Experiment Overall Design: and application to hematopoietic differentiation. Proc Natl Acad Sci U S A 1999; Experiment Overall Design: 96(6):2907-2912. Experiment Overall Design: 3. Estey EH, Thall PF, Pierce S, Cortes J, Beran M, Kantarjian H, Keating MJ, Andreeff Experiment Overall Design: M, Freireich E. Randomized phase II study of fludarabine + cytosine arabinoside + Experiment Overall Design: idarubicin +/- all-trans retinoic acid +/- granulocyte colony- stimulating factor in poor Experiment Overall Design: prognosis newly diagnosed acute myeloid leukemia and myelodysplastic syndrome. Experiment Overall Design: Blood 1999; 93(8):2478-2484 Experiment Overall Design: 4. Gelmetti V, Zhang J, Fanelli M, Minucci S, Pelicci PG, Lazar MA. Aberrant Experiment Overall Design: recruitment of the nuclear receptor corepressor-histone deacetylase complex by the acute Experiment Overall Design: myeloid leukemia fusion partner ETO. Mol Cell Biol 1998; 18(12):7185-7191.
2008-06-12 | E-GEOD-2668 | biostudies-arrayexpress
Project description:Identification of genes that regulate clonogenicity of AML cells is hindered by the difficulty of isolating pure populations of cells with defined proliferative abilities. Using early passages of the OCI/AML-4 cell line we sought to determine genes differentially expressed between clonogenic and non-clonogenic cells. We previously shown that OCI/AML-4 clonal siblings display coordinated growth patterns, so that the behaviour of a single cell that is destroyed in the generation of global single cell cDNA may be predicted by the growth patterns of its clonal siblings. Cells were plated in 96 well plates at limiting dilutions. Localized clusters of four cells were identified and micromanipulated such that three of the constituent cells were placed separately into individual microtitre wells containing growth medium and a feeder layer of OP9 cells, while the fourth cell was lysed and processed for global RT-PCR. The cells in each culture well were counted at 2 -3 day intervals until growth stopped. In this manner cDNA was generated from individual clonogenic OCI/AML-4 cells (sibling cells able to generate between 9-100 cells) or from individual non-clonogenic OCI/AML-4 cells (sibling cells were not able to generate more than 8 cells). Respective single cell cDNA was then pooled and compared by hybridization to cDNA microarrays. Using early passages of the OCI/AML-4 cell line cDNA was obtained from 17 clonogenic single cells (sibling cells able to generate between 9-100 cells) and 20 non-clonogenic single cells (sibling cells were not able to generate more than 8 cells). These cDNAs were pooled and hybridized to the cDNA microarray was conducted as three replicates, including one replicate which was a dye-swap.
2011-06-01 | E-GEOD-28612 | biostudies-arrayexpress
Project description:BRD4, a member of the BET family of histone readers, binds to acetylated lysine of histone H3 and promotes assembly of super-enhancer complexes that drive expression of key oncogenes in acute myeloid leukemia (AML) and other cancers. ARV-825 is a proteolysis-targeting chimera (PROTAC) that targets BRD4 for CRBN-mediated ubiquitination and degradation. We treated the AML cell line OCI-AML3, as well as primary tumor cells from a case of AML, with ARV-825 in vitro. At low concentrations, ARV-825 caused profound and sustained reduction in BRD4 protein levels. This caused reduction in transcription of key genes including MYC, anti-apoptotic BCL2 and BCLXL, PIM1, and CD44. Downstream effects included loss of CXCR4 surface expression and mitochondrial respiration; increased reactive oxygen species; toxicity to AML cells in vitro; and efficacy vs. OCI-AML3 cells in a mouse model of AML.
2019-10-01 | GSE101380 | GEO
Project description:Identification of genes that regulate clonogenicity of AML cells is hindered by the difficulty of isolating pure populations of cells with defined proliferative abilities. Using early passages of the OCI/AML-4 cell line we sought to determine genes differentially expressed between clonogenic and non-clonogenic cells. We previously shown that OCI/AML-4 clonal siblings display coordinated growth patterns, so that the behaviour of a single cell that is destroyed in the generation of global single cell cDNA may be predicted by the growth patterns of its clonal siblings. Cells were plated in 96 well plates at limiting dilutions. Localized clusters of four cells were identified and micromanipulated such that three of the constituent cells were placed separately into individual microtitre wells containing growth medium and a feeder layer of OP9 cells, while the fourth cell was lysed and processed for global RT-PCR. The cells in each culture well were counted at 2 -3 day intervals until growth stopped. In this manner cDNA was generated from individual clonogenic OCI/AML-4 cells (sibling cells able to generate between 9-100 cells) or from individual non-clonogenic OCI/AML-4 cells (sibling cells were not able to generate more than 8 cells). Respective single cell cDNA was then pooled and compared by hybridization to cDNA microarrays.
2011-06-01 | GSE28612 | GEO
Project description:Define and compare H3K4me2 enrichment in OCI-Ly1 and OCI-Ly7 cell lines.
2015-08-28 | GSE67381 | GEO
Project description:Transcriptomic Profile of OCI-AML-20 Cell Line in response to PRMT5 inhibition
| PRJNA685733 | ENA
Project description:MicroRNAs (miRNAs) play a pivotal role in the regulation of hematopoiesis and development of leukemia. Great interest emerged in modulating miRNA expression for therapeutic purposes. In order to identify miRNAs, which specifically suppress leukemic growth of AML with t(8;21), inv(16) or MLL-rearrangement by inducing differentiation, we conducted a miRNA expression profiling in a cohort of 90 cytogenetically characterized, de novo pediatric AML cases. Four miRNAs, specifically downregulated in MLL-rearranged, t(8;21) or inv(16) AMLs, were characterized by their tumor suppressive properties in cell lines representing those respective cytogenetic groups. Among those, forced expression of miR-9 reduced leukemic growth and induced monocytic differentiation of t(8;21) AML cell lines in vitro and in vivo. The tumor suppressive functions of miR-9 were specifically restricted to AML cell lines and primary leukemic blasts with t(8;21). On the other hand, these functions were not evident in AML blasts from patients with MLL-rearrangements. We showed that miR-9 exerts its effects through the cooperation with let-7 to repress the oncogenic LIN28B/HMGA2 axis. Thus, miR-9 is a tumor suppressor-miR which acts in a stringent cell context-dependent manner. In order to identify miRNAs, which specifically suppress leukemic growth of AML with t(8;21) (n=21), inv(16) (n=17) or MLL-rearrangement (n=35) by inducing differentiation, we conducted a miRNA expression profiling in a cohort of 90 cytogenetically characterized, de novo pediatric AML cases, which also included 12 t(15;17) and 5 t(7;12) samples.
2014-01-01 | E-GEOD-52541 | biostudies-arrayexpress