Gene expression of myeloma cell line (U266) transduced with Scr or shKDM3A cultured in normoxia or hypoxia
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE96858 | GEO | 2017/04/01
SECONDARY ACCESSION(S): PRJNA379947
REPOSITORIES: GEO
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Project description:In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, U266HR, derived from U266 cells cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used U266 cells and U266HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from U266 cells (normoxia or hypoxia) and exosomes derived from U266HR cells (hypoxia-resistant sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the U266HR cells significantly increased tube formation of HUVECs than those from U266 cells. To identify intercellular and exosomal miRNAs specifically expressed in hypoxia-resistant cells, we assess the expression profiles of intercellular and extracellular miRNAs in U266 cells and U266HR cells using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA).
2014-10-15 | GSE48910 | GEO
Project description:In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, U266HR, derived from U266 cells cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used U266 cells and U266HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from U266 cells (normoxia or hypoxia) and exosomes derived from U266HR cells (hypoxia-resistant sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the U266HR cells significantly increased tube formation of HUVECs than those from U266 cells. To identify intercellular and exosomal miRNAs specifically expressed in hypoxia-resistant cells, we assess the expression profiles of intercellular and extracellular miRNAs in U266 cells and U266HR cells using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA). U266 cells were cultured for 24 hours under hypoxic conditions (1% O2) or normoxic conditions (20% O2). The exosome fraction was obtained from culture medium using Exoquick Exosome Precipitation Solution (System Biosciences, Mountain View, CA, USA). Isolation of cellular and exosomal miRNAs was performed using the miRNsasy kit (Qiagen). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). RNU6B and a spike control (ath-miR159) were used as an invariant control for the cell and exosome, respectively. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturerM-bM-^@M-^Ys recommended program. Finally, all the raw data from each array was run on Data Assist Software ver.3.1 (Applied Biosystems).
2014-10-15 | E-GEOD-48910 | biostudies-arrayexpress
Project description:We used microarrays to examine changes in gene expression in multiple myeloma cell lines following treatment with arsenic trioxide and darinaparsin Experiment Overall Design: Four multiple myeloma cell lines (U266, MM.1s, KMS11, 8226/S) were treated with either arsenic trioxide (ATO) for 6, 24, or 48 hours or darinaparsin (DAR) for 6 or 24 hours; RNA was extracted from treated and control cells for microarray analysis
2009-02-01 | E-GEOD-14519 | biostudies-arrayexpress
Project description:Multiple myeloma (MM) is a malignant disorder characterized by the clonal proliferation of plasma cells (PCs) in the bone marrow (BM). The genetic background and clinical course of the disease are largely heterogeneous, and MM pathophysiology ranges from the premalignant condition of monoclonal gammopathy of undetermined significance (MGUS) to smoldering MM, symptomatic MM, and extramedullary MM/plasma cell leukemia (PCL). Recent genome-wide sequencing efforts have provided the rationale for molecularly aimed treatment approaches, identifying mutations that can be specifically targeted, such as those in the mitogen-activated protein kinase (MAPK) pathway, which represent the most prevalent mutations in MM. Among these, mutations affecting BRAF gene, detected in 4-15% of patients, are of potential immediate clinical relevance due to the availability of effective inhibitors of this serine-threonine kinase which are in fact being explored also in myeloma. In this study, we screened by next generation sequencing (NGS) a large and representative series of intramedullary and extramedullary MM patients, including primary and secondary plasma cell leukemia (pPCL and sPCL, respectively), for mutations in BRAF, NRAS and KRAS genes. We evaluated the relationship of identified variants with other clinical and biological features and determined the transcriptional signature associated with MAPK pathway activation in MM. To further elucidate the transcriptional programs modulated by BRAF activation in MM, we used the PLX4032 drug to inhibit BRAF activity in U266 human myeloma cell line (HMCL), carrying K601N mutation and showing constitutive activation of MEK/ERK signaling. After confirming its ability to suppress MAPK pathway and myeloma cell proliferation in culture in the U266 cell line, we investigated the specific modulation of gene expression induced by the drug. U266 cells were treated with PLX4032 (30 µM) or DMSO for 12 hours and subjected to gene expression profiling (GEP) analysis by using Affymetrix GeneChip Human Gene 1.0ST arrays.
2015-07-01 | E-GEOD-66292 | biostudies-arrayexpress
Project description:In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others. A part of the BM milieu is considered highly hypoxic, and myeloma cells in situ may be influenced by circumstances other than normoxia in vitro. Hence, we attempted to confirm the role of hypoxic MM-derived exosomes in the BM milieu. We established a novel hypoxia-resistant cell line, RPMI8226-HR derived from RPMI8226 cells, KMS-11-HR derived from KMS-11, U266-HR derived from U266, and IM-9-HR derived from IM-9 cultured for >4 months under hypoxia (1% O2), as a model of MM cells localizing in an extensively hypoxic milieu. We used RPMI8226 cells and RPMI8226-HR cells, as donor cells, and HUVECs as recipient cells. Exosomes derived from RPMI8226 cells (normoxia or hypoxia) and exosomes derived from RPMI8226-HR cells (hypoxia-resistant, HR sub-line) were used for validation of angiogeneic activity, such as tube formation assay. Exosomes derived from the RPMI8226-HR cells significantly increased tube formation of HUVECs than those from RPMI8226 cells.
2018-02-06 | GSE110113 | GEO
Project description:Purpose: We examined how transcriptional state changes relate to clonal selection as BRAF inhibitor resistance develops in BRAF-mutated myeloma. Methods: To this end we generated three single-cell clones from U266, a BRAFK601N -mutated myeloma cell line and DP6- a BRAFV600E myeloma cell line. All three U266 and DP6 clones were subjected to long-term dabrafenib treatment at their established IC50 doses (U266: 10uM, DP6 1nM). Bulk RNA-seq was performed before treatment, day 7, day 14, day 42 and at time of resistance. Results: Transcriptional adaptation after seven days was homogeneous for all clones, but was different across both cell lines. Oxidative phosphorylation (OxPhos) emerged as the most consistently enriched signaling pathway in persistent cells from both cell lines as compared to baseline. Conclusions: BRAF inhibition in BRAF-mutated myeloma cells leads to transcriptional reprogramming with induction of OxPhos-related genes within a brief period of time.
2022-03-13 | GSE168950 | GEO
Project description:Gene expression (GE) profiling of multiple myeloma (MM) cells is a promising means of identifying high-risk MM patients. The analyses depend on plasma cell purification by CD138+ cell separation. Considering the sensitivity of gene transcription, we wanted to test if cell separation distorts true in vivo GE patterns. We performed a controlled study of running 4 human myeloma cell lines (HMCLs: U266, INA-6, RPMI 8226, and NCI H929) through a CD138+ separation procedure identical to the handling of clinical samples. We then compared the resulting effects on gene expression. Using U266 as a screening model, we performed global GE analysis using the Affymetrix Human Gene 1.0 ST array. Sample cells showed significant changes (adj. p<0,05) in 670 genes compared to the non-separated controls. We searched for upregulated genes of myeloma and/or cancer relevance and chose (in decending fold change order) FOS, DUSP1, MIRN21, NFKBIA, and ATF4 for PCR validation. Note: Only U266 cells were used for microarray analysis. The other cell lines were used later to validate the array results.
2012-03-01 | E-MEXP-2961 | biostudies-arrayexpress
Project description:To identify epigenetically silenced genes in multiple myeloma (MM) cell lines and to determine the effects of 5-aza-2-deoxycytidine and trichostatin A on gene expression. We treated 3 multiple myeloma cell lines (MM1, NCI-H929, U266) with 5-aza-2-deoxycytidine and/or trichostatin A.
2008-02-01 | E-MEXP-1269 | biostudies-arrayexpress
Project description:Bortezomib therapy has been proven successful for the treatment of relapsed and/or refractory multiple myeloma (MM). However, both intrinsic and acquired resistance has already been observed. In this study, we explored the relationship between CD9 expression and bortezomib sensitivity in MM Both intrinsic and acquired resistance has already been observed. In this study, we explored the relationship between CD9 expression and bortezomib sensitivity in MM. We found that down-regulation of CD9 by methylation decreased bortezomib sensitivity in multiple myeloma. A six chip study using total RNA recovered from three separate wild-type cultures of U266 cells and three separate cultures of U266 with CD9 overexpression. Each chip measures the expression level of 45,033 genes from Homo sapiens with fourteen 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
2014-03-13 | E-GEOD-55818 | biostudies-arrayexpress
Project description:Here we report the use of high-throughput sequencing technologies (RNA-seq, ChIP-seq) to identify the molecular programme of PBX1 and FOXM1 in multiple myeloma cells (MM1S, U266 cell lines). We performed Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) against PBX1 in MM1S and U266 cells (n=2). In addition, we identifed the transcriptome of PBX1-depleted and FOXM1-depleted myeloma cells 3 days after transduction with shRNA-expressing lentiviral vectors. Molecular characterization revealed PBX1 as a novel epigenetic regulator of myeloma cell survival and proliferation. PBX1 directly and unilaterally controls the FOXM1 transcriptional programme and, together,they regulate the high-risk transcriptional signature of chr1q-amplified cells. Pharmacological inhibition of the unified PBX1-FOXM1 axis with thiostrepton showed selectivity against chr1q-amplified MM. Altogether, these data reveal PBX1-FOXM1 axis as a novel therapeutic avenue against chr1q-amplified MM.
2022-01-16 | GSE165060 | GEO