Transcription profiling of human myeloma versus lymphoma cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Louis Staudt
PROVIDER: E-GEOD-9031 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:To identify genes more highly expressed in Myeloma celllines v.s lymphoma cell lines. Keywords: cell type comparison design
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Project description:The transcriptional profile of the human multiple myeloma (MM) cell line MM.1S treated with MLN4924 vs control MM.1S cells was characterized by oligonucleotide microarray analysis, using the human U133 plus 2.0 Affymetrix GeneChip, according to previously described protocols for total RNA extraction and purification; cDNA synthesis; in vitro transcription reaction for production of biotin-labeled cRNA; hybridization of cRNA with U133plus2.0 Affymetrix gene chips; and scanning of image output files. Scanned image output files were analyzed using DNA-Chip Analyzer (dChip) (www.dchip.org), including conversion to DCP files, normalization and modeling. The gene expression profile of MM.1S cells for each time point of MLN4924 treatment was compared to the profile of control MM.1S cells. The NEDD8 activating enzyme (NAE) is upstream of the 20S proteasome in the ubiquitin/proteasome pathway and catalyzes the first step in the neddylation pathway. NEDD8 modification of cullins is required for ubiquitination of cullin-ring ligases (CRLs), which regulate degradation of a distinct subset of proteins. The more targeted impact of NAE on protein degradation prompted us to study MLN4924, an investigational NAE inhibitor, in preclinical multiple myeloma (MM) models. In vitro treatment with MLN4924 led to dose-dependent decrease of viability in a panel of human MM cell lines. In this analysis, we evaluated the molecular changes triggered in MM.1S myeloma cells by their in vitro treatment with MLN4924. The transcriptional profiles of each experimental condition were characterized by oligonucleotide microarray analysis, using the human U133 plus 2.0 Affymetrix GeneChip. The human multiple myeloma (MM) cells MM.1S were cultured in vitro in the presence or absence of the NEDD8 activating enzyme (NAE) inhibitor MLN4924 for 8, 16 or 24hrs. The gene expression profiles of drug treated cells were compared with the profiles of control MM.1S cells.
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2006-07-04 | E-GEOD-4732 | biostudies-arrayexpress
Project description:We recently defined a gene expression-based signature of high-risk multiple myeloma; this predictive signature was developed with and independently validated for newly diagnosed patients treated with high dose therapy and stem cell rescue. Here we use Phase 3 clinical trial data to show that this signature also predicts short survival in relapsed disease treated with single agent bortezomib or high dose dexamethasone. In addition, a survival signature derived with relapsed myeloma samples identified newly diagnosed patients with short survival. Taken together these data suggest that a similar biology underlies poor outcome in both newly diagnosed and relapsed myeloma and provide strong evidence that the high-risk signature is a powerful tool to identify patients who are candidates for new therapeutic regimens. Keywords: Model validation See above (Series_summary)
2011-08-19 | E-GEOD-8991 | biostudies-arrayexpress
Project description:Attempts at modeling chromosomal translocations involving MALT1 gene, hallmarks of human mucosa-associated lymphoid tissue (MALT) lymphoma, have failed to reproduce the disease in mice. Here we describe a transgenic model in which MALT1 expression was targeted to mouse hematopoietic stem/progenitor cells. In Sca1-MALT1 mice, MALT1 deregulation activated the NF-kappaB pathway in Sca1+ cells, promoting selective B-cell differentiation and mature lymphocyte accumulation in extranodal tissues, progressively leading to the development of clonal B-cell lymphomas. These tumors recapitulated the histopathological features of human MALT lymphomas, presenting typical lymphoepithelial lesions and plasmacytic differentiation. Transcriptional profiling of Sca1-MALT1 murine lymphomas revealed overlapping molecular signatures with human MALT lymphomas, including MALT1-mediated NF-kappaB activation, pro-inflammatory signaling and XBP1-induced plasmacytic differentiation. Moreover, murine Malt1 showed proteolytic activity by cleaving Bcl10 in Sca1-MALT1 lymphomas. Our novel technological approach has allowed modeling human MALT lymphoma in mice, which represent unique tools study MALT lymphoma biology and evaluate anti-MALT1 therapies. Keywords: lymphoma profiling, MALT lymphoma 97 samples were analized of which 13 were normal B-cell purified subpopulations and 84 lymphoma samples (31 MALT lymphomas, 26 DLBCL, 15 FCL and 12 SMZL)
2012-07-09 | E-GEOD-25638 | biostudies-arrayexpress
Project description:This laboratory studies the T cell recognition of glycolipid antigens, including the biochemical characterization of glycolipid antigens, the cell biology of glycolipid antigen presenting machinery, the chemical synthesis of self and foreign glycolipids, and the cellular immunology that might shed light on finding glycolipid targets for adjuvant and vaccine development. In myeloid patients, the suppression of NKT cells has been reported. This suppression is mediated by endogenous glycolipid antigens presented by CD1d, a non-classic MHC molecule. Tumor B cells express CD1d molecule and preserve the capacity in presenting glycolipid antigens to NKT cells. However, the identity of the tumor glycolipid antigens remain unknown. We recently identified isoglobotrihexosylceramide (iGb3), as one endogenous ligand for human NKT cells. We have also purified iGb3 from thymuses of pediatric patients. Thus we hypothesize that iGb3 might be directly linked to the NKT suppression in myeloma patients. The processing of iGb3 requires the “assembly line” of glycosyltransferases, the glycosidases and sphingolipid activator proteins. The loading of iGb3 antigen is dependent on lipid transfer proteins such as saposins, and the more recently characterized CD1e molecule. Thus we used the Glyo-chip approach to have a systemic survey of the above enzyme and protein components. We hope to find clues to help us in understanding the glycolipid antigen presentation in tumor B cells. EXPERIMENT: We purified RNA from 2 myeloma cell lines (U226 and 8226) by the RNAqueous kit from Ambion, TX. RNA was also purified from 2 lymphoma cell lines (Daudi and RL). 4 samples were provided to Core E of Consortium of Functional Genomics for Glyco-chip version 2 array.
2011-03-02 | E-GEOD-27600 | biostudies-arrayexpress
Project description:Conventional anti-cancer drug screening is typically performed in the absence of accessory cells (e.g. stromal cells) of the tumor microenvironment, which can profoundly alter anti-tumor drug activity. To address this major limitation, we have developed assays (e.g. the tumor cell-specific in vitro bioluminescence imaging (CS-BLI) assay) to selectively quantify tumor cell viability, in presence vs. absence of non-malignant stromal cells or drug treatment. These assays have allowed us to identify that neoplastic cells from diverse malignancies exhibit stroma-induced resistance to different anti-tumor agents. In this analysis, we evaluated the molecular changes triggered in myeloma cells by their in vitro interaction with stromal cells. The transcriptional profile of 3 human multiple myeloma (MM) cell lines (MM.1S, MM.1R, INA-6) co-cultured with stromal cells vs. when cultured alone was characterized by oligonucleotide microarray analysis, using the human U133 plus 2.0 Affymetrix GeneChip. Three human multiple myeloma (MM) cell lines (MM.1S, MM.1R, INA-6) stably expressing green fluorescent protein (GFP) were cultured in vitro for 24hrs either alone or in the presence of the human bone marrow stromal cell line HS-5. Fluorescence activated cell sorting was used to separate the GFP+ MM cells from GFP- stromal cells. The gene expression profiles of MM cells after their co-culture with stromal cells were compared with the profiles of MM cells cultured alone, according to previously described protocols for total RNA extraction and purification; cDNA synthesis; production of biotin-labeled cRNA; hybridization of cRNA with U133plus2.0 Affymetrix gene chips; and scanning of image output files. Scanned image output files were analyzed using DNA-Chip Analyzer (dChip) (www.dchip.org), including conversion to DCP files, normalization and modeling, and averaging of duplicate chips according to standard parameters recommended by the software. For each cell line, the gene expression profile in the presence of stomal cells was compared to the profile of the same cell line cultured in the absence of stromal cells. Technical replicates for each condition were analyzed (total of 12 gene expression profiles).
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