Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

EphA3 silencing in Multiple Myeloma Endothelial Cells

ABSTRACT: Transcription profiling analysis was performed on Multiple Myeloma Endothelial cells (MMECs) transiently transfected with EphA3-siRNA or control siRNA

ORGANISM(S): Homo sapiens

SUBMITTER: Vittorio Simeon

PROVIDER: E-MTAB-2519 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Proteogenomic landscape of multiple myeloma

Project description:Multiple myeloma is a plasma cell malignancy of the bone marrow. Despite therapeutic advances, multiple myeloma remains incurable and better risk stratification as well as new therapies are therefore highly needed. The proteome of multiple myeloma has not been systematically assessed before and holds the potential to uncover additional insight into disease biology and improved prognostic models. Here, we provide a comprehensive multi-omics analysis including deep tandem mass tag (TMT)-based quantitative global (phospho)proteomics, RNA sequencing and nanopore DNA sequencing of 138 primary patient-derived plasma cell malignancies encompassing treatment-naive multiple myeloma patients treated in clinical trials, plasma cell leukemia, and the premalignancy monoclonal gammopathy of undetermined significance (MGUS), as well as healthy controls. We found that the (phospho)proteome of malignant plasma cells is highly deregulated as compared to healthy plasma cells and is both defined by chromosomal alterations and extensive post-transcriptional regulation. A protein signature was identified that is associated with aggressive disease and more predictive for outcome than cytogenetic-based risk assessment in newly diagnosed multiple myeloma. Integration with functional genetics and single-cell sequencing revealed generally and genetic subtype-specific deregulated proteins and pathways in plasma cell malignancies that include novel potential targets for (immuno)therapies. These findings provide new insights in the biology of multiple myeloma and will be a unique resource for investigating new therapeutic approaches.

2024-07-09 | PXD043580 | Pride

Proteomic profiling reveals CDK6 upregulation as a targetable resistance mechanism for lenalidomide in multiple myeloma

Project description:The immunomodulatory drugs (IMiDs) lenalidomide and pomalidomide are highly effective treatments for multiple myeloma. However, virtually all patients eventually relapse due to acquired drug resistance with resistance-causing genetic alterations being found only in a small subset of cases. Here, we performed integrated global quantitative tandem mass tag (TMT)-based proteomic and phosphoproteomic analyses and RNA sequencing in five paired pre-treatment and relapse samples from multiple myeloma patients to investigate non-genetic resistance mechanisms. These analyses revealed a CDK6-governed protein resistance signature that includes myeloma high-risk factors such as TRIP13 and RRM1. Overexpression of CDK6 in multiple myeloma cell lines reduced sensitivity to IMiDs while CDK6 inhibition by palbociclib or CDK6 degradation by proteolysis targeting chimeras (PROTACs) is highly synergistic with IMiDs in vitro and in vivo. In conclusion, we found upregulation of CDK6 to cause lenalidomide resistance in multiple myeloma that can be overcome by pharmacological intervention.

2021-12-17 | PXD021265 | Pride

Transcription profiling of human samples of multiple myeloma patients with and without bone lytic lesion by MRI

Project description:This series represents samples of multiple myeloma patients with and without bone lytic lesion by MRI.

2007-09-25 | E-GEOD-755 | biostudies-arrayexpress

microRNA profiling of multiple myeloma bone marrow

Project description:Bone marrow microenvironment in MM contains a unique miR signature, which is partially present and detectable in the peripheral blood. A subset of miRs (let-7i, miR-106b, miR-15a, and miR16) shows aberrant expression in the precursor lesion of MGUS, while aberrant expression of other miRs (let-7a, miR-15a/b, miR-19b, miR-20a, miR-21, miR-223, and miR-361) is associated with cell proliferation and disease progression. miRNA profiling was performed using Agilent miRNA array platforms with RNAs isolated from the bone marrow supernatant of multiple myeloma.

2016-07-01 | E-GEOD-49261 | biostudies-arrayexpress

Transcription profiling of human samples from multiple myeloma patients treated with bortezomib or dexamethasone

Project description:The aims of this study were to assess the feasibility of prospective pharmacogenomics research in multicenter international clinical trials of bortezomib in multiple myeloma and to develop predictive classifiers of response and survival with bortezomib. Patients with relapsed myeloma enrolled in phase 2 and phase 3 clinical trials of bortezomib and consented to genomic analyses of pretreatment tumor samples. Bone marrow aspirates were subject to a negative-selection procedure to enrich for tumor cells, and these samples were used for gene expression profiling using DNA microarrays. Data quality and correlations with trial outcomes were assessed by multiple groups. Gene expression in this dataset was consistent with data published from a single-center study of newly diagnosed multiple myeloma. Response and survival classifiers were developed and shown to be significantly associated with outcome via testing on independent data. The survival classifier improved on the risk stratification provided by the International Staging System. Predictive models and biologic correlates of response show some specificity for bortezomib rather than dexamethasone. Informative gene expression data and genomic classifiers that predict clinical outcome can be derived from prospective clinical trials of new anticancer agents. Experiment Overall Design: Purified myeloma samples were collected prior to enrolment in clinical trials of bortezomib (PS-341). Samples were subject to replicate gene expression profiling using the Affymetrix 133A/B microarray. Data was normalized in MAS5.0 and the median of replicates is reported. Data was normalized to a Ttimmed mean of 15o and is NOT log transformed. Various patient parameters are reported as well as response, TTP and survival upon treatment with bortezomib or dexamethasone.

2008-06-17 | E-GEOD-9782 | biostudies-arrayexpress

RNA-seq of human multiple myeloma cell lines JJN3, OPM2 and XG7 with PRMT5 inhibitor EPZ015938 versus untreated controls.

Project description:Evaluation of anti-myeloma effects of inhibition of PRMT5, involved in arginine methylation. Three human multiple myeloma cell lines were treated with the PRMT5 inhibitor EPZ015938. Transcriptional profiles were compared to untreated controls.

2022-03-11 | E-MTAB-11489 | biostudies-arrayexpress

Transcription profiling of human plasma cell samples from multiple myeloma patients

Project description:Samples in this series are pre-treatment bone marrow aspirates from multiple myeloma patients. Experiment Overall Design: Samples in this series are: Experiment Overall Design: 1. CD-138-selected plasma cells from bone marrow of patients with newly diagnosed multiple myeloma subsequently treated with high dose therapy and stem cell transplants termed Total Therapy 2 (pre-treatment TT2) Experiment Overall Design: 2. CD-138-selected plasma cells from bone marrow of patients with newly diagnosed multiple myeloma subsequently treated with Total Therapy 3 (pre treatment TT3). Experiment Overall Design: Overall Design: Experiment Overall Design: Gene expression signatures were used to: 1) develop unsupervised hierarchical cluster classes; 2) establish links with outcome following stem cell transplantation

2008-06-13 | E-GEOD-2658 | biostudies-arrayexpress

Transcription profiling of human U266, MM.1s, KMS11, 8226/S multiple myeloma cell lines treated with arsenic

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

Transcription profiling by array of human multiple myeloma cells and cell lines; bone marrow stromal cells, bone marrow CD3 cells, bone marrow CD14 cells, bone marrow CD15 cells and in vitro generated osteoclastic cells from myeloma patients; and normal plasmablasts and normal memory B cells.

Project description:Multiple Myeloma primary myeloma cells of 131 patients, 10 human myeloma cell lines, bone marrow stromal cells of 5 myeloma patients, bone marrow CD3 cells of 5 myeloma patients, bone marrow CD14 cells of 5 myeloma patients, bone marrow CD15 cells of 5 myeloma patients, in vitro generated osteoclastic cells of 7 myeloma patients, 7 normal plasmablasts and 6 normal memory B cells.

2011-03-08 | E-TABM-937 | biostudies-arrayexpress

Transcription profiling by array of human myeloma cell lines

Project description:30 human myeloma cell lines

2010-12-23 | E-TABM-1088 | biostudies-arrayexpress