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Expression data from chronic lymphocytic leukemia (CLL) tumors and sorted CD19pos B cells from healthy donors

ABSTRACT: As part of a large study regarding the epigenetics of CLL we also acquired 3UTR expression arrays.

ORGANISM(S): Homo sapiens

PROVIDER: GSE50006 | GEO | 2015/12/01

SECONDARY ACCESSION(S): PRJNA215791

REPOSITORIES: GEO

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The Proteome Landscape of Chronic Lymphocytic Leukemia (CLL)

Project description:Many functional consequences of mutations on tumor phenotypes in chronic lymphocytic leukemia (CLL) are only partially known. This is in part due to a scarcity of information on the proteome of CLL. We profiled the proteome of 117 CLL samples with data-independent acquisition mass spectrometry (DIA-MS) and integrated the results with genomic, transcriptomic, functional data and clinical outcome. We found trisomy 12 and IGHV to be major determinants of proteome variation in CLL (1055 and 542 differential proteins FDR of 5%). Trisomy 12 was associated with limited protein abundance buffering. Protein complex analyses detected functional units involved in BCR/PI3K/AKT signaling in CLL with trisomy 12. We associated protein expression with response to anticancer drugs, and STAT2 protein expression emerged as a biomarker for the prediction of response to kinase inhibitors including BTK and MEK inhibitors. STAT2 protein levels were determined by gene dosage (trisomy 12), stabilization in a protein complex and linked to interferon signaling in CLL. This study highlights the emerging importance of protein abundance profiling in CLL biology.

2021-09-24 | PXD022198 | Pride

Genome-wide analysis of impact of B cells from the peripheral blood of chronic lymphocytic leukemia (CLL) patients versus B cells from healthy donors on CD14+ PBMCs from healthy donors

Project description:CD14+ cells in the PBMCs of CLL patients are converted into NLCs. CD14+ PBMCs from healthy donors when cultured with CLL cells give rise to differentiated cells called CD14CLL-cells, which are immunophenotypically similar to NLCs. CD14+ PBMCs from healthy donors when cultured with non-malignant B cells give rise to differentiated cells called CD14B-cells. Transcriptome wide analysis reveals genes involved in immune response to be significantly deregulated between CD14B-cells and CD14CLL-cells/NLCs.

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Expression data from chronic lymphocytic leukemia (CLL) tumors in two time points

2013-02-21 | GSE37168 | GEO

Genome-wide analysis of impact of B cells from the peripheral blood of chronic lymphocytic leukemia (CLL) patients versus B cells from healthy donors on CD14+ PBMCs from healthy donors

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Expression data from chronic lymphocytic leukemia (CLL) cells

Project description:We compared gene expression profiles of CLL patients with and without MYD88 L265P mutations, taking into consideration IGHV mutation status.

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Identification of NOTCH1 bound genes in chronic lymphocytic leukaemia (CLL) cells

Project description:NOTCH1 is mutationally activated in ~15% of cases of chronic lymphocytic leukaemia (CLL), but its role in B-cell development and leukemogenesis is not known. Here, we report that the active intracellular portion of NOTCH1 (ICN1) is detectable in ~50% of peripheral blood CLL cases lacking gene mutations. We identify a ‘NOTCH1 CLL gene expression signature’ in CLL cells, and show that this signature is significantly enriched in primary CLL cases expressing ICN1, independent of NOTCH1 mutation. NOTCH1 target genes include key regulators of B-cell proliferation, survival and signal transduction physiology. In particular, we show that MYC is a direct target of NOTCH1 via B-cell specific distal regulatory elements, thus implicating this oncogene in the pathogenesis of the disease.

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Expression data from chronic lymphocytic leukemia (CLL) tumors in two time points

Project description:As part of a large genetic evolution study we also acquired 3'UTR expression arrays at two time points for the same 18 patients with CLL. We have analysed the data to evaluate whether genetic evolution (somatic mutations and Somatic copy number alterations) also manifested at the transcriptome level, either globally, or at the level of pre-defined curated geneset that correspond to specfic evolving genetic lesions. Samples were collected at two time points along the patients clinical course, with 13 patients having samples before treatment and at relapse, and 5 patients that were long term non progressors had sampling at two time points without intevening therapy.

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Analysis of chronic lymphocytic leukemia CLL cells and normal B cells

Project description:We have analyzed 2 normal B cells isolated from peripheral blood and 5 CLL specimens with affy 133A microarray for expression. We used microarrays to analyze gene expression in normal B cells and CLL cells.

2009-09-10 | GSE18026 | GEO

CD40 stimulation of chronic lymphocytic leukemia (CLL) cells

Project description:In this experiment we in vitro activated CLL cells on a layer of fibroblasts expressing CD40L (3T40) or nothing (3T3) for 48 hours. After the 48 hours, cells were taken off the fibroblasts and sorted for viable CD19+ cells. Then we performed RNA sequencing.

2022-05-20 | GSE201341 | GEO

Expression data from healthy and malignant (chronic lymphocytic leukemia, CLL) human B-lymphocytes after B-cell receptor stimulation

Project description:Three different cell populations (6 healthy B-lymphocytes, 6 leukemic CLL B-lymphocyte of indolent form and 5 leukemic CLL B-lymphocyte of aggressive form) were stimulated in vitro with an anti-IgM antibody, activating the B-cell receptor (BCR). We analyzed the gene expression at 4 time points (60, 90, 210 and 390 minutes). Each gene expression measurement is performed both in stimulated cells and in control unstimulated cells. For one aggressive CLL case, we silenced expression of DUSP1 by transfecting DUSP1-specific RNAi and, as a control, transfected cells with a non-targeting RNAi. We then stimulated the BCR of these cells and analyzed the gene expression at the same time points in stimulated cells and in control unstimulated cells.

2013-01-04 | GSE39411 | GEO

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