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MicroRNA signature in b-cell lymphomas and control human B cells from fresh tonsils

ABSTRACT: 147 B-cell lymphomas were studies for miRNA expression miRNA profiling of control human B cell populations Comparison of miRNA expression profiles of naive B cells (CD19+ IgD+ CD27-) from 3 individuals and germinal center B cells (CD10+ CD19+) from 4 individuals 147 B-cell lymphomas were hybridized on a human miRNA one-color platform containing probes for 470 human miRNAs. Each lymphoma type was compared to all set of NHLs. Burkitt Lymphoma was also directly compared to DLBCL miRNA expression signature is different in human naive B cells compared to Germinal Center B cells

ORGANISM(S): Homo sapiens

SUBMITTER: Lorena Di Lisio

PROVIDER: E-GEOD-29493 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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microRNA signature in b-cell lymphomas and control human B cells from fresh tonsils

Project description:147 B-cell lymphomas were studies for miRNA expression miRNA profiling of control human B cell populations Comparison of miRNA expression profiles of naive B cells (CD19+ IgD+ CD27-) from 3 individuals and germinal center B cells (CD10+ CD19+) from 4 individuals

2014-04-12 | GSE29493 | GEO

Comprehensive analysis of miRNA expression in T-cell subsets of Rheumatoid arthritis patients and healthy controls reveals defined miRNA signatures of naive and memory Tregs

Project description:Disturbed expression of microRNAs (miRNAs) in regulatory T-cells (Tregs) leads to development of autoimmunity in experimental mouse models. However, the miRNA expression signature characterizing Tregs of autoimmune diseases, such as rheumatoid arthritis (RA) has not been determined yet. Moreover, the technical limitations prevented the analysis of such minute T-cell population as naive and memory Tregs. In this study we have used a microarray approach to comprehensively analyze miRNA expression signatures of naive Tregs (CD4+CD45RO-CD25++), memory Tregs (CD4+CD45RO+CD25+++), as well as conventional naive (CD4+CD45RO-CD25-) and memory (CD4+CD45RO+CD25-) T-cells (Tconvs) derived from peripheral blood of RA patients, and matched healthy controls. Differential expression of selected miRNAs was validated by TaqMan-based qRT-PCR. We found a positive correlation between increased expression of miR-451 in T-cells of RA patients and disease activity score (DAS28), ESR levels, and serum levels of IL-6. Moreover, we found characteristic, disease and treatment independent, global miRNA expression signatures defining naive Tregs, memory Tregs, naive Tconvs and memory Tconvs. The analysis allowed us to define miRNAs characteristic for a general naive phenotype (e.g. miR-92a), a general memory phenotype (e.g. miR-21, miR-155), and most importantly miRNAs specifically expressed in both naive and memory Tregs, defining as such the Treg phenotype (i.e. miR-146a, miR-3162, miR-1202, miR-1246a, and miR-4281). MicroRNA profiling was performed in four CD4+ T-cell subsets: naive Tconventional (CD3+CD8-CD45RO-CD25-), naive Tregulatory (CD3+CD8-CD45RO-CD25+), memory Tconventional (CD3+CD8-CD45RO+CD25-), and memory Tregulatory (CD3+CD8-CD45RO+CD25+) derived from 2 healthy controls, and 6 rheumatoid arthritis patients (total n=8).

2014-01-22 | E-GEOD-50646 | biostudies-arrayexpress

Transcriptome profiling of Peyer’s patch naive and germinal center B cells

Project description:Germinal center (CD19+Fas+GL7+) and naive (CD19+Fas-GL7-) B cells were sorted from Peyer's patches of littermate 12 weeks old WT C57BL/6 mice. Three biological replicates were analyzed, each composed of a pool of 5 female mice. RNA was purified from pellets of 2-2.5x10^⁴ cells and sequencing libraries were prepared from 100ng of total RNA per replicate.

2017-05-22 | GSE98086 | GEO

Effect of Odc knockout on amino acid homeostasis of Eu-Myc Lymphomas

Project description:Amino acid levels analysis of lymphomas isolated from Eu-Myc;CD19-Cre;Odc fl/fl mic and their wild-type counterparts Eu-Myc;CD19-Cre;Odc +/+

2016-09-08 | ST000461 | MetabolomicsWorkbench

miRNA profiles of tonsillar B cell subsets

2011-02-25 | GSE27504 | GEO

miRNA profiles of tonsillar B cell subsets

Project description:In order to assess the miRNA signature of B cells undergoing the germinal center reaction, we isolated three subsets of B cells from tonsils--naive (N), germinal center (GC), and memory (M) and looked at their miRNA profile. We looked at three subsets of B cells, isolated from tonsils obtained from four different donors. Thus, we profiled a total of 12 samples, and each tonsillar subset--N, GC, and M, had four biological replicates.

2011-02-25 | E-GEOD-27504 | biostudies-arrayexpress

A combined omics approach to generate the surface protein atlas of human naive CD4+ T cells during early TCR activaion

Project description:To increase the dataset of our proteomic naive CD4+ T cell surface atlas, we applied whole genome microarray expression analysis. The NCBI RefSeq accession number of all transcripts which were detected in naive and stimulated CD4+ T cells (aCD3/aCD28 for 3h) of four different donors, was mapped to the corresponding UniProtKB accession number. For these UniProtKB ACs, we extracted the subcellular localization (UniProt_SL) annotation from the UniProtKB/Swiss-Prot database or if not available the subcellular localization was predicted unsing LocTree3 and PolyPhobius. This led to the identification of 908 genes coding for proteins located on the surface of human naive and/or activated CD4+ T cells. Gene expression in human naive T cells and naive T cells which were stimulated with aCD3/aCD28 for 3h was measured. Naive T cells from four different human blood donors were analyzed.

2014-11-01 | E-GEOD-61983 | biostudies-arrayexpress

miRNA profiling of normal mature B cells

Project description:miRNA profiling has been performed on normal mature B cells at different stages of differentiation (naive, germinal center and memory). The main goal is to identify miRNA signatures associated with differentiation stages of normal B cells. Keywords: miRNA, normal mature B cells Cells were isolated by magnetic cell sorting from tonsil tissues obtained from pediatric donors. Each phenotype is represented by 6 samples, each isolated from a different donor. The experiment does not include technical replicates.

2010-05-16 | E-GEOD-15144 | biostudies-arrayexpress

Human melanoma transcriptom is modulated by cold plasma treatment

Project description:Treatment of tumor progression and metastasis continues to be of major importance in the field of cancer. It is reported that cancer cells often show a pronounced sensitivity towards oxidative stress. Cold plasma offers the ability to deliver a delicate mix of reactive oxygen and nitrogen species directly into cells or tissues. Using a well-described argon plasma jet, we investigated the biological responses of plasma on tumor cell death, cell migration, and expression of adhesion-associated genes as well as cytoskeletal modifications. Using the human melanoma cancer cell line SK-Mel-147 we were able to show that plasma induced only little apoptosis but had profound effects on tumor cell motility. Plasma treatment of cells was associated with an inhibition of migration and disorganization of the actin cytoskeleton which were mediated through multiple signaling pathways, as transcriptome-wide gene analysis suggested. Specifically, changes in cell adhesion were regulated by differential expression of cell junction and cell-matrix proteins. These results provide evidence that plasma may be able to disturb the migration and adhesion in metastatic SK-Mel-147 cells. Microarrays were used to analyze and investigate the biological effects of cold plasma on human melanoma cell line SK-Mel-147. Using an argon plasma jet kinpen, regulated transcripts were analyzed and further described in Schmidt et al. (2015): M-bM-^@M-^\Human melanoma cell migration and adhesion is decreased by cold plasma treatmentM-bM-^@M-^]. A study using total RNA recovered from human SK-Mel-147, treated with cold plasma as well as H2O2-treated and untreated SK-Mel-147 controls.

2015-02-18 | E-GEOD-65972 | biostudies-arrayexpress

Development of gene expression signatures for miR-218 overexpression

Project description:To investigate differences in gene expression after overexpression miR-218 in U251MG 2 Samples, one transduced with miR-control and one with miR-218.

2013-04-19 | E-GEOD-46059 | biostudies-arrayexpress

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