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Immune Variation Project (ImmVar) [CD4]

ABSTRACT: Gene expression profiling of CD4 T-Cells (CD4+CD62L+) from human peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from healthy individuals from the Boston area. Over the course of 18 months, fresh blood samples from healthy participants were collected following a rigorous, standardized set of procedures (SOP). 15ml of blood was collected and used to isolate peripheral blood mononuclear cells (PBMCs). From the PBMCS, cell population of interest, CD4+CD62L+, underwent a two-step sorting strategy in order to achieve cell purity >99%. mRNAs from these cells were profiled on Affymetrix GeneChip Human Gene ST 1.0 microarrays. Raw data CEL files were processed using the Robust Multichip Average (RMA) algorithm in Affymetrix PowerTools. To account for non-genetic factors such as batch effects, age, gender, and technical artifacts in gene expression data, we used Principal Component Analysis (PCA). PCs were estimated separately from the gene expression matrix for each population and cell type. The optimal numbers of PCs for association analysis were determined based on the PC that resulted in maximum number of cis-eQTLs. This procedure identified 20, 12 and 12 PCs in EU, EA and AA CD4+ T-cells, respectively. GSE56033_GSM.ImmVarCD4.*.PC*.txt supplementary files: For each population EU, AA, and EA, individual PC-corrected matrices for samples that have passed both Expression QC and Genotyping QC. These are the same expression matrices that were used for the eQTL association analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Richard Cruse

PROVIDER: E-GEOD-56033 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Immune Variation Project (ImmVar) [CD14]

Project description:Gene expression profiling of Monocytes (CD14+CD16-) from human peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from healthy individuals from the Boston area. Over the course of 18 months, fresh blood samples from healthy participants were collected following a rigorous, standardized set of procedures (SOP). 15ml of blood was collected and used to isolate peripheral blood mononuclear cells (PBMCs). From the PBMCS, cell population of interest, CD14+CD16-, underwent a two-step sorting strategy in order to achieve cell purity >99%. mRNAs from these cells were profiled on Affymetrix GeneChip Human Gene ST 1.0 microarrays. Raw data CEL files were processed using the Robust Multichip Average (RMA) algorithm in Affymetrix PowerTools. To account for non-genetic factors such as batch effects, age, gender, and technical artifacts in gene expression data, we used Principal Component Analysis (PCA). PCs were estimated separately from the gene expression matrix for each population. The optimal numbers of PCs for association analysis were determined based on the PC that resulted in maximum number of cis-eQTLs. This procedure identified 20, 10, and 14 PCs in EU, EA and AA monocytes, respectively. GSE56034_GSM.ImmVarCD14.*.PC*.txt supplementary files: For each population EU, AA, and EA, individual PC-corrected matrices for samples that have passed both Expression QC and Genotyping QC. These are the same expression matrices that were used for the eQTL association analysis.

2014-05-02 | E-GEOD-56034 | biostudies-arrayexpress

Immune Variation Project (ImmVar) [CD4]

Project description:Gene expression profiling of CD4 T-Cells (CD4+CD62L+) from human peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from healthy individuals from the Boston area.

2014-05-02 | GSE56033 | GEO

Transcription profiling of human CD4 positive T cell subsets

Project description:Peripheral Blood Mononuclear Cells (PBMCs) were isolated from a buffy coat (Australian Blood Bank) using Ficoll methodology. CD4+ T cells were isolated using Dynal Beads kit. Pure CD4+ T cells were then stained using a cocktail of monoclonal antobodies (mAbs), including: anti-CD4PE, CD45RO ECD, CD62L APC-Cy7, CD25 APC, CD127 Pacific Blue. After incubation, cells were washed twice in PBS/FCS (0.2%), and sorted into five different cell subsets: CD4+CD25+CD127low CD62L+CD45RO- (naive regulatory T cells), CD4+CD25+CD127low CD62L+/- CD45RO+ (activated regulatory T cells), CD4+CD25+CD127hi CD62L+/- CD45RO+ (memory T cells), CD4+CD25-CD127low CD62L+/- CD45RO+ (effector T cells) and CD4+CD25-CD127hi CD62L+ CD45RO- (naive T cells).

2011-02-10 | E-MEXP-2578 | biostudies-arrayexpress

BAFF and CD4+ T cells are major survival factors for long-lived splenic plasma cells in a B-cell–depletion context

Project description:Previous data have suggested that B-cell–depletion therapy may induce the settlement of autoreactive long-lived plasma cells (LLPCs) in the spleen of patients with autoimmune cytopenia. To investigate this process, we used the AID-CreERT2-EYFP mouse model to follow PCs engaged in an immune response. Multiplex-PCR at the single-cell level revealed that only a small fraction of splenic PCs had a long-lived signature, whereas PCs present after anti-CD20 antibody treatment appeared more mature, similar to bone-marrow PCs. It suggested that, in addition to a process of selection, a maturation induced upon B-cell depletion drove PCs toward a long-lived program. We showed that BAFF and CD4+ T cells play a major role in PC survival niche, because combining anti-CD20 with anti-BAFF or anti-CD4 antibody greatly reduce the number of splenic PCs. Similar results were obtained in the lupus-prone NZB/W model. These different contributions of soluble and cellular components of the PC niche in the spleen demonstrate that the LLPC expression profile is not cell-intrinsic but largely depends on signals provided by the splenic microenvironment, implying that interfering with these components at the time of B cell depletion might improve the response rate in autoimmune cytopenia.

2018-02-19 | E-MTAB-6449 | biostudies-arrayexpress

Network analysis identifies proinflammatory plasma cell polarization for secretion of ISG15 in human autoimmunity

Project description:Plasma cells (PCs) as effectors of humoral immunity produce immunoglobulins to match pathogenic insult. However, emerging data suggests more diverse roles for PCs as regulators of immune and inflammatory responses via secretion of factors other than immunoglobulins. The extent to which such responses are pre-programmed in B-lineage cells or can be induced in PCs by the microenvironment is unknown. Here we dissect the impact of IFNs on the regulatory networks of human plasma cells. We show that core PC programs are unaffected, while PCs respond to IFNs with distinctive transcriptional responses. The ISG15-system emerges as a major transcriptional output induced in a sustained fashion by IFN-Î± in PCs and linked both to intracellular conjugation and ISG15 secretion. This leads to the identification of ISG15-secreting plasmablasts/PCs in patients with active SLE. Thus ISG15-secreting PCs represent a distinct pro-inflammatory PC subset providing an immunoglobulin-independent mechanism of PC action in human autoimmunity B-cells were isolated from the peripheral blood of three adult donors and differentiated in vitro (see individual samples for culture conditions)

2016-07-22 | E-GEOD-75007 | biostudies-arrayexpress

Transcription profiling of human fetal thymocytes and circulating naive T cells

Project description:Subpopulations of human fetal thymocyte and circulating naÃ¯ve T cells were obtained through FACS sorting, including CD3-CD4+CD8- intrathymic T progenitor cells (ITTP), CD3intCD4+CD8+ "double positive" thymocytes (DP), CD3highCD4+CD8- "single positive" thymocytes (SP4), CD3+CD4+CD8-CD45RA+CD62L+ naÃ¯ve T cells from cord blood (CB4+), and CD3+CD4+CD8-CD45RA+CD62L+ naÃ¯ve T cells from adult blood (AB4+).

2007-08-06 | E-GEOD-1460 | biostudies-arrayexpress

Gene Expression Profile during human CD4+ T cell differentiation

Project description:Subpopulations of human fetal thymocyte and circulating naïve T cells were obtained through FACS sorting, including CD3-CD4+CD8- intrathymic T progenitor cells (ITTP), CD3intCD4+CD8+ "double positive" thymocytes (DP), CD3highCD4+CD8- "single positive" thymocytes (SP4), CD3+CD4+CD8-CD45RA+CD62L+ naïve T cells from cord blood (CB4+), and CD3+CD4+CD8-CD45RA+CD62L+ naïve T cells from adult blood (AB4+). Keywords = Microarray Keywords = gene expression Keywords = thymocytes Keywords = naïve CD4+ T cell Keywords = recent thymic emigrants Keywords: other

2004-07-01 | GSE1460 | GEO

Tumor cells in light-chain amyloidosis and multiple myeloma show different transcriptional rewiring of the normal plasma cell development [bulk RNA-seq]

Project description:Transcriptional atlas of normal PC development in secondary lymphoid organs (SLO), peripheral blood (PB) and BM for comparison with the transcriptional programs (TPs) of tumor PCs in AL, MM and MGUS based on bulk and single-cell RNAseq

2021-06-29 | GSE175384 | GEO

Tumor cells in light-chain amyloidosis and multiple myeloma show different transcriptional rewiring of the normal plasma cell development [single-cell RNA-seq]

2021-06-29 | GSE175385 | GEO

The angiopoietin-Tie2 pathway regulates Purkinje cell dendritic morphogenesis in a cell-autonomous manner

Project description:Neuro-vascular communication is essential to synchronize central nervous system development. Yet, the specific cellular players, defined developmental processes and molecular mechanisms involved in this crosstalk remain poorly characterized. Here we identify the angiopoietin/Tie2 signaling axis as a crucial regulator of dendritic morphogenesis of Purkinje cells (PC) during cerebellum development. We show that in the developing cerebellum Tie2 expression is not restricted to blood vessels but it is also in PCs. Its ligands angiopoietin-1 (Ang1) and angiopoietin-2 (Ang2) are expressed in neural cells and endothelial cells (ECs), respectively. PC-specific deletion of Tie2 results in reduced dendritic arborization, which is recapitulated in neural-specific Ang1-knockout and Ang2 full-knockout mice. Mechanistically, RNA sequencing reveals that Tie2 deficient PCs present alterations in gene expression of multiple genes involved in cytoskeleton organization, dendritic formation, growth and branching. Functionally, those morphological changes are accompanied by alterations in PC network electrophysiology. Altogether, our data propose that the Ang/Tie2 signaling axis serve as mediator of intercellular communication between neural cells, ECs and PCs, required to regulate PC dendritic morphogenesis and function.

2021-12-31 | GSE178659 | GEO

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