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BLUEPRINT DNA methylation profiling of B-cell differentiation using Illumina HumanMethylation 450K BeadArray

ABSTRACT: We performed DNA methylation analysis in 6 different mature B-cell subpopulations using the Illumina HumanMethylation 450K BeadArray. In particular, we analyzed naive B cells from peripheral blood (naiBC); naive B cells from tonsil (t-naiBC); germinal center B cells (gcBC); plasma cells from tonsil (t-PC); memory B cells from peripheral blood (memBC) and plasma cells from bone marrow (bm-PC). All the samples were isolated from healthy donors and we analyzed 3 to 9 biological replicates of each subtype.

PROVIDER: EGAS00001001196 | EGA |

REPOSITORIES: EGA

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Transcription profiling of human Waldenstroms macroglobulinemia CD19+ WM B cells (WM-BC) and CD138+ WM plasma cells (WM-PC) with those of normal CD19+ peripheral blood B cells (PB-BC), tonsil-BC (T-BC), CD138+ T-PC and bone marrow PC (N-PC) reveals biological insights into its pathophysiology

Project description:Waldenströms macroglobulinemia (WM) is a rare lymphoproliferative disorder with apparent morphologic and immunophenotypic heterogeneity and its origins are still poorly understood. In this study, using Gene-Expression Profiling (GEP), we compared the global mRNA expression patterns of CD19+ WM B cells (WM-BC) and CD138+ WM plasma cells (WM-PC) with those of normal CD19+ peripheral blood B cells (PB-BC), tonsil-BC (T-BC), CD138+ T-PC and bone marrow PC (N-PC). Experiment Overall Design: The sample cohort studied consisted of CD19-selected peripheral blood B cells (PB-BC; n = 7), tonsil B cells (T-BC; n = 7), bone marrow B cells from WM (WM-BC; n = 12), tonsil plasma cells (T-PC; n = 9), bone marrow plasma cells from healthy donors (N-PC; n = 10), WM plasma cells (WM-PC, n = 9), and MM plasma cells (MM-PC; n = 11).

2008-12-05 | E-GEOD-9656 | biostudies-arrayexpress

BLUEPRINT Gene expression analysis during human B-cell differentiation using the Affymetrix Human Genome U219 Array

Project description:We performed gene expression analysis using the Affymetrix Human Genome U219 Array of 9 subpopulations covering the complete B-cell maturation program: hematopoietic progenitor cells (HPC); pre-B-I cells (preB1C); pre-B-II cells (preB2C); naive B cells from peripheral blood (naiBC); naive B cells from tonsil (t-naiBC); germinal center B cells (gcBC); plasma cells from tonsil (t-PC); memory B cells from peripheral blood (memBC) and plasma cells from bone marrow (bm-PC). All the samples were isolated from healthy donors and, with the exception of bm-PC (only 1 replicate), we used 3 to 11 biological replicates of each subtype.

| EGAS00001001197 | EGA

Gene Expression Profiling Reveals Biological Insights into the Pathophysiology of Waldenströms macroglobulinemia

2012-10-01 | GSE9656 | GEO

ena-DATASET-BLUEPRINT-23-03-2015-14:16:11:295-606 - samples

Project description:We used whole-genome bisulfite sequencing (WGBS) to generate unbiased DNA methylation maps of six purified B-cell subpopulations: hematopoietic progenitor cells (HPC); pre-B-II cells (preB2C); naive B cells from peripheral blood (naiBC); germinal center B cells (gcBC); memory B cells from peripheral blood (memBC) and plasma cells from bone marrow (bm-PC). WGBS was performed in 2 biological replicates from each subpopulation.

| EGAD00001001304 | EGA

Assessment of genome-wide chromatin accessibility of subsets of bone marrow-resident antigen presenting cells [ATAC_BMACs]

Project description:Chromatin accessibility of bone marrow-resident Aire expressing cells was compared to those of bone marrow plasma cells and B cells via ATAC-seq Bone marrow (BM) harbors a large repertoire of regulatory T (Treg) cells, which are essential in hematopoiesis and peripheral tolerance. Treg cell accumulation in BM has been viewed as a consequence of preferential immigration of thymus-derived Treg cells. Here we report a novel subset of antigen presenting cells, which expresses the autoimmune regulator (Aire). These BM Aire-expressing cells resemble a subset of CD138+B220-TACI+Blimp-1+MHC-II+ plasma cells (pc-BMACs) and express a diverse repertoire of tissue-restricted self-antigens. pc-BMACs present self-antigens to na ve CD4+ T cells and can efficiently convert these into functionally competent CD25+Foxp3+ bona fide peripheral Treg cells (pTregs) capable of exerting immune suppression in vitro and in vivo. Aire expression may contribute to the tolerogenic function of pc-BMACs as it regulates the expression of genes involved in pTreg induction and function, including Icosl and retinoic acid synthesis-related genes, Aldh1a2 and Aldh1b1. Our data thus demonstrate an Aire-expressing plasma cell subset in the BM capable to promote peripheral tolerance by ectopically expressing tissue-restricted self-antigens and generating pTregs.

2022-08-26 | GSE136649 | GEO

Deciphering the fate of slan+-monocytes in tonsils by gene expression profiling

Project description:slan+-monocytes represent a subset of the “non-classical” CD14dim/-CD16++ monocytes, which are characterized by the expression of the so-called “slan” antigen, recognized by specific monoclonal antibodies. slan+-cells can be identified in peripheral tissues including tonsils. However, their origin from slan+-monocytes as well as their terminal differentiation state (toward macrophages/dendritic cells) were only partially resolved. In this study, we performed transcriptomic studies of tonsil slan+-cells,CD1c+DCs/DC2 and CD11b+ CD14+macrophages, as well as subsets of peripheral blood monocytes and we report that tonsil slan+-cells mainly represent macrophage-like cells with features distinct from those of tonsil CD11b+CD14+macrophages or CD1c+DCs/DC2. Moreover we provide a number of molecular evidence indicating that tonsil slan+-cells derive from peripheral slan+-monocytes.

2021-11-19 | GSE136107 | GEO

Protein landscape for human B-cell differentiation

Project description:The present project reports the quantitative proteome of different B-cell populations corresponding to the last steps of B-cell differentiation (i.e., naive (N), centroblast (CB), centrocytes (CC), memory cells (M), plasmablasts (PC).

2021-05-03 | PXD006191 | Pride

The forkhead transcription factor FOXP1 profile in B-cells and B-cell lymphoma cell lines

Project description:Expression of the forkhead transcription factor FOXP1 is essential for early B cell development, whereas downregulation of FOXP1 at the germinal center (GC) stage is required for GC B cell function. Aberrantly high FOXP1 expression is frequently observed in diffuse large B cell lymphoma (DLBCL) and mucosa-associated lymphoid tissue (MALT) lymphoma, being associated with poor prognosis. Here, by gene expression microarray [GSE51382] and quantitative RT-PCR analysis upon ectopic overexpression of FOXP1 in primary human memory B cells (MBCs) and B-cell lines, combined with chromatin immunoprecipitation-sequencing (ChIP-seq), we established that FOXP1 directly represses expression of PRDM1, IRF4, and XBP1, transcriptional master regulators of plasma cell (PC) differentiation. In accordance, FOXP1 is prominently expressed in primary human naive and MBCs but expression strongly decreases during plasma PC differentiation. Moreover, as compared to IgM+ MBCs, IgG+ MBCs combine lower expression of FOXP1 with an enhanced intrinsic PC differentiation propensity, and constitutive (over)expression of FOXP1 in B cell lines and primary human MBCs represses their ability to differentiate into PCs. Taken together, our data indicate that proper control of FOXP1 expression plays a critical role in PC differentiation, whereas aberrant overexpression of FOXP1 might contribute to lymphomagenesis by blocking terminal B cell differentiation. OXP1 ChIP-seq profile in primary human memory B cells (MBCs) and B-cell lines

2015-05-19 | E-GEOD-69009 | biostudies-arrayexpress

Evaluation of Genome-wide chromatin accessibility of BM T cell subsets [ATAC_TC]

Project description:Chromatin accessibility of bone marrow conventional T cells, pTregs, tTregs, BMAC-induced Tregs and in vitro-induced Tregs were compared Bone marrow (BM) harbors a large repertoire of regulatory T (Treg) cells, which are essential in hematopoiesis and peripheral tolerance. Treg cell accumulation in BM has been viewed as a consequence of preferential immigration of thymus-derived Treg cells. Here we report a novel subset of antigen presenting cells, which expresses the autoimmune regulator (Aire). These BM Aire-expressing cells resemble a subset of CD138+B220-TACI+Blimp-1+MHC-II+ plasma cells (pc-BMACs) and express a diverse repertoire of tissue-restricted self-antigens. pc-BMACs present self-antigens to na ve CD4+ T cells and can efficiently convert these into functionally competent CD25+Foxp3+ bona fide peripheral Treg cells (pTregs) capable of exerting immune suppression in vitro and in vivo. Aire expression may contribute to the tolerogenic function of pc-BMACs as it regulates the expression of genes involved in pTreg induction and function, including Icosl and retinoic acid synthesis-related genes, Aldh1a2 and Aldh1b1. Our data thus demonstrate an Aire-expressing plasma cell subset in the BM capable to promote peripheral tolerance by ectopically expressing tissue-restricted self-antigens and generating pTregs.

2022-08-26 | GSE136648 | GEO

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

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