Single cell transcriptomic profiling of human CD19+ B cells enriched for CD5+ Innate-like B cells
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ABSTRACT:
PROVIDER: PRJNA913177 | ENA |
REPOSITORIES: ENA
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Project description:We have previously observed that regulatory B cells expressing the apoptosis-inducing surface molecule Fas ligand were enriched in the B cell fraction denoted by a surface phenotype of CD5+CD1dhigh. To identify potential growth factors, transcriptional regulators, or surface markers that might better characterize regulatory B cells, we compared global gene expression by microarray in two B cells subsets isolated by FACS. Splenocytes from 20 DBA/1 male mice were harvested, pooled, and CD19+ B cells were isolated by positive selection using MACS. B cells were then stained for CD5 and CD1d and sorted by FACS into CD5+CD1dhigh and CD5-CD1dhigh populations.
2013-06-30 | GSE46245 | GEO
Project description:We have previously observed that regulatory B cells expressing the apoptosis-inducing surface molecule Fas ligand were enriched in the B cell fraction denoted by a surface phenotype of CD5+CD1dhigh. To identify potential growth factors, transcriptional regulators, or surface markers that might better characterize regulatory B cells, we compared global gene expression by microarray in two B cells subsets isolated by FACS. Splenocytes from 20 DBA/1 male mice were harvested, pooled, and CD19+ B cells were isolated by positive selection using MACS. B cells were then stained for CD5 and CD1d and sorted by FACS into CD5+CD1dhigh and CD5-CD1dhigh populations. Single replicates of both CD5+CD1dhigh and CD5-CD1dhigh B cells from pooled mouse splenocytes were isolated and assay using the Affymetrix GeneChip Mouse 430 2.0 Array.
2013-06-30 | E-GEOD-46245 | biostudies-arrayexpress
Project description:Aryl hydrocarbon receptor is a ligand-activated transcription factor whose activation can regulate B cell-mediated immune responses. Given the diverse nature of human B cell subsets, scRNA-seq transcriptomic profiling was used to ascertain the heterogeneity of AHR expression in discrete B cell subpopulations. We identified a unique cell cluster enriched in expression of AHR and CD9. Further, these cells were diminished in their expression of canonical B cell-associated genes and enriched with a myeloid cell-specified gene signature. These results were confirmed in vitro as CD14 expressing B cells were readily detectable in human donor PBMC and expressed significantly more AHR protein. Following activation in vitro, CD9+ B cells secreted IgM, IL-10, TGFβ1, and several myeloid-associated pro-inflammatory mediators, specifically CXCL8. These results demonstrate CD14 expression by B cells is readily detectable in healthy human donors and their release of CXCL8 could implicate these cells in inflammatory diseases and autoimmunity.
2024-12-04 | GSE221199 | GEO
Project description:CD5 is characterized as an inhibitory co-receptor with important regulatory role during T cell development. To study the molecular mechanism by which CD5 operates, we used quantitative mass spectrometry to analyze the components of the CD5 signaling machinery in primary T cells. In a first set of experiments, CD5-containing complexes were immunoprecipitated from thymocytes of wild-type (WT) C57BL/6 mice. Thymocytes were treated with pervanadate to induce widespread activation of protein tyrosine kinases. Corresponding samples prepared from thymocytes of Cd5−/− mice were used as controls, to discriminate CD5-binding molecules from the background of contaminant proteins. Eight biological replicates were prepared for both conditions, and samples were analyzed in duplicate LC-MS runs. This first set of experiment is presented in TableS1 of the paper, and is associated to the MaxQuant result file “Interactome WT” in the present PX dataset. We analyzed the CD5 interactome at different time of stimulation with pervanadate (1min and 10min) using thymocytes from wild-type (WT) C57BL/6 mice. Corresponding samples prepared from thymocytes of Cd5−/− mice were used as controls. Three biological replicates were prepared for both conditions (WT and KO) and each time point (1min and 10min). This set of experiments is presented in TableS2 of the paper and is associated to the MaxQuant result file “Interactome at 1min and 10min” in the present PX dataset. We checked that the activation of CD5 (phosphorylation sites) and the formation of the signaling complex was comparable in different stimulatory conditions (comparison of WT thymocytes stimulated with either pervanadate or anti-CD3+anti-CD4 antibodies). We also analyzed the binding of CD5 interactors in thymocytes from a c-Cbl-/- mouse model (comparison of WT and c-Cbl-/-thymocytes stimulated with pervanadate). These experiments and the associated experimental design of the comparisons are summarized in TableS3 of the paper, and are based on the MaxQuant result file “Comparison of different stimulatory conditions” in this dataset. To check the phosphorylation status of the CD5 tyrosine residues at different time of stimulation, we analyzed samples immunoprecipitated from thymocytes of wild-type (WT) C57BL/6 mice, following stimulation with anti-CD3+anti-CD4 antibodies for 1min, 3min and 10min. This set of experiment is presented in TableS4 of the paper and is associated to the MaxQuant result file “CD5 pY kinetics” in the present PX dataset. To determine the role of Y429 in the context of CD5 signaling, we expressed a wild-type (CD5tgWt) or a mutated form of CD5, containing a tyrosine to phenylalanine substitution at position 429 (CD5tgY429F) in transgenic mice. We analyzed the CD5 interactome by comparing samples immunoprecipitated from thymocytes of these 2 mice models (following pervanadate stimulation, 6 and 5 biological replicates respectively) with samples prepared in the same way from Cd5−/− mice as controls (6 biological replicates). The results are shown in TableS5 of the paper, and correspond to the MaxQuant result file “interactome CD5tgWt_CD5tgY429F”.
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Project description:We recently found that a unique subset of innate-like γδ T cells develop from the DN2a-stage of the fetal thymus independent of the zinc-finger transcription factor B-cell leukemia/lymphoma 11b (Bcl11b). Herein we characterized these Bcl11b-independent γδ T cells in the periphery as CD5−NK1.1+ and Granzyme B+, and show that they are capable of producing interferon (IFN)-γ upon T cell receptor stimulation without Ca2+ influx. In wild-type mice, these cells were sparse in lymphoid tissues but abundant in non-lymphoid tissues such as the liver. Bcl11b-independent CD5−NK1.1+ γδ T cells appeared and contributed to early protection before Bcl11b-dependent CD5+NK1.1− γδT cells following Listeria monocytogenes infection, recapitulating their appearance during thymic development.
2017-10-11 | GSE89906 | GEO
Project description:The induction of proinflammatory T cells by dendritic cell (DC) subtypes is critical for anti-tumor responses and effective immune checkpoint blockade (ICB) therapy. Here we show that human CD1c+CD5+ dendritic cells are reduced in melanoma-affected lymph nodes, with CD5 expression on DCs correlating with patient survival. Activating CD5 on DCs enhanced T-cell priming and improved survival after immune checkpoint blockade therapy. CD5+ DC numbers increased during ICB treatment, and low IL-6 levels promoted their de novo differentiation. Mechanistically, CD5 expression by DCs was required to generate optimally protective CD5hi T helper and CD8+ T cells; further, deletion of CD5 from T cells dampened tumor elimination in response to ICB therapy in vivo. Thus, CD5+ dendritic cells are an essential component of optimal immune checkpoint blockade therapy.
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Project description:To assess the impact of CD5 on the transcriptome in B cells, we studied changes in mRNA levels in Jok-E1A/Jok-E1B cells compared with Jok-1 cells. Gene expression was performed in untransfected CD5-negative hairy B cell leukemia line (Jok-1), transfected with cDNA for either the membrane isoform of CD5 (E1A; Jok-E1A) or the cytoplasmic E1B isoform (Jok-E1B). Three biological replicates were performed.
2013-09-11 | E-GEOD-50714 | biostudies-arrayexpress
Project description:CD5-positive (CD5+) diffuse large B-cell lymphoma (DLBCL) has a poor prognosis and high incidence of central nervous system (CNS) relapse, even in the rituximab era. To determine the gene expression profile of CD5+ DLBCL, total RNA from 90 patients with DLBCL, including 33 CD5+ DLBCL and 57 CD5-negative (CD5-) DLBCL patients, was examined using Agilent human oligo microarrays. These cases were separated into 78 activated B-cell-like (ABC) DLBCLs and 12 germinal center B-cell-like (GCB) DLBCLs. All cases of CD5+ DLBCL were classified as ABC DLBCLs. The classifier based on gene expression used in a supervised analysis correctly identified CD5 expression in the DLBCL and ABC DLBCL samples. The gene most relevant to CD5 expression was SH3BP5. The enriched GO categories in the CD5+ ABC DLBCL signature gene set were multicellular organismal signaling, transmission of nerve impulse, and synaptic transmission. This present study, which includes the largest reported number of patients with CD5+ DLBCL, confirmed that most CD5+ DLBCLs are ABC DLBCLs, suggesting that therapeutic strategies for ABC DLBCL may be effective for the treatment of CD5+ DLBCL. Our CD5+ ABC DLBCL signature gene set may provide insights into the cause of the high frequency of CNS relapse in CD5+ DLBCL.
2015-05-19 | GSE66770 | GEO
Project description:The source of IgA and the mechanism for deposition of IgA in the mesangium remain unknown for primary IgA nephropathy. Because CD19(+)CD5(+) B cells are important producers of IgA and contribute to several autoimmune diseases, they may play an important role in IgA nephropathy. In this study, flow cytometry, quantitative PCR, and confocal microscopy were used to assess the frequency, distribution, Ig production, CD phenotypes, cytokine production, and sensitivity to apoptosis of CD19(+)CD5(+) B cells in the peripheral blood, peritoneal fluid, and kidney biopsies of 36 patients with primary IgA nephropathy. All patients with IgA nephropathy were significantly more likely to have CD19(+)CD5(+) B cells in the peripheral blood, peritoneal fluid, and kidney biopsies than were five control subjects and 10 patients with active systemic lupus erythematosus. The 33 patients who had IgA nephropathy and responded to treatment demonstrated a significant decrease in CD19(+)CD5(+) B cells in the peripheral blood, peritoneal fluid, and kidney (all P < 0.01). In the three patients who had IgA nephropathy and did not respond to treatment, the frequency of CD19(+)CD5(+) B cells did not change. CD19(+)CD5(+) B cells isolated from patients with untreated IgA nephropathy expressed higher levels of IgA, produced more IFN-gamma, and were more resistant to CD95L-induced apoptosis than cells isolated from control subjects and patients with lupus; these properties reversed with effective treatment of IgA nephropathy. In conclusion, these results strongly suggest that CD19(+)CD5(+) B cells play a prominent role in the pathogenesis of primary IgA nephropathy.
| S-EPMC2573008 | biostudies-other
Project description:CD5-positive (CD5+) diffuse large B-cell lymphoma (DLBCL) has a poor prognosis and high incidence of central nervous system (CNS) relapse, even in the rituximab era. To determine the gene expression profile of CD5+ DLBCL, total RNA from 90 patients with DLBCL, including 33 CD5+ DLBCL and 57 CD5-negative (CD5-) DLBCL patients, was examined using Agilent human oligo microarrays. These cases were separated into 78 activated B-cell-like (ABC) DLBCLs and 12 germinal center B-cell-like (GCB) DLBCLs. All cases of CD5+ DLBCL were classified as ABC DLBCLs. The classifier based on gene expression used in a supervised analysis correctly identified CD5 expression in the DLBCL and ABC DLBCL samples. The gene most relevant to CD5 expression was SH3BP5. The enriched GO categories in the CD5+ ABC DLBCL signature gene set were multicellular organismal signaling, transmission of nerve impulse, and synaptic transmission. This present study, which includes the largest reported number of patients with CD5+ DLBCL, confirmed that most CD5+ DLBCLs are ABC DLBCLs, suggesting that therapeutic strategies for ABC DLBCL may be effective for the treatment of CD5+ DLBCL. Our CD5+ ABC DLBCL signature gene set may provide insights into the cause of the high frequency of CNS relapse in CD5+ DLBCL. This present study involved 90 cases (33 patients with CD5+ DLBCL and 57 with CD5- DLBCL) of de novo consecutive DLBCL diagnosed at Mie University Hospital with available frozen biopsy specimens and total RNA samples. Lymphoma tissue RNA from 90 patients was extracted for target preparation and hybridization onto Agilent microarrays. The expression of CD5 in tumor cells was confirmed by means of immunohistochemistry using frozen sections.
2015-05-19 | E-GEOD-66770 | biostudies-arrayexpress