Identification of novel activation marker and regulator of human basophils via transcriptomic analysis of IL-3-stimulated basophils
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE144096 | GEO | 2021/01/01
REPOSITORIES: GEO
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Project description:To investigate the mechanisms by which C/EBPa drives basophil differentiation and maintains basophil identity, we examined whether or not C/EBPa promotes basophil molecular programming and simultaneously represses mast cell molecular programming. We performed genome-wide gene expression profiling on basophils and mast cells and found that 6798 genes were shared by mast cells and basophils; 2033 genes were expressed 2-10 (log2 1-3.3)-fold higher in basophils (differentially expressed in basophils); and 413 genes were expressed greater than 10 (log2 3.3)-fold in basophils (highly expressed in basophils). On the other hand, we found 569 genes were expressed 2-10 (log2 -1 to -3.3) fold higher in mast cells and 171 genes were highly expressed in mast cells [greater than 10 fold (log2 -3.3)]. We treated purified basophils prepared from Cebpaf/f RosaYFP/creER mice and Cebpa+/+ RosaYFP/creER control mice with or without 4HT treatment for five days. Gene expression in the treated basophils was analyzed using microarray analysis. Overall, deletion of C/EBPa in basophils resulted in a reduction of mRNA expression for 248 genes and led to an increase in mRNA expression for 255 genes. The majority of the C/EBPa-regulated genes were either differentially or highly expressed in basophils or mast cells. In this study, we compared gene expression in basophils and mast cell and identified genes which specifically expressed in basophils and mast cells. By using Cebpa conditional knock out mice, we identified Cebpa regulated genes in basophils.
2013-04-01 | E-GEOD-41596 | biostudies-arrayexpress
Project description:Basophils are the least common granulocytes which represent less than 1% of peripheral blood leukocytes. Recent development of analytical tools for basophils enables us to understand their critical roles in allergic reactions and protection from parasitic infections. Nevertheless, the differentiation trajectory of basophils remains unclear. We have identified previously-unappreciated pre-basophil subpopulation which encompasses previously-defined basophil precursors (BaPs) in a series of experiments including scRNA-seq analysis (deposited to GSE206589). In this study, we explored gene expression profiles of pre-basophils and mature basophils activated by antigen/IgE-stimulation or IL-3-stimulation. We have revealed that IL-3 activated pre-basophils displayed distinct gene expression profiles from antigen/IgE- or IL-3-stimulated mature basophils, suggesting the unuque property of pre-basophils.
2023-03-21 | GSE222701 | GEO
Project description:Basophils are important effector cells in allergic inflammation, anti-parasitic immune response and skin disorders. A number of activators including interleukin 3 (IL-3) and IgE have been identified in the regulation of human basophils expressing mediators such as histamine and leukotriene C4 (LTC4) and cytokines, including IL-4 and IL-13. Human basophils express high levels of IL-2 receptors. However, the function of the IL-2 pathway in basophils remains unknown. Here, we identify that IL-2-stimulated human basophils in vitro express a variety of inflammatory cytokines and chemokines including IL-5, IL-13, GM-CSF and CCL-17. Of note, one of the top regulated cytokines, IL-5, was for the first time identified to be expressed in human basophils and was distinctly regulated by IL-2, independently of IL-3 and IgE. Immunofluorescence analysis of skin specimens from bullous pemphigoid and eczema revealed that infiltrating basophils in skin lesions widely express IL-5 and GM-CSF. Together, our findings reveal IL-2 as a novel regulator of human basophils to express IL-5 and GM-CSF in skin disorders. This adds a new layer to support the importance of basophils in skin disorders.
2018-10-01 | GSE74375 | GEO
Project description:In this study, we explored gene expression profiles of CD34-CLEC12Ahi pre-basophils isolated from the bone marrow as well as CD34-CLEC12Alo mature basophils from the bone marrow and CD34+ basophil progenitors. We revealed that the gene expression of mature basophils isolated from the bone marrow and spleen resembled each other whereas pre-basophils and mature basophils showed distinct gene expression profiles.
2023-03-21 | GSE206591 | GEO
Project description:To investigate the mechanisms by which C/EBPa drives basophil differentiation and maintains basophil identity, we examined whether or not C/EBPa promotes basophil molecular programming and simultaneously represses mast cell molecular programming. We performed genome-wide gene expression profiling on basophils and mast cells and found that 6798 genes were shared by mast cells and basophils; 2033 genes were expressed 2-10 (log2 1-3.3)-fold higher in basophils (differentially expressed in basophils); and 413 genes were expressed greater than 10 (log2 3.3)-fold in basophils (highly expressed in basophils). On the other hand, we found 569 genes were expressed 2-10 (log2 -1 to -3.3) fold higher in mast cells and 171 genes were highly expressed in mast cells [greater than 10 fold (log2 -3.3)]. We treated purified basophils prepared from Cebpaf/f RosaYFP/creER mice and Cebpa+/+ RosaYFP/creER control mice with or without 4HT treatment for five days. Gene expression in the treated basophils was analyzed using microarray analysis. Overall, deletion of C/EBPa in basophils resulted in a reduction of mRNA expression for 248 genes and led to an increase in mRNA expression for 255 genes. The majority of the C/EBPa-regulated genes were either differentially or highly expressed in basophils or mast cells.
2013-04-01 | GSE41596 | GEO
Project description:Basophils are the least common granulocytes which represent less than 1% of peripheral blood leukocytes. Recent development of analytical tools for basophils has enabled us to understand their critical roles in allergic reactions and protection from parasitic infections. Nevertheless, the differentiation trajectory of basophils remain unclear. To explore differentiation trajectory of basophils, we conducted highly sensitive single cell RNA sequencing (scRNA-seq) of bone marrow-derived basophils (BMBAs) and basophils under homeostatic conditions. As a result, we identified previously-unappreciated pre-basophils which are located down-stream of bi-potential basophil and mast cell common precursors and upstream of mature basophils along the ontogeny of basophlis.
2023-03-21 | GSE206589 | GEO
Project description:Basophil functional state was determined using the Flow2CAST Basophil Activation Test (BAT). Human basophils were isolated from whole blood of three house dust mite (HDM) responsive donors with reactive basophils and two donors with anergic basophils. Basophil isolation was performed using the EasySep Human Basophil Enrichment kit (Stemcell). Purity of the basophils was determined by flow cytometry and ranged from 96 - 99%. For stimulation, 75,000 basophils were incubated for 4 hr with or without 50 ul of anti-FCERI antibody (Bühlmann Laboratories) in a total volume of 200 ul of Stimulation Buffer provided by the Flow2CAST kit. After incubation, the basophils were collected and re-suspended in TRIzol Reagent (Life Technologies). Total RNA was extracted using double extraction protocol using the guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen), followed by a Qiagen RNeasy Micro clean-up procedure. cDNA and ST-ssDNA were prepared, fragmented and labeled according to Nugen WT Ovation Pico RNA Amplification and WT Ovation Exon kit and Encore Biotin protocols. The labeled ssDNA was hybridized on the Affymetrix Human GeneChip 1.0 ST Arrays, which subsequently were processed and stained using GeneChip Fluidics Station 450. The stained GeneChip Arrays were scanned in the Microarray Facility at the Biopolis Shared Facility using a GeneChip Scanner 3000. Quality control for the Arrays was performed using the Affymetrix Expression Console Software.
2017-06-15 | GSE70013 | GEO
Project description:Whole transcriptome analysis of genes expressed by spleen basophils in response to gasttrointestinal helminth infection, compared to naïve animals, analyzing the role of basophil-intrinsic Notch signaling using a basophil specific inhibition of Notch (Mcpt8Cre-DNMAML)
2019-04-08 | GSE129056 | GEO
Project description:Mast cells and basophils are developmentally related cells whose activation is a hallmark of allergy. Functionally, mast cells and basophils overlap in their ability to produce several mediators, including histamine and granule proteases, but studies have increasingly demonstrated non-redundant roles. To characterize the transcriptional heterogeneity of mast cells and basophils upon their activation, we performed large-scale comparative microarrays of murine bone marrow–derived mast cells (BMMCs) and basophils (BMBs) at rest, upon an adaptive-type activation (IgE crosslinking), or upon an innate-type activation (IL-33 stimulation). Hierarchical clustering demonstrated that BMMCs and BMBs shared specific activation-associated transcriptional signatures but differed in others, both between cell type and between activation mode. In BMMCs, IgE crosslinking upregulated 785 genes including Egr2, Ccl1, and Fxyd6, while IL-33 stimulation induced 823 genes including Ccl1, Egr2, and Il1b. Focused bioinformatics pathway analysis demonstrated that IgE activation aligned with processes such as oxidative phosphorylation, angiogenesis, and the p53 pathway. The IL-33–activated transcriptome was enriched in genes commonly altered by NF-B in response to TNF, by IL-6 via STAT3, and in response to IFN. Furthermore, BMBs activated via IgE crosslinking selectively induced immune response genes Ccl1, Il3, and Il2 compared to IL-33–stimulated BMBs. Principal-component analysis revealed key cell- and activation-specific clustering. Overall, our data demonstrate that mast cells and basophils have cell- and activation-specific transcriptional responses and suggest that context-specific gene networks and pathways may shape how the immune system responds to allergens and innate cytokines.
2017-03-17 | GSE96696 | GEO
Project description:Gene expression profiles of basophil progenitors, CD34- pre-basophils and mature basophils
| PRJNA851433 | ENA