Epigenomic analysis of primary human T cells reveals novel enhancers associated with Th2 memory differentiation and asthma susceptibility (3 cell types)
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ABSTRACT: A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4+ T cells that produce Th2 cytokines (Th2 cells). By mapping genome-wide histone modification profiles of T cell subsets isolated from peripheral blood of healthy and asthmatic individuals, we identified enhancers with known and potential roles in the normal differentiation of human Th1 and Th2 cells. In addition, we discovered disease-specific T cell enhancers that differ between healthy and asthmatic individuals. Examination of H3K4me2 histone modifications in 3 human cell types in 11 healthy and 12 asthmatic individuals .
Project description:A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4+ T cells that produce Th2 cytokines (Th2 cells). By comparing gene expression profiles of T cell subsets isolated from peripheral blood of healthy and asthmatic individuals, we identified genes with known and potential roles in the normal differentiation of human Th1 and Th2 cells. Examination of gene expression in 3 human cell types in healthy and asthmatic individuals.
Project description:To estimate the reproducibility of standard and micro-scaled H3K4me2 ChIP-Seq assay we performed the genome-wide correlation analysis of H3K4me2 enrichment patterns from 7 independent standard ChIP-Seq assays (2 million D10 cells), and micro-scaled ChIP-Seq 100,000 cells sample M-bM-^@M-^S(N=12), 10,000 cells sampleM-bM-^@M-^S(N=3), and 1000 cell sample M-bM-^@M-^S (N=4) Examination of H3K4me2 histone modifications in mouse derived lymphoblastic cell line (D10.G4.1 cells, ATCC).
Project description:Background: A specific subset of regulatory IL-10 producing B cells has been extensively studied in autoimmune and inflammatory pathologies. These cells are able to constrain exacerbated inflammation by inhibiting T cell mediated responses and maturation of antigen presenting cells. In allergic diseases, observations that increase of regulatory B cells is necessary for allergen tolerance suggest that development of allergic asthma would be associated with a defect in the regulatory B cells compartment. Objective: We sought to (i) characterize regulatory IL-10+ regulatory B cell subset in Balb/c mice by microarray and flow cytometry and (ii) investigate their regulatory capacity in vivo in a house dust mite model of allergic asthma. Results: We identified an IL-10 producing B cells subset able to control T cell proliferation in vitro in both control and asthmatic mice. This subset is decreased in allergic mice. IL-10+ Breg cells express high levels of CD9 and upregulate CD70 and CD73 after activation. Expression of CD9 allows identifying more than 50% of Bregs. Interestingly CD9+ B cells inhibit TH2-TH17 allergic airway inflammation in vivo after adoptive transfer in an IL-10 dependent manner. Conclusions: Herein, we demonstrate that induction of allergic asthma dampens the generation of Bregs contributing to exacerbated airway inflammation. We identified a distinct CD9+ Breg-cell population decreased in lung of HDM mice and able to control asthma and allergic airway inflammation by producing IL-10 after adoptive transfer. This study points B cells as an interesting therapeutic target in allergic asthma. IL-10+ B cells (n=3) and 3 IL-10- B cells (n=3) in control mice + IL-10+ B cells (n=3) and 3 IL-10- B cells (n=3) from asthmatic allergic (HDM) mice
Project description:Microarray analyses were performed to compare gene expression in cultured mouse Th9, Th2 and Treg cells and resting versus activated Th9 cells. Three replicates were analyzed for each culture condition; Th9 unstim, Th2 unstim, Treg unstim, Th9 stim
Project description:A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4+ T cells that produce Th2 cytokines (Th2 cells). By mapping genome-wide histone modification profiles of T cell subsets isolated from peripheral blood of healthy and asthmatic individuals, we identified enhancers with known and potential roles in the normal differentiation of human Th1 and Th2 cells. In addition, we discovered disease-specific T cell enhancers that differ between healthy and asthmatic individuals.
Project description:Single-cell RNA-seq analysis of mouse CD4 T cells to understand the function of HDAC1 for pathogenic Th2 cells. Wildtype and HDAC1 KO cell from several sorted populations are covered. Hashtag oligos were used to enable multiplexing before analysis on a 10x chromium.
Project description:Transcription profiling by array of bronchial epithelial cells from severe asthmatic, mild-moderate asthmatic and non-asthmatic patients
Project description:Background: Evidence suggests that immune responses to rhinovirus A and C are altered in asthmatic children and rhinovirus species induce different types of antibody responses. Objective: To ascertain and compare the T-cell memory response induced by RV-A and RV-C in asthmatic and non-asthmatic children. Methods: Peripheral blood mononuclear cells from children who previously suffered asthma exacerbation (asthmatics) and non-asthmatic controls were stimulated in vitro with peptide formulations to induce representative species-specific responses to RV-A and RV-C. Expression of genes was measured by RNA-seq and differentially expressed genes were further analysed to identify enriched pathways and upstream regulators. Results: Responses to RV-A showed markedly higher upregulation of IFNG and the IFNG responsive genes CXCL9, 10 and 11 and STAT1 compared to RV-C. There was no reciprocal upregulation of Th2 cytokine genes or the Th2 chemokine genes CCL11, CCL17 and CCL22. RV-C but not RV-A induced high upregulation of CCL24 (eotaxin-2) in both non-asthmatic and asthmatic responses. Upstream regulator analysis showed both RV-A and, although to a diminished extent, RV-C induced predominant Th1 and inflammatory cytokine expression. The responses of asthmatics compared to non-asthmatics was diminished to both RV-A and RV-C while retaining the pattern for gene expression and upstream regulators characteristic of each species and there was no upregulation of Th2-type responses. All groups showed activation of the IL-17A pathway. Conclusions: RV-C induced memory cells with a lower IFNG type response than RV-A without Th2 upregulation. Asthmatics had lower recall responses than non-asthmatics while largely retaining the same gene activation profile for each species.
Project description:A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4+ T cells that produce Th2 cytokines (Th2 cells). By comparing gene expression profiles of T cell subsets isolated from peripheral blood of healthy and asthmatic individuals, we identified genes with known and potential roles in the normal differentiation of human Th1 and Th2 cells.