The 11q13.5 immune disease risk locus contains a distal enhancer required for Treg-mediated suppression of gut inflammation [ATAC-Seq]
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ABSTRACT:
PROVIDER: PRJNA600871 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10876147_1.fastq.gz | Fastqsanger.gz | |||
| SRR10876147_2.fastq.gz | Fastqsanger.gz | |||
| SRR10876148_1.fastq.gz | Fastqsanger.gz | |||
| SRR10876148_2.fastq.gz | Fastqsanger.gz | |||
| SRR10876149_1.fastq.gz | Fastqsanger.gz |
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Project description:The 11q13.5 immune disease risk locus contains a distal enhancer required for Treg-mediated suppression of gut inflammation
| PRJNA600868 | ENA
Project description:Much of the genetic variation underlying susceptibility to common autoimmune and allergic diseases is concentrated within protein non-coding regulatory elements termed enhancers{Enhancer; Hsniz}. It has been difficult to assign functions to a majority of enhancers that overlap immune disease-associated variants due to their distance from the genes they regulate, our lack of understanding of the cell types in which they operate and our inability to recapitulate the biology of immune-mediated diseases in vitro. Here, using syntenic analysis and CRISPR-based mutagenesis to model enhancer function in mice, we show that a prominent human autoimmune/allergic disease risk locus at 11q13.5 contains a distal enhancer commissioned in Foxp3+ regulatory T (Treg) cells and required for Treg-mediated resistance to gut inflammation. Highly conserved binding sites within the enhancer recruit the transcription factor STAT5 to mediate interleukin (IL)-2-driven expression of Lrrc32, encoding Glycoprotein A Repetitions Predominant (GARP). Whereas disruption of the Lrrc32 gene results in loss of embryonic viability, mice lacking the enhancer (hereinafter Lrrc32 +70k) are viable but lack GARP expression on Foxp3+ Treg cells which subsequently are unable to control gut inflammation. In human Treg cells disease-risk alleles at 11q13.5 reduce levels of histone acetylation and are associated with reduced levels of LRRC32 expression. These findings define a function for the 11q13.5 risk locus in Treg-mediated immunoregulation and provide evidence of a causal involvement of Treg cells in the pathophysiology of polymorphic immune-mediated diseases at the intersection of genetics and the environment.
2020-03-02 | GSE128198 | GEO
Project description:Much of the genetic variation underlying susceptibility to common autoimmune and allergic diseases is concentrated within protein non-coding regulatory elements termed enhancers{Enhancer; Hsniz}. It has been difficult to assign functions to a majority of enhancers that overlap immune disease-associated variants due to their distance from the genes they regulate, our lack of understanding of the cell types in which they operate and our inability to recapitulate the biology of immune-mediated diseases in vitro. Here, using syntenic analysis and CRISPR-based mutagenesis to model enhancer function in mice, we show that a prominent human autoimmune/allergic disease risk locus at 11q13.5 contains a distal enhancer commissioned in Foxp3+ regulatory T (Treg) cells and required for Treg-mediated resistance to gut inflammation. Highly conserved binding sites within the enhancer recruit the transcription factor STAT5 to mediate interleukin (IL)-2-driven expression of Lrrc32, encoding Glycoprotein A Repetitions Predominant (GARP). Whereas disruption of the Lrrc32 gene results in loss of embryonic viability, mice lacking the enhancer (hereinafter Lrrc32 +70k) are viable but lack GARP expression on Foxp3+ Treg cells which subsequently are unable to control gut inflammation. In human Treg cells disease-risk alleles at 11q13.5 reduce levels of histone acetylation and are associated with reduced levels of LRRC32 expression. These findings define a function for the 11q13.5 risk locus in Treg-mediated immunoregulation and provide evidence of a causal involvement of Treg cells in the pathophysiology of polymorphic immune-mediated diseases at the intersection of genetics and the environment.
2020-03-02 | GSE143515 | GEO
Project description:The 11q13.5 immune disease risk locus contains a distal enhancer required for Treg-mediated suppression of gut inflammation [RNA-Seq]
| PRJNA526721 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2020-03-01 | GSE143516 | GEO
Project description:Regulatory T (Treg) cells play an important role in the induction and maintenance of peripheral tolerance. Treg cells also suppress a variety of other immune responses, including anti-tumor and alloimmune responses. We have previously reported that tumor-activated Treg cells express granzyme B and that granzyme B is important for Treg cell-mediated suppression of anti-tumor immune responses (GSE13409). Here, we report that allogeneic mismatch also induces the expression of granzyme B. Granzyme B-deficient mice challenged with fully mismatched allogeneic P815 mastocytoma cells have markedly improved survival compared to WT and other granzyme- or perforin-deficient mice, suggesting an immunoregulatory role for granzyme B in this setting. Treg cells harvested from the tumor environment of P815-challenged mice express granzyme B. Treg cells also express granzyme B in vitro during mixed lymphocyte reactions and in vivo in a mouse model of graft-versus-host disease (GVHD). However, in contrast to findings from our previously published tumor model, granzyme B is not required for the suppression of effector T cell (Teff) proliferation in in vitro Treg suppression assays stimulated by either Concanavalin A or allogeneic antigen presenting cells. Additionally, in an ex vivo assay, sort-purified in vivo-activated CD4+Foxp3+ Treg cells from mice with active GVHD -- under conditions known to induce granzyme B expression in Treg cells -- suppressed Teff cell proliferation in a granzyme B-independent manner. Adoptive transfer of naive granzyme B-deficient CD4+CD25+ Treg cells into a mouse model of GVHD rescued hosts from lethatlity equivalently to naive wild-type Treg cells. Serum analysis of GVHD-associated cytokine production in these recipients also demonstrated that Treg cells suppressed production of IL-2, IL-4, IL-5, GM-CSF, and IFN-gamma in a granzyme B-independent manner. In order to determine whether the context in which Treg cells are activated alters the intrinsic properties of Treg cells, we used Foxp3 reporter mice to obtain gene expression profiles of CD4+Foxp3+ Treg cells purifed from naive resting spleens, spleens from mice with acute GVHD, and from ascites fluid of mice challenged intraperitoneally with allogeneic P815 tumor cells. Unsupervised analyses revealed distinct activation signatures of Treg cells among the 3 experimental groups. Taken together, these findings demonstrate that granzyme B is not required for Treg cell-mediated suppression of GVHD, which is in contrast to what we have previously reported for Treg cell function in the setting of tumor challenge. Cell intrinsic differences could partially account for these differential phenotypes. These data also suggest the therapeutic potential of targeting specific Treg cell suppressive functions in order to segregate GVHD and graft-versus-tumor effector functions. Experiment Overall Design: Six replicates of Naive CD4+Foxp3+ Treg cells were purified from resting spleens, five replicates of allogeneic tumor-activated Treg cells and three samples of GVHD-activated Treg cells. Experiment Overall Design: Naive reps 1-3 are controls for the GVHD-activated samples. Experiment Overall Design: Naive reps 4-6 are controls for the Allogeneic tumor-activated samples.
2009-09-15 | E-GEOD-16210 | biostudies-arrayexpress
Project description:Regulatory T (Treg) cells, as central mediators of immune suppression, play crucial roles in many aspects of immune system physiology and pathophysiology. Treg cells are characterized by a distinct pattern of gene expression, including upregulation of immune-suppressive genes and silencing of inflammatory cytokine genes. However, the molecular mechanisms that establish and/or maintain such gene regulation in Treg cells remain largely unknown. We recently reported that Nr4a family nuclear orphan receptors are essential for the development of Treg cells. The fact that Treg cells maintain high levels of expression of all Nr4a family components suggests that they may also play critical roles beyond Treg cell development. Here, we show that Nr4a factors are essential for maintaining Treg-specific gene expression programs, mediating two defined characteristics of Treg cells: lineage stability and suppressive activity. A compound knockout mouse strain in which all Nr4a genes were specifically deleted in Treg cells developed systemic immunopathology with accelerated Th2/Tfh/IgE reactions. Treg cells in these mice showed global reduction of 'Treg signature' gene expression, including Foxp3, Il2ra and Ikzf4. These findings demonstrate that Nr4a controls a genetic program indispensable for Treg cell maintenance and function. mRNA from wild-type and Nr4a-deficient Treg cells were analyzed.
2013-12-23 | E-GEOD-53574 | biostudies-arrayexpress
Project description:Foxp3+ regulatory T (Treg) cells prevent inflammatory disease but the mechanistic basis of suppression is not understood completely . Gene silencing by RNA interference can act in a cell-autonomous and non-cell-autonomous manner, providing mechanisms of inter-cellular regulation. Here, we demonstrate that non-cell-autonomous gene silencing, mediated by miRNA-containing exosomes, is a mechanism employed by Treg cells to suppress T cell-mediated disease. Treg cells transferred microRNAs (miRNA) to various immune cells, including T helper 1 (Th1) cells, suppressing Th1 cell proliferation and cytokine secretion. Use of Dicer-deficient or Rab27a and Rab27b double-deficient Treg cells to disrupt miRNA-biogenesis or the exosomal pathway, respectively, established a requirement for miRNAs and exosomes for Treg cell-mediated suppression. Transcriptional analysis and miRNA inhibitor studies showed that exosome-mediated transfer of Let-7d from Treg cell to Th1 cells contributed to suppression and prevention of systemic disease. These studies reveal a mechanism of Treg cell-mediated suppression mediated by miRNA-containing exosomes. Regulatory T cells (CD4+CD25hiFoxp3rfp+, Treg) were isolated from naive mice. RNA as extracted form some Treg cells, while others were cultured in complete IMDM media for 3 days, stimulated with anti-CD3 anti-CD3 (1ug/ml) and anti-CD28 (10ug/ml). Exosomes were recovered from Treg cell supernatant, as described, and RNA was extracted form the purified exosomes. To identify which miRNAs were transferred to Dicer-deficient (KO) cells from Treg cells, we cultured Dicer KO cells alone, or co-cultured Dicer KO cells with Treg cells. RNA was extracted form Dicer KO cells cultured alone or from Dicer KO cells cultured in the presence of Treg cells. 3 x biological replicates were used. Each biological replicate was derived from a pool of 3-5 samples.
2014-08-27 | E-GEOD-60615 | biostudies-arrayexpress
Project description:Drak2¬-deficient (Drak2-/-) mice are resistant to multiple models of autoimmunity, yet effectively eliminate pathogens and tumors. Thus, DRAK2 is an ideal target to treat autoimmune diseases. However, the mechanisms by which DRAK2 contributes to autoimmunity, particularly type 1 diabetes (T1D), remain unresolved. Our data indicate that DRAK2 contributes to autoimmunity in multiple ways by regulating thymic Treg development and by impacting the sensitivity of conventional T cells to Treg-mediated suppression.
2023-02-09 | PXD037922 | Pride
Project description:Regulatory T (Treg) cells, as central mediators of immune suppression, play crucial roles in many aspects of immune system physiology and pathophysiology. Treg cells are characterized by a distinct pattern of gene expression, including upregulation of immune-suppressive genes and silencing of inflammatory cytokine genes. However, the molecular mechanisms that establish and/or maintain such gene regulation in Treg cells remain largely unknown. We recently reported that Nr4a family nuclear orphan receptors are essential for the development of Treg cells. The fact that Treg cells maintain high levels of expression of all Nr4a family components suggests that they may also play critical roles beyond Treg cell development. Here, we show that Nr4a factors are essential for maintaining Treg-specific gene expression programs, mediating two defined characteristics of Treg cells: lineage stability and suppressive activity. A compound knockout mouse strain in which all Nr4a genes were specifically deleted in Treg cells developed systemic immunopathology with accelerated Th2/Tfh/IgE reactions. Treg cells in these mice showed global reduction of 'Treg signature' gene expression, including Foxp3, Il2ra and Ikzf4. These findings demonstrate that Nr4a controls a genetic program indispensable for Treg cell maintenance and function.
2013-12-23 | GSE53574 | GEO