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RNA-sequencing of Aire-ILC3 cells from wild-type and Aire-deficient mice

ABSTRACT: Autoimmune regulator (Aire) plays an indispensable role in the induction of central immune tolerance. We identify a novel subset of Rorγt-dependent innate lymphoid cell-type in secondary lymphoid organs, which presents endogenously generated antigens and contributes to peripheral T cell tolerance. In this experiment, transcriptomes of these Aire-ILC3 cells are characterized in wild-type Balb/C and Aire-/- Balb/C mice [Ramsey, C. et al. (2002) Hum Mol Genet 11:397-409] using RNA-seq method. To obtain the cells, peripheral lymph nodes were minced, enzymatically digested, and Aire-ILC3 cells were FACS-sorted as Lin-, MHCII+, CD80+, IL7Ra+ cells.

REANALYSIS of: E-MTAB-7088

ORGANISM(S): Mus musculus

PROVIDER: E-MTAB-7088 | ExpressionAtlas | 2019-01-16

REPOSITORIES: ExpressionAtlas

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RNA-sequencing of Aire-ILC3 cells from wild-type and Aire-deficient mice

Project description:Autoimmune regulator (Aire) plays an indispensable role in the induction of central immune tolerance. We identify a novel subset of Rorγt-dependent innate lymphoid cell-type in secondary lymphoid organs, which presents endogenously generated antigens and contributes to peripheral T cell tolerance. In this experiment, transcriptomes of these Aire-ILC3 cells are characterized in wild-type Balb/C and Aire-/- Balb/C mice [Ramsey, C. et al. (2002) Hum Mol Genet 11:397-409] using RNA-seq method. To obtain the cells, peripheral lymph nodes were minced, enzymatically digested, and Aire-ILC3 cells were FACS-sorted as Lin-, MHCII+, CD80+, IL7Ra+ cells.

2019-03-14 | E-MTAB-7088 | ArrayExpress

Identification of a novel Aire-regulating cis-regulatory element using H3K27ac ChIP-seq

Project description:Thymic central tolerance is essential to preventing autoimmunity. In medullary thymic epithelial cells (mTECs), the Autoimmune regulator (Aire) gene plays an essential role in this process by driving the expression of a diverse set of tissue-specific antigens (TSAs), which are presented and help tolerize self-reactive thymocytes. Interestingly, Aire has a highly tissue-restricted pattern of expression, with only mTECs and peripheral extrathymic Aire-expressing cells (eTACs) known to express detectable levels in adults. Despite this high level of tissue specificity, the cis-regulatory elements that control Aire expression have remained obscure. We used sequence conservation analysis and ChIP-seq against the enhancer-associated histone mark H3K27ac to identify a candidate Aire cis-regulatory element. There is enrichment of H3K27ac near this element, ACNS1, in mTECs and the element also has characteristics of being NF-κB-responsive. Finally, we find that this element is essential for Aire expression in vivo and necessary to prevent spontaneous autoimmunity, reflecting the importance of this regulatory DNA element in promoting immune tolerance. Overall design: Two experimental groups (GFP neg mTECs and GFP pos mTECs), each with three samples, and one control sample (D10 Th2 cells).

| GSE74257 | GEO

Identification of a novel Aire-regulating cis-regulatory element using H3K27ac ChIP-seq

Project description:Thymic central tolerance is essential to preventing autoimmunity. In medullary thymic epithelial cells (mTECs), the Autoimmune regulator (Aire) gene plays an essential role in this process by driving the expression of a diverse set of tissue-specific antigens (TSAs), which are presented and help tolerize self-reactive thymocytes. Interestingly, Aire has a highly tissue-restricted pattern of expression, with only mTECs and peripheral extrathymic Aire-expressing cells (eTACs) known to express detectable levels in adults. Despite this high level of tissue specificity, the cis-regulatory elements that control Aire expression have remained obscure. We used sequence conservation analysis and ChIP-seq against the enhancer-associated histone mark H3K27ac to identify a candidate Aire cis-regulatory element. There is enrichment of H3K27ac near this element, ACNS1, in mTECs and the element also has characteristics of being NF-κB-responsive. Finally, we find that this element is essential for Aire expression in vivo and necessary to prevent spontaneous autoimmunity, reflecting the importance of this regulatory DNA element in promoting immune tolerance. Two experimental groups (GFP neg mTECs and GFP pos mTECs), each with three samples, and one control sample (D10 Th2 cells).

2015-10-23 | E-GEOD-74257 | ArrayExpress

Deletional Tolerance Mediated by Extrathymic Aire-Expressing Cells

Project description:The prevention of autoimmunity requires elimination of self-reactive T cells during their development and maturation. Expression of diverse self-antigens by stromal cells in the thymus is essential to this process, and depends, in part, on the activity of the Autoimmune Regulator (Aire) gene. Here we report the identification of extrathymic Aire-expressing cells (eTACs) resident within the secondary lymphoid organs. These stromally-derived eTACs express a diverse array of unique self-antigens and are capable of interacting with and deleting naive autoreactive T cells. Using two-photon microscopy we observe stable, antigen-specific interactions between eTACs and autoreactive T cells. We propose that such a secondary network of self-antigen-expressing stromal cells may help reinforce immune tolerance by preventing the maturation of autoreactive T cells that escape thymic negative selection. A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out. Keywords: genetic_modification_design Overall design: 8 samples

2008-08-08 | GSE12388 | GEO

The effect of the autoimmune regulator (Aire) gene on the transcriptional expression profile of 3.10 mouse medullary thymic epithelial cell line

Project description:Medullary thymic epithelial cells (mTECs) contribute to self-tolerance through the ectopic expression of peripheral tissue antigens (PTAs) in the thymus. PTA expression in mTECs is largely dependent on the autoimmune regulator (Aire) gene. Here we used a Mus musculus mTEC cell line (3.10 mTEC line, which constitutively express Aire in culture) to knockdown Aire gene by means of siRNA transfection. Aire knockdown was confirmed by means of qRT-PCR and RNA-FISH (for Aire mRNA levels), immunofluorescence and western blot (for AIRE protein levels).The Agilent oligo microarrays were used to determine the large scale transcriptional expression profiles of control or Aire-knockdown 3.10 mTECs.

2015-12-31 | E-MTAB-3879 | ArrayExpress

The effect of the Autoimmune regulator (Aire) gene on microRNA transcriptional profile of 3.10 mTEC cell line

Project description:Medullary thymic epithelial cells (mTECs) contribute to self-tolerance through the ectopic expression of peripheral tissue antigens (PTAs) in the thymus. Autoimmune regulator (Aire) is to date the best characterized transcriptional regulator known to at least partially coordinate PTA expression in mTECs. Furthermore the expression of Aire-dependent and -independent genes is also modulated by microRNAs. Given the transcriptional regulation exerted by Aire in mTEC cells and the role of miRNAs in post-transcriptional control, we used a Mus musculus mTEC cell line (3.10) which constitutively express Aire in culture) to knockdown Aire gene by means of siRNA transfection and then observe the effect of Aire knockdown in the transcriptional profile of miRNAs by means of oligomicroarrays. The Agilent oligomicroarrays were used to determine the large scale the miRNA transcriptional profiles of control or Aire-knockdown 3.10 mTECs.

2016-06-27 | E-MTAB-4596 | ArrayExpress

Messenger RNA expression profile of medullary thymic epithelial-mTEC-cells by in vivo thymus Aire knockdown-BALB-c mice

Project description:Small interfering RNA (siRNA) was used to knockdown Autoimmune regulator(Aire) gene by in vivo electroporation of the thymus of BALB-c mice. In This set of data we include control and Aire-silenced mTEC cells isolated from thymus of BALB-c mice.

2012-08-11 | E-MEXP-3343 | ArrayExpress

MicroRNA profiling by array of control and Aire-knockdown medullary thymic epithelial cells isolated from thymus of BALB-c mice.

Project description:Small interfering RNA ( siRNA) was used to knockdown Autoimmune regulator (Aire) gene by in vivo electroporation of the thymus of BALB-c mice. In this set of data we include control and Aire-knockdown mTEC cells isolated from thymus of BALB-c mice.

2013-06-28 | E-MEXP-3665 | ArrayExpress

Transcription profiling by high throughput sequencing of primary cTEC, mTEClo, and mTEChi harvested from wild type and Aire-deficient mice

Project description:Promiscuous gene expression (pGE) of numerous self-antigens in thymic epithelial cells (TEC) enables the elimination of self-reactive T cells. The autoimmune regulator (Aire) is the only known molecular determinant driving pGE in the thymus but the existence of Aire-independent mechanisms has been inferred. Here, we analyzed the poly(A)+ transcriptome of TEC populations by RNA-sequencing (RNA-seq) in order to reveal differential features of Aire-induced vs. –independent pGE. We report an unanticipated effect of Aire deletion on the proliferation and differentiation of cortical TEC. Moreover, the RNA-seq data reveal the breath of Aire-induced and –independent pGE in medullary TEC (mTEC) subsets and the extent of thymic peripheral tissue representation. The results suggest that Aire-induced promiscuously expressed transcripts affect several functions with far reaching biological consequences in mTEC. High-throughput characterization of TEC transcriptomes will enable progress in understanding TEC biology and the establishment of self-tolerance. The mRNA profiles of cTEC, mTEClo and mTEChi from 6-8 week-old wild type (WT) and Aire-/- (KO) mice were generated by RNA-sequencing using Illumina HiSeq2000.

2015-05-19 | E-GEOD-65617 | ArrayExpress

RNA-Seq of lymph node fibroblastic reticular cells isolated from bone marrow transplant recipient mice with or without acute Graft-versus-host disease on day 7 or untransplanted control mice

Project description:Acute GVHD is known to damage the structure of peripheral lymphoid organs. This study investigates how peripheral tolerance induction is affected by lymph node stroma damage in the context of graft-versus-host disease. Fibroblastic reticular cells (FRC) were flow sorted on day 7 post allo-BMT in mice developing acute GVHD, transplanted no GVHD-recipients or untransplanted control mice. The single miHA-mismatch female into male transplantation model was used (acute GVHD group: T-cell depleted bone marrow (TCDBM) + HY-specific TCR-transgenic MataHari CD8+ T cells into C57BL/6 male recipients; no GVHD group: TCDBM only).

2020-01-14 | E-MTAB-8255 | ArrayExpress

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