BATF represses BIM to sustain tolerant T cells in the periphery (ATAC-Seq)
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE244276 | GEO | 2023/10/17
REPOSITORIES: GEO
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Project description:T cells that encounter self-antigens after exiting the thymus avert autoimmunity through peripheral tolerance. Pathways for this include an unresponsive state known as anergy, clonal deletion, and T regulatory (Treg) cell induction. The transcription factor cues and kinetics that guide distinct peripheral tolerance outcomes remain unclear. Here, we found that anergic T cells are epigenetically primed for regulation by the non-classical AP-1 family member BATF. Tolerized BATF-deficient CD4+ T cells were resistant to anergy induction and instead underwent clonal deletion due to pro-apoptotic BIM (Bcl2l11) upregulation. During prolonged antigen exposure, BIM de-repression resulted in fewer PD-1+ conventional T cells as well as loss of peripherally-induced FOXP3+ Treg cells. Simultaneous Batf and Bcl2l11 knockdown meanwhile restored anergic T cell survival and Treg cell maintenance. The data identify the AP-1 nuclear factor BATF as a dominant driver of sustained T cell anergy and illustrate a mechanism for divergent peripheral tolerance fates.
2023-10-17 | GSE244278 | GEO
Project description:Peripheral tolerance induction is critical for the maintenance of self-tolerance and can be mediated by immunoregulatory T cells or by direct induction of T cell anergy or deletion. While the molecular processes underlying anergy have been extensively studied, little is known about the molecular basis for peripheral T cell deletion. Here, we determined the gene expression signature of peripheral CD8+ T cells undergoing deletional tolerance, relative to those undergoing immunogenic priming or lymphopenia-induced proliferation. From these data, we report the first detailed molecular signature of cells undergoing deletion. Consistent with defective cytolysis, these cells exhibited deficiencies in granzyme up-regulation. Furthermore, they showed antigen-driven Bcl-2 down-regulation and early up-regulation of the pro-apoptotic protein Bim, consistent with the requirement of this BH3-only protein for peripheral T cell deletion. Bim up-regulation was paralleled by defective IL-7Ra chain re-expression, suggesting that Bim-dependent death may be triggered by loss of IL-7/IL-7R signaling. Finally, we observed parallels in molecular signatures between deletion and anergy suggesting that these tolerance pathways may not be as molecularly distinct as previously surmised.
2009-02-10 | GSE14699 | GEO
Project description:Activation of peripheral T lymphocytes in the absence of pathogen induced inflammation or costimulatory signals results in tolerance. Two different tolerance mechanisms have been described, deletion and anergy. We recently demonstrated that an important variable which is responsible for the decision between anergy and deletion for CD8 T cells is the strength of signaling through the T cell receptor(Redmond and Sherman, Immunity 22:275,2005). However, it is not know what the downstream signals are that result in death(deletion) vs. survival(anergy)of the activated cells. Here we analysze additional conditions: 1) Wild Type mice were injected injected only once with a strain of vaccinia virus that express hemagglutinin from influenza; 2) BIM KO Clone 4 transgenic T cells were transferred into B10D2 mice then injected daily for 3 days with 1ug of KdHA peptide and sorted by flow cytometry according to their expression of CD8 and thy1.1; 3) Mice injected with 1 ug (deleted condition) of influenza hemaglutinin antigen (HA), 24 hours post injection CD8 T CL4 cells were sorted by flow cytometry (FacsARIA) and 4) WildType mice injected with 100 ug (anergic condition) of influenza hemaglutinin antigen (HA), 24 hours post injection CD8 T CL4 cells were sorted by flow cytometry (FacsARIA). Dr. Sherman's lab aims to assess the role of protein glycosylation in the decision between deletion vs. anergy in immune tolerance, they have prepared purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) or a weak antigenic signal (deletion conditions) with cognate antigen. Dr. Sherman's lab wishes to assess transcriptional differences in genes involved in protein glycosylation in these 2 cell populations. Then control population will be naïve transgenic CD8 cells. RNA preparations of mouse CD8 T cells from the B10D2 strain with three different conditions (Naïve, Deleted, and Anergic) were sent to the Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv4 microarrays.
2011-09-07 | E-GEOD-31988 | biostudies-arrayexpress
Project description:Peripheral tolerance induction is critical for the maintenance of self-tolerance and can be mediated by immunoregulatory T cells or by direct induction of T cell anergy or deletion. While the molecular processes underlying anergy have been extensively studied, little is known about the molecular basis for peripheral T cell deletion. Here, we determined the gene expression signature of peripheral CD8+ T cells undergoing deletional tolerance, relative to those undergoing immunogenic priming or lymphopenia-induced proliferation. From these data, we report the first detailed molecular signature of cells undergoing deletion. Consistent with defective cytolysis, these cells exhibited deficiencies in granzyme up-regulation. Furthermore, they showed antigen-driven Bcl-2 down-regulation and early up-regulation of the pro-apoptotic protein Bim, consistent with the requirement of this BH3-only protein for peripheral T cell deletion. Bim up-regulation was paralleled by defective IL-7Ra chain re-expression, suggesting that Bim-dependent death may be triggered by loss of IL-7/IL-7R signaling. Finally, we observed parallels in molecular signatures between deletion and anergy suggesting that these tolerance pathways may not be as molecularly distinct as previously surmised. Naïve (CD44lo) OT-I T cells were CFSE labelled and transferred in a model of deletional tolerance (RIP-OVAhi mice), a model of immunity (mice primed with OVA coated splenocytes and LPS) or a model of lymphopenia induced proliferation (Rag-/- mice). 60 hrs (RIP-OVAhi and OVA coated splenocytes) or 5 days (Rag-/-) after transfer, OT-I cells that had undergone two or more divisions as determined by CFSE dilution were sorted, RNA extracted and samples were prepared for hybridisation to Affymetrix microarrays. As a control for naive cells, CFSE labelled OT-I cells were injected into antigen-free B6 mice and the undivided naive cells were sorted after 60 hrs and also used for microarray analysis. Two replicates were prepared for the naive cells, cells from RIP-OVAhi mice and cells from OVA coated splenocyte primed mice, while one replicate was prepared for the cells from Rag-/- mice.
2009-02-10 | E-GEOD-14699 | biostudies-arrayexpress
Project description:Activation of peripheral T lymphocytes in the absence of pathogen induced inflammation or costimulatory signals results in tolerance. Two different tolerance mechanisms have been described, deletion and anergy. We recently demonstrated that an important variable which is responsible for the decision between anergy and deletion for CD8 T cells is the strength of signaling through the T cell receptor(Redmond and Sherman, Immunity 22:275,2005). However, it is not know what the downstream signals are that result in death(deletion) vs. survival(anergy)of the activated cells. Marth and co-workers have previously shown that CD8 T cell apoptosis under conditions similar to those that occur during tolerance in vivo may involve a change in protein glycosylation (Van Dyken et.al., Mol.Cell.Bio.27:1096,2007).In order to assess the role of protein glycosylation in the decision between deletion vs. anergy in immune tolerance, we have prepared purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) or a weak antigenic signal (deletion conditions) with cognate antigen. We wish to assess transcriptional differences in genes involved in protein glycosylation in these 2 cell populations. The control population will be naive trangenic CD8 cells. Dr. Sherman's lab aims to assess the role of protein glycosylation in the decision between deletion vs. anergy in immune tolerance, they have prepared purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) or a weak antigenic signal (deletion conditions) with cognate antigen. Dr. Sherman's lab wishes to assess transcriptional differences in genes involved in protein glycosylation in these 2 cell populations. Then control population will be naïve transgenic CD8 cells. RNA preparations of mouse CD8 T cells from the B10D2 strain with three different conditions (Naïve, Deleted, and Anergic) were sent to the Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv4 microarrays.
2011-09-07 | E-GEOD-31987 | biostudies-arrayexpress
Project description:Activation of peripheral T lymphocytes in the absence of pathogen induced inflammation or costimulatory signals results in tolerance. Two different tolerance mechanisms have been described, deletion and anergy. We recently demonstrated that an important variable which is responsible for the decision between anergy and deletion for CD8 T cells is the strength of signaling through the T cell receptor(Redmond and Sherman, Immunity 22:275,2005). However, it is not know what the downstream signals are that result in death(deletion) vs. survival(anergy)of the activated cells. Marth and co-workers have previously shown that CD8 T cell apoptosis under conditions similar to those that occur during tolerance in vivo may involve a change in protein glycosylation (Van Dyken et.al., Mol.Cell.Bio.27:1096,2007).In order to assess the role of protein glycosylation in the decision between deletion vs.anergy in immune tolerance, we have prepared purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) or a weak antigenic signal (deletion conditions) with cognate antigen. We wish to assess transcriptional differences in genes involved in protein glycosylation in these 2 cell populations. The control population will be naive trangenic CD8 cells. Dr. Sherman's lab aims to assess the role of protein glycosylation in the decision between deletion vs. anergy in immune tolerance, they have prepared purified TCR transgenic CD8 T cells stimulated in vivo using a strong antigenic signal (anergy conditions) or a weak antigenic signal (deletion conditions) with cognate antigen. Dr. Sherman's lab wishes to assess transcriptional differences in genes involved in protein glycosylation in these 2 cell populations. Then control population will be naïve transgenic CD8 cells. RNA preparations of mouse CD8 T cells from the B10D2 strain with three different conditions (Naïve, Deleted, and Anergic) were sent to the Microarray Core (E). The RNA was amplified, labeled, and hybridized to both the GLYCOv3 and Mouse 430A_2.0 microarrays.
2011-06-14 | E-GEOD-29935 | biostudies-arrayexpress
Project description:T cell anergy is one of the mechanisms contributing to peripheral tolerance, particularly in the context of progressively growing tumors and in tolerogenic treatments promoting allograft acceptance. We recently reported that early growth response gene 2 (Egr2) is a critical transcription factor for the induction of anergy in vitro and in vivo, which was identified based on its ability to regulate the expression of inhibitory signaling molecules diacylglycerol kinase (DGK)-a and -z. We reasoned that other transcriptional targets of Egr2 might encode additional factors important for T cell anergy and immune regulation. Thus, we conducted two sets of genome-wide screens: gene expression profiling of wild type versus Egr2-deleted T cells treated under anergizing conditions, and a ChIP-Seq analysis to identify genes that bind Egr2 in anergic cells. Merging of these data sets revealed 49 targets that are directly regulated by Egr2. Among these are inhibitory signaling molecules previously reported to contribute to T cell anergy, but unexpectedly, also cell surface molecules and secreted factors, including lymphocyte-activation gene 3 (Lag3), Class-I-MHC-restricted T cell associated molecule (Crtam), Semaphorin 7A (Sema7A), and chemokine CCL1. These observations suggest that anergic T cells might not simply be functionally inert, and may have additional functional properties oriented towards other cellular components of the immune system. T cell-specific Egr2 deletion was mediated by use of a Cre-expressing adenovirus and a CAR Tg x Egr2flox/flox mouse in which CAR is expressed exclusively in the T cell compartment from a Lck promoter/CD2 enhancer cassette. OVA-specific Th1 cell clones were generated from CAR Tg x Egr2flox/flox mice. CAR Tg x Egr2flox/flox Th1 T cells were infected with an empty (EV) or a Cre-expressing adenovirus. Upon confirmation of Egr2 deletion by immunoblot, the T cells were left untreated (Control) or anergized (Anergic) by immobilized anti-CD3 for 16 hours, and microarray was conducted after 1 day of rest in culture medium. The microarray analysis was performed three times using three sets of independently manipulated samples
2013-04-21 | E-GEOD-46242 | biostudies-arrayexpress
Project description:Establishment of a diverse B-cell receptor (BCR) repertoire by V(D)J recombination generates autoreactive B-cells that are eliminated by central tolerance in the bone marrow or down-regulate their BCR responsiveness to self-antigen during anergy induction in peripheral B-cells. The loss of anergy combined with hyperactivation of nucleic acid-sensing Toll-like receptors (TLRs) is thought to break B-cell tolerance leading to autoimmunity, although the transcriptional factors controlling these processes are still unknown. Here, we describe a critical role of Ikaros in promoting B-cell anergy and restraining TLR signaling by analyzing mice with specific deletion of Ikaros in mature B-cells, which resulted in systemic autoimmunity. While regulating many anergy-associated genes, Ikaros also activated the Zfp318 gene, implicated in down-tuning of the BCR responsiveness by shifting expression from IgM to IgD in anergic B-cells. TLR signaling was hyperactive in Ikaros-deficient B-cells, which failed to up-regulate feedback inhibitors of the MyD88-NF-?B signaling pathway. Systemic inflammation was lost upon expression of a non-self-reactive BCR or loss of MyD88 in Ikaros-deficient B-cells, which identified Ikaros as a guardian preventing autoimmunity by coordinately regulating anergy induction and TLR signaling.
2019-07-01 | GSE122313 | GEO
Project description:T cell anergy is one of the mechanisms contributing to peripheral tolerance, particularly in the context of progressively growing tumors and in tolerogenic treatments promoting allograft acceptance. We recently reported that early growth response gene 2 (Egr2) is a critical transcription factor for the induction of anergy in vitro and in vivo, which was identified based on its ability to regulate the expression of inhibitory signaling molecules diacylglycerol kinase (DGK)-a and -z. We reasoned that other transcriptional targets of Egr2 might encode additional factors important for T cell anergy and immune regulation. Thus, we conducted two sets of genome-wide screens: gene expression profiling of wild type versus Egr2-deleted T cells treated under anergizing conditions, and a ChIP-Seq analysis to identify genes that bind Egr2 in anergic cells. Merging of these data sets revealed 49 targets that are directly regulated by Egr2. Among these are inhibitory signaling molecules previously reported to contribute to T cell anergy, but unexpectedly, also cell surface molecules and secreted factors, including lymphocyte-activation gene 3 (Lag3), Class-I-MHC-restricted T cell associated molecule (Crtam), Semaphorin 7A (Sema7A), and chemokine CCL1. These observations suggest that anergic T cells might not simply be functionally inert, and may have additional functional properties oriented towards other cellular components of the immune system.
2013-04-21 | GSE46242 | GEO
Project description:Chronic HCV infection remains a global health concern due to its involvement in hepatic and extrahepatic diseases, including B cell non-Hodgkin’s lymphoma (BNHL). Clinical and epidemiological evidence support a causal role for HCV in BNHL development, although mechanistic insight is lacking. We performed RNA-sequencing on peripheral B cells from patients with HCV, BNHL, and HCV-associated BNHL to identify unique and shared transcriptional profiles associated with transformation. In patients with HCV-associated BNHL, we observed enrichment of an anergic gene signature and evidence of clonal expansion that was correlated with expression of epigenetic regulatory genes. Our data support a role for viral-mediated clonal expansion of anergic-like B cells in HCV-associated BNHL development, and suggest epigenetic dysregulation as a potential mechanism driving expansion. We propose epigenetic mechanisms may be involved in both HCV-associated lymphoma and regulation of B cell anergy, representing an attractive target for clinical interventions.
2022-10-22 | GSE215876 | GEO