Differential gene expression microarray analysis of Tregs and Teff cells expanded by TCR-dependent Vs independent methods
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE136582 | GEO | 2019/08/29
REPOSITORIES: GEO
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Project description:NOD mice were treated with PBS or OX40L and Jagged-1 proteins once a week for three weeks. A week after final treatment CD4+CD25- Teff cells and CD4+CD25hi Treg cells were sorted by FACS. Genomic DNA isolated from sorted cells and differences in DNA methylation pattern in these cell types between PBS and OX40L-Jagged-1 treated mice was analyzed by whole genome bi-sulfite sequencing.
2019-05-03 | GSE130617 | GEO
Project description:Analysis of Foxp3(+)epigenetics(-) T cells, Foxp3(-)epigenetics(+) T cells, and Foxp3(+)epigenetics(+) T cells. Results indicate regulatory T cell (Treg) ontogenesis requires two independent processes, expression of the transcription factor Foxp3 and establishment of Treg epigenetic programs induced by T cell receptor (TCR) stimulation. GFP+CD4+ and GFP-CD4+ splenocytes were sorted from DEREG and DEREG/Scurfy mice. These cells were activated with anti-CD3/CD28 antibodies, and then transduced with Foxp3-expressing retrovirus (pGCSamIN, NGFR marker). NGFR+ T cells sorted were subjected to microarray analysis (Affymetrix, mouse genome 430 2.0 array). To normalize the experimental conditions, Tregs (GFP+ T cells from DEREG) and Tconv (GFP- T cells from DEREG) were also activated and transduced with empty vector. Two replicates each.
2012-11-05 | E-GEOD-25252 | biostudies-arrayexpress
Project description:Human FOXP3+CD25+CD4+ regulatory T cells (Tregs) play a dominant role in the maintenance of immune homeostasis. Several genes are known to be important for murine Tregs, but for human Tregs the genes and underlying molecular networks controlling the suppressor function still largely remain unclear. We here performed a high-time-resolution dynamic analysis of the transcriptome during the very early phase of human Treg/ CD4+ T-effector cell activation. After constructing a correlation network specific for Tregs based on these dynamic data, we described a strategy to identify key genes by directly analyzing the constructed undirected correlation network. Six out of the top 10 ranked key hubs are known to be important for Treg function or involved in autoimmune diseases. Surprisingly, PLAU (the plasminogen activator urokinase) was among the 4 new key hubs. We here show that PLAU was critical for expression regulation of FOXP3, EOS and several other important Treg genes and the suppressor function of human Tregs. Moreover, we found Plau inhibits murine Treg development and but promotes the suppressive function. Further analysis unveils that PLAU is particularly important for memory Tregs and that PLAU mediates Treg suppressor function via STAT5 and ERK signaling pathways. Our study shows the potential for identifying novel key genes for complex dynamic biological processes using a network strategy based on high-time-resolution data, and highlights a critical role of PLAU in both human and murine Tregs. The construction of a dynamic correlation network of human Tregs provides a useful resource for the understanding of Treg function and human autoimmune diseases. The high-time-resolution time-series transcriptomic data during the very early phase of human Treg/Teff activation could be generally used for further mechanistic analysis of human Treg function. These data could be further used for biological network analysis, dynamic analysis, modeling by experimental researchers, bioinformaticians, computational biologists and systems biologists. We have measured the genome-wide expression of 38,500 genes (probes) by performing a high-time-resolution time-series analysis during the activation process of human regulatory T cells /CD4+ T-effector cells at 19 time points for the first 6h with an equal interval of 20 min. We have also overexpressed the GARP gene in human effector T cells and measured the genome-scale expression for the GARP-overexpressed cells and ThGFP cells at time point 0, 100 and 360min following activation. The stimulation source used in this work is a combination of anti-CD3/-CD28 Dynal beads with IL2 100U/ml.
2012-11-23 | E-GEOD-11292 | biostudies-arrayexpress
Project description:Disorders in regulatory T cell (Treg) function can result in the break-down of immunological self-tolerance. Thus, the identification of mechanisms controlling the activity of Treg is of great relevance. We used Treg from individuals carrying the C77G polymorphism as human models to study the role of CD45 molecules. The C77G mutation occurs with low frequency in healthy individuals and prevents splicing of CD45 exon A thereby leading to an aberrant expression pattern of CD45 isoforms in affected individuals. Resting and in vitro expanded/activated CD4+CD25highFoxp3+ Treg from carriers of C77G strongly expressed CD45RA isoforms whereas they were almost absent in cells from individuals with wild-type CD45. The expression patterns of CD45RB and CD45RC did not differ between C77G and control Treg but CD45R0 molecules were reduced in C77G cells. Resting C77G Treg showed diminished upregulation of activation markers and a reduced proliferative potential when stimulated with anti-CD3/TcR or anti-CD3/CD28 mAb suggesting decreased responsiveness to activating stimuli. This is in line with the observation that CD3/CD28-mediated activation of in vitro expanded Treg resulted in lower levels of TGF-? and IL-10 transcripts in C77G cells compared to controls. Furthermore, microarray studies revealed distinct gene expression patterns in Treg from C77G carriers and individuals with wild-type CD45. In addition, the capacity to suppress proliferation of conventional CD4+ T cells was reduced in C77G Treg. These data suggest that the changes in CD45 isoform combination resulting from C77G alter the responsiveness of Treg to CD3/TcR- and/or CD28-mediated signalling. Targeting of CD45 isoforms might be an approach to modulate Treg function. Total RNA was isolated from expanded and stimulated (2h with 1:5 CD3/CD28 beads) Treg of wild-type and C77G carriers using RNeasy Plus Micro Kit (Qiagen). Two pools of three wild-type individuals and three C77G individuals were prepared using equal amounts of RNA from each single donors. The two samples were each hybridised twice on an Agilent human Gene Expression Microarray 4x44K. cell type comparison
2012-12-31 | E-GEOD-31209 | biostudies-arrayexpress
Project description:Effector (Teff) and regulatory (Treg) CD4 T cells undergo metabolic reprogramming to support proliferation and immune function. While Phosphatidylinositide 3-kinase (PI3K)/Akt/mTORC1 signaling induces the glucose transporter Glut1 and aerobic glycolysis for Teff proliferation and inflammatory function, mechanisms that regulate Treg metabolism and function remain unclear. We show that TLR signals that promote Treg proliferation increase Glut1, PI3K/Akt/mTORC1 signaling, and glycolysis. However, TLR-induced mTORC1 signaling also impaired Treg suppressive capacity. Conversely, FoxP3 opposed PI3K/Akt/mTOR signaling to reduce glycolysis and anabolic metabolism while increasing oxidative and catabolic metabolism. Importantly, Glut1 expression was sufficient to increase Treg numbers but reduced suppressive capacity and FoxP3 expression. Thus, inflammatory signals and FoxP3 balance mTORC1 signaling and glucose metabolism to control Treg proliferation and suppressive function.
2016-08-30 | GSE84919 | GEO
Project description:Whole genome bisulfite genome analysis of OX40L-Jagged-1 expanded Treg and Teff cells
| PRJNA540788 | ENA
Project description:Disorders in regulatory T cell (Treg) function can result in the break-down of immunological self-tolerance. Thus, the identification of mechanisms controlling the activity of Treg is of great relevance. We used Treg from individuals carrying the C77G polymorphism as human models to study the role of CD45 molecules. The C77G mutation occurs with low frequency in healthy individuals and prevents splicing of CD45 exon A thereby leading to an aberrant expression pattern of CD45 isoforms in affected individuals. Resting and in vitro expanded/activated CD4+CD25highFoxp3+ Treg from carriers of C77G strongly expressed CD45RA isoforms whereas they were almost absent in cells from individuals with wild-type CD45. The expression patterns of CD45RB and CD45RC did not differ between C77G and control Treg but CD45R0 molecules were reduced in C77G cells. Resting C77G Treg showed diminished upregulation of activation markers and a reduced proliferative potential when stimulated with anti-CD3/TcR or anti-CD3/CD28 mAb suggesting decreased responsiveness to activating stimuli. This is in line with the observation that CD3/CD28-mediated activation of in vitro expanded Treg resulted in lower levels of TGF-? and IL-10 transcripts in C77G cells compared to controls. Furthermore, microarray studies revealed distinct gene expression patterns in Treg from C77G carriers and individuals with wild-type CD45. In addition, the capacity to suppress proliferation of conventional CD4+ T cells was reduced in C77G Treg. These data suggest that the changes in CD45 isoform combination resulting from C77G alter the responsiveness of Treg to CD3/TcR- and/or CD28-mediated signalling. Targeting of CD45 isoforms might be an approach to modulate Treg function.
2012-12-31 | GSE31209 | GEO
Project description:Investigation of the role of FOXP3 in CD4+ T effector cells. FOXP3 is transiently upregulated in T effector cells under activation. This temporary expression in Teff cells is insufficient to suppress expression of reported targets of FOXP3 repressor activity. The role of FOXP3 in T effector cells remains unclear. We used microarray analysis to detail the differentially expressed genes between FOXP3 wild type and 2T>C(mut) clones and identified classes of up-regulated or down-regulated genes based upon FOXP3 expression. We used T effector cells from one IPEX disease carrier mother that consist of a mixed population ofFOXP3 wild type and 2T>C(mut) clones. We activated them using anti-CD3, anti-CD28. We compareFOXP3 wild type and 2T>Cl clones at different stages: resting phase and activated phase at 72hrs.
2013-03-08 | E-GEOD-41087 | biostudies-arrayexpress
Project description:Naïve T cell activation involves at least two signals from an antigen presenting cell (APC), one through the T cell receptor via interaction with APC peptide-MHC complexes and a second through interaction of CD28 with APC B7 ligands. Following activation, T cells up-regulate a host of other membrane-bound costimulatory molecules which can either promote or inhibit further T cell maturation and proliferation. In some cases, it is necessary to attenuate T cell activation to prevent deleterious inflammation, and inhibitory members of the B7/Butyrophilin family of ligands have evolved to balance the strong stimuli the activating B7 ligands confer. Human genetic association and in vitro studies have implicated one such ligand, BTNL2, in controlling inflammation at mucosal surfaces. Here we show that recombinant mouse BTNL2 modifies B7/CD28 signaling to promote expression of Foxp3, a transcription factor necessary for murine Treg development and function. BTNL2 blocks Akt-mediated inactivation of Foxo1, a transcription factor necessary for Foxp3 expression. Immunophenotyping and gene profiling reveal that BTNL2-induced Treg share many properties with natural Treg, and in vivo they suppress enteritis induced by mouse effector T cells. These findings describe a mechanism by which environmental antigen-driven formation of Treg may be orchestrated by APC expressing specific modulators of costimulatory signals. CD4+CD25- cells isolated from spleen were stimulated on plates coated with anti-mouse CD3 and human IgG (negative control), anti-mouse CD3, rB7-2, and IgG (positive control), and anti-mouse CD3, rB7-2, and rBTNL2 (experimental). Culturing was performed in duplicate for each condition.
2013-01-31 | E-GEOD-42385 | biostudies-arrayexpress
Project description:Co-stimulatory molecules of the CD28 family on T lymphocytes integrate cues from innate immune system sensors, and modulate activation responses in conventional CD4+ T cells (Tconv) and their FoxP3+ regulatory counterparts (Treg). To better understand how costimulatory and co-inhibitory signals might be integrated, we profiled the changes in gene expression elicited in the hours and days after engagement of Treg and Tconv by anti-CD3 and either anti-CD28, -CTLA4, -ICOS, -PD1, -BTLA or -CD80.
2012-11-15 | GSE42276 | GEO