DNA demethylation in CD4-CD8-TCR-ab compared to CD8+ T cells in B6.MRL-FASlpr mice
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ABSTRACT:
PROVIDER: PRJNA649258 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12340405_1.fastq.gz | Fastqsanger.gz | |||
| SRR12340405_2.fastq.gz | Fastqsanger.gz | |||
| SRR12340406_1.fastq.gz | Fastqsanger.gz | |||
| SRR12340406_2.fastq.gz | Fastqsanger.gz | |||
| SRR12340407_1.fastq.gz | Fastqsanger.gz |
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Project description:To understand the DNA methylation differences associated with CD4-CD8-TCR-ab (DN) T cells that accumulate in the B6.MRL-FASlpr mouse model we performed reduced representation bisulfite sequencing on these cells compared to CD8+ T cells derived from the lymph nodes. Overall we observed that 95% of the differential CpG were demethylated in DN T cells compared to CD8+ T cells.
2020-10-06 | GSE155293 | GEO
Project description:In this study, miRNA expression in splenic lymphocytes from three genetically disparate lupus-prone mouse models (MRL-lpr, B6-lpr and NZB/WF1) were profiled. 49 miRNAs were found to be differentially expressed in MRL-lpr mice compared to MRL mice; and 24 miRNAs were differentially expressed in B6-lpr mice compared to B6 mice. Among these dysregulated miRNAs, we noted that 15 miRNAs were common to both lpr strains. Interestingly, microarray analysis of NZB/W and NZW at 3 months of age, an age when overt lupus disease is not evident in NZB/W mice, revealed that only one miRNA, miR-148a was significantly upregulated in NZB/W mice. The aim of this porject is to determine the common miRNA expression changes in splenocytes from different strains of murine lupus models. The splenocytes were prepared from genetically lupus-prone female mice including MRL/MpJ-Faslpr/J (MRL-lpr), NZBWF1/J (NZB/W), B6.MRL-Faslpr/J (B6-lpr) and their control mice MRL/MpJ (MRL), NZW/LacJ (NZW) and C57BL/6J (B6) mice (The Jackson laboratory, ME). Total RNAs, containing miRNAs were isolated from whole splenocytes using mirVana miRNA isolation kits (Ambion) following manufactory’s instructions and sent to LC Sciences (http://www.lcsciences.com/) for the microarray assay. The mouse miRNA array chips (Chip ID miRMouse 12.0 version), which included 617 unique, mature, mouse miRNA, based on the Sanger miRBase Release 12.0, were used in the assay.
2011-12-17 | E-GEOD-22359 | biostudies-arrayexpress
Project description:MRL/Faslpr mice is a lupus prone strain that exhibits lupus disease features at 12-16 weeks of age, including high-titer circulating anti-DNA antibodies, splenomegaly, lymphadnopathy, skin lesions, and IgG deposits in the kidney. At 16-24 weeks of age, CD4+ B220- CD44+ T cells were sorted into three populations based on the expression of two cell surface molecules, CD62L and PSGL1. CD62Lhi PSGL1hi, CD62Llo PSGL1hi, and CD62Llo PSGL1lo CD4+ T cells were isolated directly ex vivo. There was no treatment given to the animals. Naive (CD62Lhi CD44lo) CD4+ B220- T cells were isolated from young 6-8 week old female mice for comparison. We used a microarray to identify unique features of the CD62Llo PSGL1lo population in comparison to naïve CD4+ T cells and other activated CD4+ T cells. Cells were isolated from the spleens of aged (16-24 weeks) female MRL/Faslpr mice directy ex vivo, and immediatley sorted into 3 populations; CD62Lhi PSGL1hi, CD62Llo PSGL1hi, and CD62Llo PSGL1lo. All 3 populations of cells were previously gated on TCRb+, CD4+, B220-, CD44+. Naive CD4 T cells were isolated directly ex vivo from the spleens of young (6-8 weeks) female MRL/Faslpr mice, and immediately sorted by gating on TCRb+, CD4+, B220-, CD62Lhi, CD44lo. Three indepedent sorts were performed. RNA was isolated using Qiagen's RNAeasy kit and total RNA was submitted to the W.M. Keck Foundation Biotechnology Resource Laboratory at Yale for amplification and hybridization to Affymetrix Mouse Genome 430 2.0 GeneChips.
2010-03-18 | E-GEOD-20735 | biostudies-arrayexpress
Project description:We performed genome-wide RNA sequencing to analyze gene expression in CD4 and CD8 LN T cells from B6 and FlipFlop mice. We first identified 335 genes in B6 mice that were differentially expressed in CD4 helper and CD8 cytotoxic T cells. Assessment of these genes in FlipFlop mice further revealed that FlipFlop CD4 T cells resembled B6 CD8 T cells, while FlipFlop CD8 T cells resembled B6 CD4 T cells.
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Project description:Global DNA hypomethylation in CD4+ cells in SLE patients was suggested to play a key role in the pathogenesis. To identify new methylation-sensitive genes, we integrated genome-wide DNA methylation and mRNA profiling in CD4+ cells of MRL/lpr (MRL) and C57BL6/J (B6) mice. We identified Ctse, in which 13 methyl-CpGs within 583 bp region of intron 1 were hypomethylated, and mRNA upregulated in MRL compared with B6 mice. One of methyl-CpGs, mCGCG was hypomethylated and mutated to CGGG in MRL mice. Kaiso is known to bind mCGCG and we hypothesized that it represses expression of Ctse. The binding of Kaiso to mCGCG site in B6 was reduced in MRL mice revealed by ChIP-PCR. EL4 cells treated with 5-azaC and/or TSA showed the suppression of the binding of Kaiso to mCGCG motif and the overexpression of Ctse was demonstrated by qPCR. Ctse gene silencing by siRNA in EL4 cells resulted in reduction of IL-10 secretion. Accordingly, IL10 and CTSE mRNAs up-regulated in CD4+ T cells both in MRL mice and the patients with SLE. The hypomethylation of mCGCG motif, reduced recruitment of Kaiso, and increased expression of Ctse and Il-10 in CD4+ cells may be involved in the pathogenesis of SLE.
2017-08-13 | GSE102421 | GEO
Project description:Thymocyte-thymocyte interaction can be very efficiently occur in CIITAtgpIV-/- mouse. We analyzed the gene expression profile between CD8+ T cells generated in CIITAtgpIV-/- mouse, and compared it to that of CD8+ T cells from B6 WT mouse. In this dataset, we include the expression data obtained from CD8 single positive thymocytes generated in CIITAtgpIV-/- mouse and B6 WT mouse. These data are used to obtain 279 genes that showed differentially increased expression in CIITAtgpIV-/- mouse. Total 1 sample from 2-4 CIITAtgpIV-/- mice and B6 WT mice were analyzed. We compared these using Affymetrix Expression console1.1, R affy-package(2.9.2), DAVID. Genes with an FDR≤10% and a fold-change ≥2 were selected.
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Project description:Thymocyte-thymocyte interaction can be very efficiently occur in CIITAtgpIV-/- mouse. We analyzed the gene expression profile between CD8+ T cells generated in CIITAtgpIV-/- mouse, and compared it to that of CD8+ T cells from B6 WT mouse. In this dataset, we include the expression data obtained from CD8 single positive thymocytes generated in CIITAtgpIV-/- mouse and B6 WT mouse. These data are used to obtain 279 genes that showed differentially increased expression in CIITAtgpIV-/- mouse.
2010-12-18 | GSE26090 | GEO
Project description:MRL/Faslpr mice is a lupus prone strain that exhibits lupus disease features at 12-16 weeks of age, including high-titer circulating anti-DNA antibodies, splenomegaly, lymphadnopathy, skin lesions, and IgG deposits in the kidney. At 16-24 weeks of age, CD4+ B220- CD44+ T cells were sorted into three populations based on the expression of two cell surface molecules, CD62L and PSGL1. CD62Lhi PSGL1hi, CD62Llo PSGL1hi, and CD62Llo PSGL1lo CD4+ T cells were isolated directly ex vivo. There was no treatment given to the animals. Naive (CD62Lhi CD44lo) CD4+ B220- T cells were isolated from young 6-8 week old female mice for comparison. We used a microarray to identify unique features of the CD62Llo PSGL1lo population in comparison to naïve CD4+ T cells and other activated CD4+ T cells.
2010-03-18 | GSE20735 | GEO
Project description:We used 6 male 4 week old C57BL/6 (B6) mice, three with wild-type (WT) genes, the other 3 with conditional knockout (KO) of both Ezh2 alleles. Knockout was achieved by breading B6 mice with floxed alleles of Ezh2 (Ezh2-fl/fl) to B6 mice expressing Cre recombinase under the control of a CD4 promotor to generate T-cell specific homozygous Ezh2 conditional knockout (CKO) mice. CD8 T-cells were purified using anti-mouse CD8 antibody (Ab)-conjugated magnetic beads from the spleen and lymph nodes of WT and CKO mice. The purity was consistently more that 93% as assessed by flow cytometry analysis. Freshly isolated mature T cells were named naïve CD8 T cells. These naïve CD8 T cells (two million cells / ml) were cultured in media containing 10% fetal bovine serum-IMDM in the presence of plate-coated anti-CD3 Ab (3 mg /ml) + anti-CD28 Ab (3 mg /ml). Three days later, these in vitro stimulated CD8 T cells were collected and named activated CD8 T cells. About 200 ng total RNA was extracted, and amplified using small-sample methods to make biotin-labeled cDNA targets that were hybridized to Affymetrix HT Mouse 430 PM arrays. This resulted in 4 groups of samples: naive or activated cells that were either KO or WT for Ezh2, each group having three biological replicates. The samples are in theory paired, since pairs of samples came from the same mouse, however we did not find many significant mouse to mouse effects, and do not think they need to be modeled. We provide a supplementary Excel workbook that holds the expression data, but it also holds probe-set annotation, and some statistical calculations (and the functions used to compute them), and may be convenient for some users. As of Dec 20, 2018, we were not expecting to use this data in a publication in the near future, and so released it to the public.
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Project description:CD8 T cell memory differentiation endows T cells with an ability to rapidly induce effector functions upon pathogen re-encounter. While it is well established that substantial epigenetic remodeling occurs during the effector stage of the immune response, the signaling events that imprint CD8 T cells with these stable epigenetic programs are not well-defined. To gain insight into the signaling determinants of effector-associated epigenetic programming among CD8 T cells, we explored the role of IL-12 in the imprinting of IFNg expression during human CD8 T cell priming. We observe that anti-CD3/CD28-mediated stimulation of human naïve CD8 T cells is not sufficient to induce substantial demethylation of the IFNg promotor. However, anti-CD3/CD28 stimulation in the presence of the inflammatory cytokine, IL-12, resulted in significant and stable demethylation of the IFNg locus that was commensurate with an increase in IFNg expression. We further show that IL-12-associated demethylation of the IFNg locus is coupled to cell division through TET2-dependent demethylation in an ex vivo human CAR T cell model system and an in vivo immunologically competent murine system. Collectively, these data illustrate that IL-12 signaling promotes TET2-mediated effector epigenetic programming in CD8 T cells during the primary immune response and serve as proof of concept that signal 3 cytokines can be used to guide the induction of epigenetically regulated traits among T cells used for adoptive immunotherapies.
2021-08-31 | GSE182968 | GEO