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| Status |
Public on Sep 01, 2015 |
| Title |
The DNA methylation signature of human TCRαβ+CD4-CD8- double negative T cells reveals CG demethylation and a unique epigenetic architecture permissive to a broad stimulatory immune response |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
T cell receptor (TCR) αβ+ CD4- CD8- double negative T cells represent a rare T cell subset implicated in the pathogenesis of several autoimmune diseases. In this study, we investigated the DNA methylation signature of double negative T cells to gain insight into the epigenetic architecture and transcriptional capacity of peripheral blood primary human double negative T cells compared to autologous CD4+ and CD8+ T cells. We identified 2,984 CG sites across the genome with unique loss of DNA methylation in double negative T cells, and showed significant reduction in mRNA expression of DNA methyltransferases DNMT1, DNMT3A, and DNMT3B. DNA methylation was increased in CD8A/CD8B and CD4 consistent with epigenetic repression of both the CD8 and CD4 genetic loci in double negative T cells. Curiously, we show consistent increase in non-CG methylation in double negative T cells, a finding suggestive of pluripotency and previously only known to occur in embryonic stem cells and developing brain tissue. Network analyses of genes hypomethylated in double negative compared to CD4+ and CD8+ T cells indicate a strong relationship between double negative T cells and functions related to cell-cell interaction, cell adhesion, and cell activation pathways. Our data also suggest a robust pro-inflammatory epigenetic signature in double negative T cells, consistent with a transcriptional permissiveness to produce key inflammatory cytokines including IFNγ, IL-17F, IL-12B, IL-5, IL-18, TNFSF11 (RANKL), and TNFSF13B (BLYS or BAFF). These findings highlight an epigenetic basis for a role of double negative T cells in autoimmunity and extend the potential pathogenic transcriptional capacity of this unique T cell subset.
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| Overall design |
Peripheral blood mononuclear cells (PBMCs) were isolated from fresh blood samples of 7 unrelated healthy women (age range 25-60) (Supplementary Table 1) by Ficoll-gradient centrifugation (GE Healthcare Bio-Sciences AB, Uppsala, Sweden). Subsequently, T cells were negatively-selected using the Human Pan T Cell Isolation II kit (Miltenyi Biotec, Cambridge, MA). T cells were then analyzed and sorted into TCRαβ+ CD4+ T cells, TCRαβ+ CD8+ T cells, and TCRαβ+ DN T cell subsets by flow cytometry. DNA was isolated from CD4+, CD8+, and DN T cell subsets using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA), then bisulfite-converted using the EZ DNA Methylation kit (Zymo Research, Irvine, CA) for DNA methylation studies.
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| Contributor(s) |
Renauer PA, Coit P, Sawalha AH |
| Citation(s) |
25451162 |
| Submission date |
Sep 08, 2014 |
| Last update date |
Mar 22, 2019 |
| Contact name |
Jonathan Daniel Wren |
| E-mail(s) |
jdwren@gmail.com
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| Organization name |
Oklahoma Medical Research Foundation
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| Department |
Arthritis & Clinical Immunology
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| Lab |
MC103
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| Street address |
825 NE 13th St
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| City |
OKC |
| State/province |
OK |
| ZIP/Postal code |
73104-5005 |
| Country |
USA |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (21)
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| Relations |
| BioProject |
PRJNA260497 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE61195_DNCD4CD8SampleMethylation_NonNormalized.txt.gz |
299.0 Mb |
(ftp)(http) |
TXT |
| GSE61195_DNCD4CD8SampleMethylation_Norm_Controls_Bkgd.txt.gz |
355.6 Mb |
(ftp)(http) |
TXT |
| GSE61195_RAW.tar |
183.1 Mb |
(http)(custom) |
TAR |
| Processed data included within Sample table |
| Processed data are available on Series record |
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