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Series GSE44380 Query DataSets for GSE44380
Status Public on Feb 20, 2013
Title An inherently bi-functional subset of Foxp3+ Treg/T-helper cells is controlled by the transcription factor Eos
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary At sites of inflammation, certain Foxp3+ Tregs have the ability to alter their phenotype and become pro-inflammatory helper/effector cells, without losing Foxp3 expression. We show that this functional reprogramming is controlled by the transcription factor Eos (Ikzf4), an obligate co-repressor for Foxp3. The ability to reprogram was restricted to a specific subset of Foxp3+ Tregs, arising as early as the thymus and identifiable by short half-life of Eos at rest, characteristic cell-surface markers (CD38+CD69+CD103NEG) and a distinct pattern of DNA methylation. Mice made selectively deficient in this subset of Eos-labile Tregs became markedly impaired in their ability to cross-present new antigens and prime CD8+ T cells. Downregulation of Eos and consequent Treg reprogramming was prevented by the immunoregulatory enzyme IDO, via activation of the aryl hydrocarbon receptor (AhR). Thus, the Foxp3+ lineage contains a committed subset of Tregs that are constitutively primed for conversion into biologically important helper cells.
Overall design Cells from thymus or spleen were incubated for 1 hr with cycloheximide (CHX), then CD4+GFP+ Tregs were FACS-sorted into Eos-labile (CD38+CD103NEG) and Eos-stable (CD103+CD38NEG) subsets. Control CD4+GFPNEG (non Treg) cells were sorted from spleen. Genome-wide differential methylation analysis was performed using Reduced Representation Bisulfite Sequencing (RRBS). The genomic DNA from each sample was digested with the methylation-insensitive restriction enzyme MspI (restriction site, CCGG) and ligated to Illumina sequencing adaptors containing methylated cytosine residues. The ligated MspI fragments were size-selected, treated with sodium bisulfite, and amplified by PCR. The PCR products were purified and sequenced using Illumina HiSeq 2000 sequencer with a read length of 100bp.
Contributor(s) Shi H, Munn DH
Citation(s) 23684987
Submission date Feb 19, 2013
Last update date May 15, 2019
Contact name Huidong Shi
Phone 706-721-6000
Organization name Augusta University
Department Georgia Cancer Center
Lab 2125 K
Street address 1120 15th Street, CN2138
City Augusta
State/province GA
ZIP/Postal code 30912
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (5)
GSM1084104 Non-Tregs_RRBS
GSM1084105 EOS-labile-thymus_RRBS
GSM1084106 EOS-labile-spleen_RRBS
BioProject PRJNA189706
SRA SRP018797

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Supplementary file Size Download File type/resource
GSE44380_RAW.tar 69.7 Mb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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