Comment[ArrayExpressAccession]	E-GEOD-39529						
MAGE-TAB Version	1.1						
Public Release Date	2012-10-03						
Investigation Title	Foxp3 expression is required for the induction of therapeutic tissue tolerance						
Comment[Submitted Name]	Foxp3 expression is required for the induction of therapeutic tissue tolerance						
Experiment Description	CD4+Foxp3+ regulatory T cells (Treg) are essential for immune homeostasis and maintenance of self-tolerance. They are produced in the thymus and also generated de novo in the periphery in a TGFB dependent manner. Foxp3+ Treg are also required to achieve tolerance to transplanted tissues when induced by co-receptor or costimulation blockade. Using TCR transgenic mice to avoid issues of autoimmune pathology we show that Foxp3 expression is necessary and sufficient for tissue tolerance by coreceptor blockade. Moreover, the known need in tolerance induction for TGFB signalling to T cells, can wholly be explained by its role in induction of Foxp3, as such signalling proved dispensable for the suppressive process. We analysed the relative contribution of TGFB and Foxp3 on the transcriptome of TGFB induced Treg. TGFB elicited a large set of downregulated signature genes. The number of genes uniquely modulated due to the influence of Foxp3 alone was surprisingly limited. Retroviral conditional Foxp3 expression proved sufficient to confer transplant-suppressive potency on CD4+ T cells, and was lost once nuclear Foxp3 expression was extinguished. Thus despite the large genetic influence of TGFB exposure on iTreg the crucial Foxp3 influenced signature independent of TGFB is small. These data support a dual role for TGFB and Foxp3 in induced tolerance, where TGFB stimulates Foxp3 expression whose sustained expression is associated with acquisition of tolerance 21 samples were analyzed. 5 replicates of Marilyn.Foxp3hCD2 activated (HY)(Untreated) and TGFB-induced (HYT) cells sorted as CD4+hCD2+ and CD4+hCD2- and 3 replicates of Marilyn.Foxp3-/- activated and TGFβ-experienced (but Foxp3-) cells sorted as CD4+CD2. Pairwise comparisons were generated for the Marilyn Foxp3hCD2 UT versus TGFB induced populations and also for the Marilyn Foxp3-/- UT versus the TGFB experienced cells sorted as CD4+CD2						
Term Source Name	ArrayExpress	EFO					
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Howie	Madhiwalla	Zhang	Howie			
Person First Name	Duncan	S	M	D			
Person Email	duncan.howie@googlemail.com						
Person Affiliation	Genzyme Corporation/Sir William Dunn School of Pathology Oxford University						
Person Phone	01865 275518						
Person Address	Genzyme Corporation/Sir William Dunn School of Pathology Oxford University, 49 New York Avenue, Framingham, MA, USA						
Person Roles	submitter						
Protocol Name	P-GSE39529-1	P-GSE39529-6	P-GSE39529-5	P-GSE39529-2	P-GSE39529-3	P-GSE39529-4	P-GSE39529-7
Protocol Description	ID_REF =  VALUE = log2 RMA normalized data at gene level from Expression Console	The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.	Hybridization to arrays was carried out at 45oC for 16 hours in an Affymetrix Model 640 hybridization oven. Arrays were washed and stained on an Affymetrix FS450 Fluidics station	Cultured splenocytes were used to generate highly purified populations of Marilyn.Foxp3hCD2 activated (HY) and TGFB-induced (HYT) cells sorted as CD4+hCD2+ and CD4+hCD2- and Marilyn.Foxp3-/- activated and TGFB-experienced (but Foxp3-) cells sorted as CD4+CD2	Total RNA was isolated from the frozen cell pellets by Asuragen, Inc., according to the company’s standard operating procedure for automated isolation on a KingFisher magnetic particle separator	biotin-labeled sense strand cDNA was prepared from 30�g cRNA generated from 1�g total RNA per sample using a modified Affymetrix GeneChip� Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix, Inc.).Intermediate cRNA and resulting cDNA yields were quantified by spectrophotometry. Fragmentation and labeling of cDNA was performed using 5 �g for Exon Arrays.	Arrays were further pre-processed in the Affymetrix Expression Console software version 1.2 which was used to normalize CEL files using the quantile normalization method and the data was summarized data at gene level by using the Robust Multichip Analysis (RMA) algorithm . All further data analysis was performed in MP Genomics software version 5.1. Batch normalization was performed across two studies for the Foxp3CD2 cells.(biological replicates 4 and 5 repeated in second study) probe group file: MoEx-1_0-st-v1.r2.pgf meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	specified_biomaterial_action	nucleic_acid_extraction	labeling	feature_extraction
Experimental Factor Name	compound	cell type	genotype				
Experimental Factor Type	compound	cell type	genotype				
Publication Title	Foxp3 expression is required for the induction of therapeutic tissue tolerance.						
Publication Author List	Regateiro FS, Chen Y, Kendal AR, Hilbrands R, Adams E, Cobbold SP, Ma J, Andersen KG, Betz AG, Zhang M, Madhiwalla S, Roberts B, Waldmann H, Nolan KF, Howie D						
PubMed ID	22988034						
Publication DOI	10.4049/jimmunol.1200449						
Comment[SecondaryAccession]	GSE39529						
Comment[GEOReleaseDate]	2012-10-03						
Comment[ArrayExpressSubmissionDate]	2012-07-20						
Comment[GEOLastUpdateDate]	2012-10-03						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-39529.sdrf.txt