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Series GSE3997 Query DataSets for GSE3997
Status Public on Dec 30, 2006
Title Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: analysis by mRNA profiling
Organism Mus musculus
Experiment type Expression profiling by array
Summary Background. T cells in the thymus undergo opposing positive and negative selection processes so that the only T cells entering circulation are those bearing a T cell receptor (TCR) with a low affinity for self. The mechanism differentiating negative from positive selection is poorly understood, despite the fact that inherited defects in negative selection underlie organ-specific autoimmune disease in AIRE-deficient people and the non obese diabetic (NOD) mouse strain. Results. Here we use homogeneous populations of T cells undergoing either positive or negative selection in vivo together with genome-wide transcription profiling on microarrays to identify the gene expression differences underlying negative selection to an Aire-dependent organ-specific antigen, including the upregulation of a genomic cluster in the cytogenetic band 2F. Analysis of defective negative selection in the autoimmune-prone NOD strain demonstrates a global impairment in the induction of the negative selection response gene set, but little difference in positive selection response genes. Combining expression differences with genetic linkage data we identify differentially expressed candidate genes including Bim, Bnip3, Smox, Pdrg1, Id1, Pdcd1, Ly6c, Pdia3, Trim30 and Trim12. Conclusions. The data provide a molecular map of the negative selection response in vivo, and by analysis of deviations from this pathway in the autoimmune susceptible NOD strain, suggest that susceptibility arises from small expression differences in genes acting at multiple points in the pathway between the TCR and cell death.
Keywords: Murine
 
Overall design Analysis of two thymic populations - early single positive thymocytes (CD4+CD8lowCD69+TCRhi) and early double positive thymocytes (CD4+CD8+CD69-TCRlow). Samples purified from the 3A9 TCR transgenic (TCR) to characterise positive selection and the 3A9 TCR x insHEL double transgenic (Dbl) to characterise negative selection towards an Aire-dependent organ-specific antigen. Both the non autoimmune C57BL10.H2k (B10) and autoimmune Non obese diabetic (NOD) strains were analysed in this method. Three biological replicates were used for each of these eight different groups.
 
Contributor(s) Liston A, Hardy K, Pittelkow Y, Wilson SR, Markaroff LE, Fahrer AM, Goodnow CC
Citation(s) 17239257
Submission date Jan 09, 2006
Last update date Jan 08, 2019
Contact name Kristine Hardy
E-mail kristine.hardy@canberra.edu.au
Organization name University of Canberra
Lab Cytokine Gene Expression
Street address University of Canberra
City Bruce
State/province ACT
ZIP/Postal code 0200
Country Australia
 
Platforms (1)
GPL339 [MOE430A] Affymetrix Mouse Expression 430A Array
Samples (24)
GSM91280 B10 TCR double positive rep 1
GSM91281 B10 TCR double positive rep 2
GSM91282 B10 TCR double positive rep 3
Relations
BioProject PRJNA94273

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE3997_RAW.tar 82.5 Mb (http)(custom) TAR (of CEL, EXP)
Raw data provided as supplementary file

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