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Open Access Research

Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling

Adrian Liston15, Kristine Hardy1, Yvonne Pittelkow2, Susan R Wilson2, Lydia E Makaroff3, Aude M Fahrer3 and Christopher C Goodnow14*

Author Affiliations

1 John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia

2 Mathematical Sciences Institute, The Australian National University, Canberra, ACT 2601, Australia

3 Biochemistry and Molecular Biology, The Australian National University, Canberra, ACT 2601, Australia

4 The Australian Phenomics Facility, The Australian National University, Canberra, ACT 2601, Australia

5 Department of Immunology, University of Washington, Seattle, WA 98195, USA

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Genome Biology 2007, 8:R12  doi:10.1186/gb-2007-8-1-r12

Published: 21 January 2007

Abstract

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.

Conclusion

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.