Research article

Transcriptional signatures of Itk-deficient CD3⁺, CD4⁺ and CD8⁺ T-cells

K Emelie M Blomberg¹ , Nicole Boucheron² , Jessica M Lindvall³ , Liang Yu¹ , Julia Raberger² , Anna Berglöf¹ , Wilfried Ellmeier² and CI Edvard Smith¹

¹  Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden

²  Division of Immunobiology, Institute of Immunology, Center for Physiology, Pathophysiology and Immunology, Medical University of Vienna, A-1090 Vienna, Austria

³  Department for Informatics, Center for Bioinformatics, Post box 1080 Blindern NO-0316, Oslo, Norway

author email corresponding author email

BMC Genomics 2009, 10:233doi:10.1186/1471-2164-10-233

Published:	18 May 2009

Abstract

Background

The Tec-family kinase Itk plays an important role during T-cell activation and function, and controls also conventional versus innate-like T-cell development. We have characterized the transcriptome of Itk-deficient CD3⁺ T-cells, including CD4⁺ and CD8⁺ subsets, using Affymetrix microarrays.

Results

The largest difference between Itk^-/- and Wt CD3⁺ T-cells was found in unstimulated cells, e.g. for killer cell lectin-like receptors. Compared to anti-CD3-stimulation, anti-CD3/CD28 significantly decreased the number of transcripts suggesting that the CD28 co-stimulatory pathway is mainly independent of Itk. The signatures of CD4⁺ and CD8⁺ T-cell subsets identified a greater differential expression than in total CD3⁺ cells. Cyclosporin A (CsA)-treatment had a stronger effect on transcriptional regulation than Itk-deficiency, suggesting that only a fraction of TCR-mediated calcineurin/NFAT-activation is dependent on Itk. Bioinformatic analysis of NFAT-sites of the group of transcripts similarly regulated by Itk-deficiency and CsA-treatment, followed by chromatin-immunoprecipitation, revealed NFATc1-binding to the Bub1, IL7R, Ctla2a, Ctla2b, and Schlafen1 genes. Finally, to identify transcripts that are regulated by Tec-family kinases in general, we compared the expression profile of Itk-deficient T-cells with that of Btk-deficient B-cells and a common set of transcripts was found.

Conclusion

Taken together, our study provides a general overview about the global transcriptional changes in the absence of Itk.