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


CONCLUSIONS
Taken together, our study provides a general overview about the global transcriptional changes in the absence of Itk.
Blomberg
K Emelie M
KE
Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-14186 Huddinge, Sweden. emelie.blomberg@ki.se
Boucheron
Nicole
N
Lindvall
Jessica M
JM
Yu
Liang
L
Raberger
Julia
J
Berglöf
Anna
A
Ellmeier
Wilfried
W
Smith
Ci Edvard
CE
D000818:Animals; D018106:CD28 Antigens / Q000378:metabolism; D017252:CD3 Complex / Q000378:metabolism; D015496:CD4-Positive T-Lymphocytes / Q000378:metabolism*; D018414:CD8-Positive T-Lymphocytes / Q000378:metabolism*; D016572:Cyclosporine / Q000494:pharmacology; D020869:Gene Expression Profiling; D008213:Lymphocyte Activation; D051379:Mice; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D050778:NFATC Transcription Factors / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D011505:Protein-Tyrosine Kinases / Q000235:genetics*; D016176:T-Lymphocyte Subsets / Q000378:metabolism; D014158:Transcription, Genetic
D018106:CD28 Antigens; D017252:CD3 Complex; D050778:NFATC Transcription Factors; D016572:Cyclosporine; D011505:Protein-Tyrosine Kinases; C080813:emt protein-tyrosine kinase