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Status |
Public on May 20, 2009 |
Title |
Transcriptional signatures of Itk-deficiency using CD3+, CD4+ and CD8+ T-cells |
Organism |
Mus musculus |
Experiment type |
Expression profiling by array
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Summary |
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. 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 (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. Taken together, our study provides a general overview about the global transcriptional changes in the absence of Itk.
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Overall design |
CD3+ CD4+ and CD8+ T-cells from pooled suspensions of spleen and lymph nodes of Wt and Itk knockout mice on C57BL/6 background were isolated after negative depletion. Unstimulated as well as stimulated T-cells were studied. Stimulations were done with anti-CD3 (1 mg/ml) for 24 hrs. For the CD4+ T-cells we collected triplicates from the Itk knockout mice and duplicates from the Wt group. For the CD8+ T-cells, we got duplicates from Itk knockout , while we obtained a single sample from Wt owing to the low cell yield for resting Wt CD8+ T-cells. After CD3-stimulation we got a single sample from the CD8+ subset of both Wt and Itk knockout, while for the CD4+ subsets we collected duplicates.
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Contributor(s) |
Blomberg KE, Boucheron N, Lindvall JM, Yu L, Raberger J, Berglöf A, Ellmeier W, Smith CI |
Citation(s) |
19450280 |
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Submission date |
Aug 15, 2008 |
Last update date |
Feb 11, 2019 |
Contact name |
Emelie Blomberg |
E-mail(s) |
emelie.blomberg@ki.se
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Organization name |
Karolinska Institutet
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Department |
Department of Laboratory Medicine, Clinical Research Center
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Lab |
MCG
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Street address |
Novum level 5
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City |
Huddinge |
ZIP/Postal code |
SE-141 86 |
Country |
Sweden |
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Platforms (1) |
GPL1261 |
[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array |
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Samples (14)
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This SubSeries is part of SuperSeries: |
GSE12466 |
Transcriptional signatures of Itk-deficient CD3+, CD4+ and CD8+ T-cells |
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Relations |
BioProject |
PRJNA114227 |
Supplementary file |
Size |
Download |
File type/resource |
GSE12465_RAW.tar |
55.6 Mb |
(http)(custom) |
TAR (of CEL) |
Processed data included within Sample table |
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