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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 14, 2014 |
| Title |
Gene expression in thymi of Tcf1 -/-, Tcf +/- or Tcf1 -/- mice with tumor. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
The HMG-box factor Tcf1 is required during T-cell development in the thymus and mediates the nuclear response to Wnt signals. Tcf1−/− mice have previously been characterized and show developmental blocks at the CD4−CD8− double negative (DN) to CD4+CD8+ double positive transition. Due to the blocks in T-cell development, Tcf1−/− mice normally have a very small thymus. Unexpectedly, a large proportion of Tcf1−/− mice spontaneously develop thymic lymphomas with 50% of mice developing a thymic lymphoma/leukemia at the age of 16 wk. These lymphomas are clonal, highly metastatic, and paradoxically show high Wnt signaling when crossed with Wnt reporter mice and have high expression of Wnt target genes Lef1 and Axin2. In wild-type thymocytes, Tcf1 is higher expressed than Lef1, with a predominance of Wnt inhibitory isoforms. Loss of Tcf1 as repressor of Lef1 leads to high Wnt activity and is the initiating event in lymphoma development, which is exacerbated by activating Notch1 mutations. Thus, Notch1 and loss of Tcf1 functionally act as collaborating oncogenic events. Tcf1 deficiency predisposes to the development of thymic lymphomas by ectopic up-regulation of Lef1 due to lack of Tcf1 repressive isoforms and frequently by cooperating activating mutations in Notch1. Tcf1 therefore functions as a T-cell–specific tumor suppressor gene, besides its established role as a Wnt responsive transcription factor. Thus, Tcf1 acts as a molecular switch between proliferative and repressive signals during T-lymphocyte development in the thymus.
Using the Tcf1−/− ΔVII/ΔVII knockout mouse (Verbeek et al. Nature 1995), thymocytes of 17 mice (5 control Tcf+/-, 4 Tcf-/- and 8 Tcf-/- with thymic lymphoma) were homogenized for RNA isolation using Qiagen RNeasy minicolumns. The quantity and quality of total RNA was determined using spectrophotometry (Nanodrop) and an Agilent Bioanalyzer. One µg of RNA was used to generate cRNA using Affymetrix One cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA, USA), after which the samples were biotinylated using an Affymetrix IVT labeling kit (Affymetrix). The samples were hybridized overnight at 42°C to GeneChip mouse genome 430 2.0 Arrays (Affymetrix). Washing and staining steps were performed on a Fluidics station 450, and the Genechips were scanned using a GeneChip scanner 3000 (Affymetrix) at the Department of Immunology, Erasmus Medical Center. Raw data were normalized and summarized using Robust Multichip Average (RMA) method.
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| Overall design |
The experiment consists of 5 control Tcf+/- thymi, 4 Tcf-/- thymi and 8 Tcf-/- thymus samples with thymic lymphoma.
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| Contributor(s) |
Tiemessen MM, Baert MR, Schonewille T, Brugman MH, Famili F, Salvatori DC, Meijerink JP, Ozbek U, Clevers H, van Dongen JJ, Staal FJ |
| Citation(s) |
23185135 |
| Submission date |
Feb 13, 2014 |
| Last update date |
Feb 11, 2019 |
| Contact name |
Martijn H Brugman |
| E-mail(s) |
m.h.brugman@lumc.nl
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| Phone |
+31-71-5261300
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| Organization name |
LUMC
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| Department |
IHB
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| Street address |
Albinusdreef 2
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| City |
Leiden |
| ZIP/Postal code |
2333 ZA |
| Country |
Netherlands |
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| Platforms (1) |
| GPL1261 |
[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA238191 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE54976_RAW.tar |
63.2 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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