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| Status |
Public on Mar 17, 2011 |
| Title |
Gene Expression Profiling Reveals a Massive, Aneuploidy-Dependent Transcriptional Deregulation and Distinct Differences between Lymph Node–Negative and Lymph Node–Positive Colon Carcinomas |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
To characterize patterns of global transcriptional deregulation in primary colon carcinomas, we did gene expression profiling of 73 tumors [Unio Internationale Contra Cancrum stage II (n = 33) and stage III (n = 40)] using oligonucleotide microarrays. For 30 of the tumors, expression profiles were compared with those from matched normal mucosa samples. We identified a set of 1,950 genes with highly significant deregulation between tumors and mucosa samples (P < 1e-7). A significant proportion of these genes mapped to chromosome 20 (P = 0.01). Seventeen genes had a >5-fold average expression difference between normal colon mucosa and carcinomas, including up-regulation of MYC and of HMGA1, a putative oncogene. Furthermore, we identified 68 genes that were significantly differentially expressed between lymph node-negative and lymph node-positive tumors (P < 0.001), the functional annotation of which revealed a preponderance of genes that play a role in cellular immune response and surveillance. The microarray-derived gene expression levels of 20 deregulated genes were validated using quantitative real-time reverse transcription-PCR in >40 tumor and normal mucosa samples with good concor- dance between the techniques. Finally, we established a relationship between specific genomic imbalances, which were mapped for 32 of the analyzed colon tumors by comparative genomic hybridization, and alterations of global transcriptional activity. Previously, we had conducted a similar analysis of primary rectal carcinomas. The systematic comparison of colon and rectal carcinomas revealed a signif- icant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/B-catenin signaling cascade, suggesting similar pathogenic pathways. [Cancer Res 2007;67(1):41-56]
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| Overall design |
Samples of tumor and/or mucosa from a total of 65 colon cancer patients, i.e. 103 arrays
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| Contributor(s) |
Grade M, Ghadimi M, Ried T |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Mar 19, 2010 |
| Last update date |
Jan 17, 2013 |
| Contact name |
Marian Grade |
| E-mail(s) |
marian.grade@gmail.com
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| Organization name |
University Medical Center Goettingen, Georg-August-University
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| Department |
Surgery
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| Street address |
Robert-Koch-Str. 40
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| City |
Goettingen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
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| Platforms (1) |
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| Samples (103)
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| Relations |
| BioProject |
PRJNA124589 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE20970_RAW.tar |
223.6 Mb |
(http)(custom) |
TAR (of GPR) |
| Processed data included within Sample table |
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