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| Status |
Public on Aug 13, 2008 |
| Title |
Chromophobe and Oncocytoma Renal Cell Carcinomas: gene expression and SNP analysis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array
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| Summary |
Chromosomal abnormalities, such as structural and numerical abnormalities, are a common occurrence in cancer. The close association of homologous chromosomes during interphase, a phenomenon termed somatic chromosome pairing, has been observed in cancerous cells, but the functional consequences of somatic pairing have not been established. Gene expression profiling studies revealed that somatic pairing of chromosome 19 is a recurrent chromosomal abnormality in renal oncocytoma, a neoplasia of the adult kidney. Somatic pairing was associated with significant disruption of gene expression within the paired regions and resulted in the deregulation of the prolyl-hydroxylase EGLN2, a key protein that regulates the oxygen-dependent degradation of hypoxia-inducible factor (HIF). Overexpression of EGLN2 in renal oncocytoma increased ubiquitin-mediated destruction of HIF and concomitantly suppressed the expression of several HIF-target genes, including the pro-death BNIP3L gene. The transcriptional changes that are associated with somatic pairing of chromosome 19 mimic the transcriptional changes that occur following DNA amplification. Therefore, in addition to numerical and structural chromosomal abnormalities, alterations in chromosomal spatial dynamics should be considered as genomic events that are associated with tumorigenesis. The identification of EGLN2 as a significantly deregulated gene that maps within the paired chromosome region directly implicates defects in the oxygen-sensing network to the biology of renal oncocytoma.
Keywords: Gene expression profiling, SNP analysis, renal, tumor
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| Overall design |
Oncocytoma and Chromophobe RCC samples - expression profiling and SNP chip analysis
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| Contributor(s) |
Dykema K |
| Citation(s) |
18773095 |
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| Submission date |
Jun 25, 2007 |
| Last update date |
Dec 22, 2017 |
| Contact name |
Karl Dykema |
| Organization name |
Van Andel Institute
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| Lab |
Lab of Computational Biology
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| Street address |
333 Bostwick Ave. NE
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| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platforms (3) |
| GPL2004 |
[Mapping50K_Hind240] Affymetrix Human Mapping 50K Hind240 SNP Array |
| GPL2005 |
[Mapping50K_Xba240] Affymetrix Human Mapping 50K Xba240 SNP Array |
| GPL4866 |
Affymetrix GeneChip Human Genome U133 Plus 2.0 Array [MBNI v6 Entrez Gene ID CDF] |
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| Samples (34)
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| Relations |
| BioProject |
PRJNA101225 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE8271_RAW.tar |
303.5 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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