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| Status |
Public on Nov 03, 2006 |
| Title |
5`aza-dC demethylation of three short term cultured glioblastomas |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Methylation profiling by array
|
| Summary |
Glioblastoma, the most aggressive and least treatable form of malignant glioma, is the most common human brain tumor. Although many regions of allelic loss occur in glioblastomas, relatively few tumor suppressor genes have been found mutated at such loci. To address the possibility that epigenetic alterations are an alternative means of glioblastoma gene inactivation, we coupled pharmacological manipulation of methylation with gene profiling to identify potential methylation-regulated, tumor-related genes. Triplicates of three short-term cultured glioblastomas were exposed to 5μM 5-aza-dC for 96 hours followed by cRNA hybridization to an oligonucleotide microarray (Affymetrix U133A). We based candidate gene selection on bioinformatics, RT-PCR, bisulfite sequencing, methylation-specific PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Two genes identified in this manner, RUNX3 and Testin (TES), were subsequently shown to harbor frequent tumor-specific epigenetic alterations in primary glioblastomas. This overall approach therefore provides a powerful means to identify candidate tumor suppressor genes for subsequent evaluation and may lead to the identification of genes whose epigenetic dysregulation is integral to glioblastoma tumorigenesis.
Keywords: expression profile following global demethylation
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| Overall design |
Duplicates of three short term cultured glioblastoma cell lines (internal IDs: GLI56;GLI60;GLI72) were either exposed to 5umol 5`aza-dC for 96h or left untreated. Total RNA was extracted of treated and untreated cells after 96h and hybridized to U133A chip. Gene expression profiles of treated and untreated cells were compared. Upregulation of gene expression in the treated (demethylated) samples was interpreted as potentially being regulated by methylation - pointing towards hypermethylation in the related cell line. Identification of novel tumor suppressor genes, regulated by methylation, was the overall goal.
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| Contributor(s) |
Mueller WC, Louis DN |
| Citation(s) |
16909125 |
| |
| Submission date |
Apr 25, 2006 |
| Last update date |
Aug 10, 2018 |
| Contact name |
Wolf C Mueller |
| E-mail(s) |
[email protected], [email protected]
|
| Phone |
+49-(0)30-450536004
|
| Fax |
+49-(0)30-450536940
|
| Organization name |
Charité Universitätsmedizin Berlin
|
| Department |
Neuropathology
|
| Street address |
Amrumer Str. 1
|
| City |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
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| Platforms (1) |
| GPL96 |
[HG-U133A] Affymetrix Human Genome U133A Array |
|
| Samples (12)
|
| GSM106370 |
short term cultured GBM_ID GLI56T1_5`aza-dc_96h_rep1 |
| GSM106377 |
short term cultured GBM_ID GLI56T2_5`aza-dc_96h_rep2 |
| GSM106398 |
short term cultured GBM_ID GLI60T1_5`aza-dc_96h_rep1 |
| GSM106401 |
short term cultured GBM_ID GLI60T2_5`aza-dc_96h_rep2 |
| GSM106404 |
short term cultured GBM_ID GLI72T1_5`aza-dc_96h_rep1 |
| GSM106406 |
short term cultured GBM_ID GLI72T2_5`aza-dc_96h_rep2 |
| GSM106497 |
short term cultured GBM_ID GLI56U1_untreated control_rep1 |
| GSM106498 |
short term cultured GBM_ID GLI56U2_untreated control_rep2 |
| GSM106500 |
short term cultured GBM_ID GLI60U1_untreated control_rep1 |
| GSM106501 |
short term cultured GBM_ID GLI60U2_untreated control_rep2 |
| GSM106502 |
short term cultured GBM_ID GLI72U1_untreated control_rep1 |
| GSM106503 |
short term cultured GBM_ID GLI72U2_untreated control_rep2 |
|
| Relations |
| BioProject |
PRJNA95605 |
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