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| Status |
Public on Aug 11, 2006 |
| Title |
Using GINI2 to identify novel mutations in candidate tumor suppressor genes in colon cancer cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Inhibition of the nonsense mediated decay (NMD) mechanism in cells results in stabilization of transcripts carrying premature translation termination codons. A strategy referred to as gene indentification by NMD inhibition (GINI) has been proposed to identify genes carrying nonsense mutations (Noensie & Dietz, 2001). Genes containing frameshift mutations in colon cancer cell line have been identifying mutatnt genes using GINI, we have now further improved the strategy. In this approach, inhibition of NMD with emetine is complemented with inhibiting NMD by blocking the phosphorylation of the hUpf1 protein with caffeine. In addition, to enhance the GINI strategy, comparing mRNA level alterations produced by inhibiting transcription alone or inhbiiting transcription together with NMD following caffeine pretreatment were used for the efficient identification of false positives produced as a result of stress response to NMD inhibition. To demonstrate the improved efficiency of this approach, we analyzed colon cancer cell lines showing microstellite instability. Bi-allelic inactivating mutations were found in the FXR1, SEC1L1, NCOR1, BAT3, PHD14, ZNF294, C190ORF5 genes as well as genes coding for proteins with yet unknown functions.
Keywords: microarray, gene expression, Affymetrix, drug treatment, emetine, caffeine, actinomycin D, novel tumor suppressor gene candidates
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| Overall design |
Using GINI2 as a method of identifying novel biallelic truncating mutations in MSI+ colon cancer cells, various treatment conditions were applied to cultured colon cancer cell lines LS180 (MSI+) and SW480 (MSI-) and gene expression profiling was measured using Affymetrix GeneChip U133 Plus 2 arrays.
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| Contributor(s) |
Ivanov I, Lo KC, Hawthorn L, Cowell JK, Ionov Y |
| Citation(s) |
17086209 |
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| Submission date |
Aug 09, 2006 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Ken Lo |
| E-mail(s) |
[email protected]
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| Phone |
716-845-3941
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| Fax |
716-845-3940
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| Organization name |
Roswell Park Cancer Institute
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| Department |
Cancer Genetics
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| Lab |
John Cowell
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| Street address |
Elm and Carlton Streets
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| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA96123 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE5486_RAW.tar |
63.9 Mb |
(http)(custom) |
TAR (of CEL) |
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