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| Status |
Public on Jul 18, 2007 |
| Title |
Effects of Phenylethyl Isothiocyanate on N-Nitrosomethylbenzylamine-induced Cytotoxicity in Rat Esophagus |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by array
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| Summary |
To date, there is little information on early molecular events in the development of N-nitrosomethylbenzylamine (NMBA) induced esophageal tumorigenesis and of the effects of chemopreventive agents on these events. In this study, we identified genes in rat esophagus that were differentially expressed in response to short–term NMBA-treatment and modulated by co-treatment with phenethylisothiocyanate (PEITC). Rats were fed AIN-76A diet or AIN-76A diet containing PEITC for three weeks. During the third week of dietary treatment, they were administered three s.c. doses of NMBA (0.5 mg/kg b.w.). Rats were sacrificed 24 h after the last treatment, esophagi excised and processed for histological grading, microarray and real-time PCR analysis. Our histopathological data showed that treatment of rats with PEITC had protective effect on NMBA-induced preneoplastic lesions in the rat esophagus. We identified 2261 genes that were differentially expressed in the NMBA-treated vs. control esophagi and 1936 genes in the NMBA+PEITC- vs. NMBA-treated esophagi. The intersection of these two sets resulted in the identification of 1323 genes in NMBA-treated esophagus that were modulated by PEITC to near-normal levels of expression. The measured changes in the expression levels of 10 selected genes were validated using real-time PCR. Principle components analysis (PCA) was applied to all twelve microarrays in the study, which suggested that in terms of global gene expression, PEITC treatment had a genome-wide modulating effect on NMBA-induced gene expression. Samples obtained from animals treated with PEITC alone or co-treated with NMBA were more similar to controls than they were to NMBA treatment alone.
Keywords: Toxicogenomics,reference design
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| Overall design |
For each treatment we used a pooling strategy to enable the inclusion of samples from numerous animals. Three replicate microarrays were completed for each of the four treatments (control, PEITC, NMBA and NMBA+PEITC) for a total of twelve microarrays. Each microarray was hybridized using a pooled RNA sample, and each pool was created from equal amounts of total RNA from two or three independent RNA samples, representing individual animals. Each of these samples was obtained from a different animal, and no sample was included in more than one pool. In total, samples from nine animals per group were pooled for control, NMBA, PEITC and NMBA+PEITC microarrays. To facilitate comparisons of gene expression across all treatments, we utilized a reference design in which each microarray was co-hybridized with a common reference sample labeled with Cy3, and RNA from the treatment pool was labeled with Cy5. Stratagene’s Universal Rat reference RNA (Stratagene, La Jolla, CA) was used as the common reference in all microarrays.
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| Contributor(s) |
Reen RK, Dombkowski AA, Kresty LA, Cukovic D, Mele JM, Salagrama S, Nines R, Stoner GD |
| Citation(s) |
17616710 |
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| Submission date |
Jan 30, 2007 |
| Last update date |
Dec 06, 2012 |
| Contact name |
Gary D Stoner |
| E-mail(s) |
[email protected]
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| Phone |
614-293-3268
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| Fax |
614-293-4072
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| Organization name |
Department of Internal Medicine
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| Department |
The Ohio State University
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| Street address |
2001 Polaris Pkwy
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| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43240 |
| Country |
USA |
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| Platforms (1) |
| GPL2877 |
Agilent-013162 Whole Rat Genome Microarray G4131A (Feature Number version) |
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| Samples (12)
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| GSM159376 |
Group 1 Control Untreated, pool #EP1 vs. reference pool |
| GSM159377 |
Group 1 Control Untreated, pool #EP2 vs. reference pool |
| GSM159378 |
Group 1 Control Untreated pool # EP3 vs. reference pool |
| GSM159381 |
Group 3 NMBA treated, pool # EP6 vs. reference pool |
| GSM159383 |
Group 3 NMBA treated, pool #EP4 vs. reference pool |
| GSM159384 |
Group 3 NMBA treated, pool #EP5 vs. reference pool |
| GSM159385 |
Group 2 PEITC treated, pool #EP13 vs. reference pool |
| GSM159386 |
Group 2 PEITC treated, pool #EP 14 vs. reference pool |
| GSM159387 |
Group 2 PEITC treated, EP#15 vs. reference pool |
| GSM159388 |
Group 4 PEITC + NMBA treated, pool # EP 16 vs. reference pool |
| GSM159389 |
Group 4 PEITC + NMBA treated, pool # EP 17 vs. reference pool |
| GSM159390 |
Group 4 PEITC + NMBA treated, pool # EP 18 vs. reference pool |
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| Relations |
| BioProject |
PRJNA98131 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE6917_RAW.tar |
133.5 Mb |
(http)(custom) |
TAR (of TXT) |
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