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| Status |
Public on Jan 01, 2018 |
| Title |
Gene expression profiling in response to radiation treatment in breast cancer [patient samples] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Introduction: Breast radiotherapy is currently “one size fits all” regardless of breast cancer subtype (eg. luminal, basal). However, recent clinical data suggests that radiation response may vary significantly among subtypes. Therefore, current practice leads to over- or under-treatment of women whose tumors are more or less radiation responsive. We hypothesized that this clinical variability may be due, in part, to differences in cellular radiation response. Methods: We exposed 16 biologically-diverse breast tumor cell lines to 0 or 5GY radiation. Microarray analysis was performed on RNA harvested from those cell lines. Samples were run in triplicate. Following quality assessment, differential gene expression analysis was performed using a two-way multiplicative linear mixed-effects model. A candidate radiation response biomarkers with biologically plausible role in radiation response, were identified and confirmed at the RNA and protein level with qPCR and Western blotting assays. Induction in human breast tumors was confirmed in 32 patients with paired pre- and post-radiation tumor samples using IHC and microarray analysis. Quantification of protein was performed in a blinded manner and included positive and negative controls.
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| Overall design |
The objective of our study was to identify genomic determinants of radiation sensitivity using clinical samples as well as breast tumor cell lines. In order to identify differences in the radiation response gene expression profiles of specific breast cancer subtypes, we exposed 16 biologically-diverse breast tumor cell lines to 0 or 5GY radiation. Microarray analysis was performed on RNA harvested from those cell lines. Samples were run in triplicate. Following quality assessment, differential gene expression analysis was performed using a two-way multiplicative linear mixed-effects model. Candidate radiation response biomarker with a biologically plausible role in radiation response, were identified and confirmed at the RNA and protein level with qPCR and Western blotting assays. Induction of the genes of interest were further evaluated and confirmed in human breast tumors in 32 breast cancer patients with paired pre- and post-radiation tumor samples using IHC and microarray analysis assays.
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| Contributor(s) |
Horton JK, Dewhirst M, Geradts J, Fels DR, Zhou Y, Lee C, Siamakpour-Reihani S, Chen W, Ashcraft K, Groth J, Kung H, Chi A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jul 24, 2014 |
| Last update date |
Jan 02, 2018 |
| Contact name |
Wei Chen |
| Organization name |
Duke University
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| Department |
Center for Genomic and Computational Biology
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| Street address |
101 Science Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platforms (1) |
| GPL18990 |
[Xcel] Affymetrix Human Almac Xcel Array |
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| Samples (19)
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| This SubSeries is part of SuperSeries: |
| GSE59734 |
Gene expression profiling in response to radiation treatment in breast cancer |
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| Relations |
| BioProject |
PRJNA256081 |
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