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| Status |
Public on Dec 05, 2007 |
| Title |
Identification of genes modulated by acid and bile in a Barrett's oesophagus cell line |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
The major aetiological risk factor for Barrett's oesophagus and oesophageal adenocarcinoma is gastroesophageal reflux. This study's aim was to identify genes involved in the celular response to reflux in vitro. The Barrett’s oesophagus cell line, CP-A hTERT, was exposed to media with acid, deoxycholic acid or a primary bile salt mixture. RNA expression was compared with controls on Affymetrix U133 Plus 2.0 arrays. In CP-A hTERT, the greatest number of changes in gene expression was observed after treatment with deoxycholic acid, pH 4.5; 152 genes were up-regulated at 2 hours (91 at 6 hours) and 10 down-regulated at 2 hours (34 at 6 hours). 12 genes were identified and were subsequently assessed in patients with non-erosive reflux disease, oesophagitis, Barrett's oesophagus and oesophageal adenocarcinoma
Background and Aims: The major etiological risk factor for Barrett’s esophagus and esophageal adenocarcinoma is gastro-esophageal reflux. This study’s aim was to identify genes involved in the cellular response to components of reflux both in vitro and in patients with reflux-related disease.
Methods: The Barrett’s cell line, CP-A hTERT, was exposed to media with acid, deoxycholic acid or a primary bile salt mixture. RNA expression was compared with controls on Affymetrix U133 Plus 2.0 arrays. 12 genes of interest were analysed by Real Time PCR both in cell line and biopsies from 110 patients with non-erosive reflux disease, esophagitis, Barrett’s esophagus and esophageal adenocarcinoma.
Results: In CP-A hTERT, the greatest number of changes in gene expression was observed after treatment with deoxycholic acid, pH 4.5. Of 12 genes analysed in biopsies, 10 were significantly different between the 4 groups with the largest change for anterior gradient homolog 2, which may modulate p53 function. This had highest expression in biopsies from Barrett’s esophagus (median gene fold change for Barrett’s esophagus versus non-erosive reflux disease, 411.2 (95% CI 290.5-682.7; p<0.01); esophageal adenocarcinoma versus non-erosive reflux disease 68.1 (20.5-161.4; p<0.01)). In addition 4 genes associated with development/differentiation were upregulated in Barrett’s biopsies compared to those from non-erosive reflux disease (SEL1L, MFNG, CRIP1 and EFNA1).
Conclusions: Novel genes have been identified, whose expression is altered after acid and bile exposure in vitro and in biopsies from patients with reflux related diseases. These genes may have utility as biomarkers of response to reflux and should be assessed in prospective studies.
Keywords: Acid (pH 4.5) and bile (mixture of primary bile salts or the secondary bile salt deoxycholic acid, both at pH 4.5) challenge to a Barrett's oesophagus cell line. RNA extraction at 2 and 6 hours. Comparison of treatment RNA to control (non-treatment) RNA,
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| Overall design |
The Barrett's oesophagus cell line CP-A hTERT was treated with a 15 minute exposure of acid (pH 4.5), a mixture of primary bile acids (pH 4.5) or deoxycholic acid (pH 4.5). RNA extraction occurred in treatment and non-treated cells at 2 hours and 6 hours. The treatments were performed in duplicate on 2 different days. RNA was compared in each treatment to each control at the relevant time points, in a 2 x 2 manner by using Affymetrex U133 Plus 2.0 arrays. Results of 12 genes were confirmed by Real Time PCR and were subsequently assessed in patients with non-erosive reflux disease, oesophagitis, Barrett's oesophagus and oesophageal adenocarcinoma.
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| Contributor(s) |
Donnellan C, Hardie L |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 04, 2007 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Clare Donnellan |
| E-mail(s) |
clare.donnellan@usa.net
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| Phone |
0044 7973 472082
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| Organization name |
Leeds University
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| Department |
Molecular Epidemiology
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| Street address |
LIGHT Laboratories
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| City |
Leeds University, Leeds |
| State/province |
West Yorkshire |
| ZIP/Postal code |
LS2 9JT |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (13)
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| GSM246400 |
CP-A hTERT-deoxycholic acid pH 4.5_2 hours_ rep 1 |
| GSM246401 |
CP-A hTERT-deoxycholic acid pH 4.5_6 hours_ rep 1 |
| GSM246402 |
CP-A hTERT-deoxycholic acid pH 4.5_2 hours_ rep 2 |
| GSM246403 |
CP-A hTERT-deoxycholic acid pH 4.5_6 hours_ rep 2 |
| GSM246404 |
CP-A hTERT-primary bile mixture pH 4.5_2 hours_ rep 1 |
| GSM246405 |
CP-A hTERT-primary bile mixture pH 4.5_6 hours_ rep 1 |
| GSM246406 |
CP-A hTERT-primary bile mixture pH 4.5_2 hours_ rep 2 |
| GSM246407 |
CP-A hTERT-acid pH 4.5_2 hours_ rep 1 |
| GSM246408 |
CP-A hTERT-acid pH 4.5_6 hours_ rep 1 |
| GSM246409 |
CP-A hTERT control_rep 1 |
| GSM246410 |
CP-A hTERT-acid pH 4.5_2 hours_ rep 2 |
| GSM246411 |
CP-A hTERT-acid pH 4.5_6 hours_ rep 2 |
| GSM246412 |
CP-A hTERT control_rep 2 |
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| Relations |
| BioProject |
PRJNA103703 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9768_RAW.tar |
223.0 Mb |
(http)(custom) |
TAR (of CEL, CHP, EXP) |
| Processed data included within Sample table |
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