Reviewer's report 
 Gene Expression Changes Associated with Barretts Esophagus and Barretts-Associated Title: 
Adenocarcinoma Cell Lines After Acid or Bile Salt Exposure 
 1  9 February 2007 Version: Date: 
 Gareth Jenkins Reviewer: 
Reviewer's report: 
General 
The paper looks at the effect of acid and bile on proliferation in vitro and ex vivo through gene expression analysis and assessment of cell turnover. There are some interesting findings in this report and a wealth of gene expression data in the supplemental files. Whilst none of the gene expression findings suggested 
proliferation, this data may provide a valuable resource for researchers looking at the biology of Barrett's 
metaplasia and subsequent carcinogenesis. ------------------------------------------------------------------------------- Major Compulsory Revisions (that the author must respond to before a decision on publication can be 
reached) 
n/a ------------------------------------------------------------------------------- Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author 
can be trusted to correct) 
1. Methods page 5. More details needed in the methods section. For example, the list of 
conjugated/unconjugated bile acids only contains conjugated ones (glyco, tauro). It is not clear why 2 
different mixtures of conjugated bile acids were used. Were these types and concentrations used to reflect 
those seen in the refluxate in vivo? 2. Page 5, line 6. tauro-c-henodeoxycholic 
------------------------------------------------------------------------------- 
Discretionary Revisions (which the author can choose to ignore) 
1. Can the authors provide brief justifications for dosing schedules (concentrations of bile acids, time 
points)? One reason for a lack of expression changes here compared to other reports (e.g. via MapK), could 
involve differences in dosing schedules, time points etc compared to other reports. 
2. The acid exposures were carried out for up to 60 minutes, followed by 4 hours recovery, whereas the bile 
exposures were carried out for 60 minutes followed by 24 hours recovery, why the difference? 
3. The acid pulses here showed no effect on proliferation, which is in contrast to earlier work. This 
inconsistency is not discussed and perhaps should be. 
4. Why were 3 measures of proliferation shown for acid, but only 1 for bile? Is the MTS and cell count data 
available for bile treated cells? If so, does it show the same thing as the thymidine data? 
 Accept after minor essential revisions What next?: 
 An article whose findings are important to those with closely related research interests Level of interest: 
 Acceptable Quality of written English: 
 No, the manuscript does not need to be seen by a statistician. Statistical review: 
Declaration of competing interests: 
I declare that I have no competing interests 
Reviewer's report 
 Gene Expression Changes Associated with Barretts Esophagus and Barretts-Associated Title: 
Adenocarcinoma Cell Lines After Acid or Bile Salt Exposure 
 1  9 February 2007 Version: Date: 
 Gareth Jenkins Reviewer: 
Reviewer's report: 
General 
The paper looks at the effect of acid and bile on proliferation in vitro and ex vivo through gene expression analysis and assessment of cell turnover. There are some interesting findings in this report and a wealth of gene expression data in the supplemental files. Whilst none of the gene expression findings suggested 
proliferation, this data may provide a valuable resource for researchers looking at the biology of Barrett's 
metaplasia and subsequent carcinogenesis. ------------------------------------------------------------------------------- Major Compulsory Revisions (that the author must respond to before a decision on publication can be 
reached) 
n/a ------------------------------------------------------------------------------- Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author 
can be trusted to correct) 
1. Methods page 5. More details needed in the methods section. For example, the list of 
conjugated/unconjugated bile acids only contains conjugated ones (glyco, tauro). It is not clear why 2 
different mixtures of conjugated bile acids were used. Were these types and concentrations used to reflect 
those seen in the refluxate in vivo? 2. Page 5, line 6. tauro-c-henodeoxycholic 
------------------------------------------------------------------------------- 
Discretionary Revisions (which the author can choose to ignore) 
1. Can the authors provide brief justifications for dosing schedules (concentrations of bile acids, time 
points)? One reason for a lack of expression changes here compared to other reports (e.g. via MapK), could 
involve differences in dosing schedules, time points etc compared to other reports. 
2. The acid exposures were carried out for up to 60 minutes, followed by 4 hours recovery, whereas the bile 
exposures were carried out for 60 minutes followed by 24 hours recovery, why the difference? 
3. The acid pulses here showed no effect on proliferation, which is in contrast to earlier work. This 
inconsistency is not discussed and perhaps should be. 
4. Why were 3 measures of proliferation shown for acid, but only 1 for bile? Is the MTS and cell count data 
available for bile treated cells? If so, does it show the same thing as the thymidine data? 
 Accept after minor essential revisions What next?: 
 An article whose findings are important to those with closely related research interests Level of interest: 
 Acceptable Quality of written English: 
 No, the manuscript does not need to be seen by a statistician. Statistical review: 
Declaration of competing interests: 
I declare that I have no competing interests 
Please review this paper.
user
Reviewer's report 
 Gene Expression Changes Associated with Barretts Esophagus and Barretts-Associated Title: 
Adenocarcinoma Cell Lines After Acid or Bile Salt Exposure 
 1  9 February 2007 Version: Date: 
 Gareth Jenkins Reviewer: 
Reviewer's report: 
General 
The paper looks at the effect of acid and bile on proliferation in vitro and ex vivo through gene expression analysis and assessment of cell turnover. There are some interesting findings in this report and a wealth of gene expression data in the supplemental files. Whilst none of the gene expression findings suggested 
proliferation, this data may provide a valuable resource for researchers looking at the biology of Barrett's 
metaplasia and subsequent carcinogenesis. ------------------------------------------------------------------------------- Major Compulsory Revisions (that the author must respond to before a decision on publication can be 
reached) 
n/a ------------------------------------------------------------------------------- Minor Essential Revisions (such as missing labels on figures, or the wrong use of a term, which the author 
can be trusted to correct) 
1. Methods page 5. More details needed in the methods section. For example, the list of 
conjugated/unconjugated bile acids only contains conjugated ones (glyco, tauro). It is not clear why 2 
different mixtures of conjugated bile acids were used. Were these types and concentrations used to reflect 
those seen in the refluxate in vivo? 2. Page 5, line 6. tauro-c-henodeoxycholic 
------------------------------------------------------------------------------- 
Discretionary Revisions (which the author can choose to ignore) 
1. Can the authors provide brief justifications for dosing schedules (concentrations of bile acids, time 
points)? One reason for a lack of expression changes here compared to other reports (e.g. via MapK), could 
involve differences in dosing schedules, time points etc compared to other reports. 
2. The acid exposures were carried out for up to 60 minutes, followed by 4 hours recovery, whereas the bile 
exposures were carried out for 60 minutes followed by 24 hours recovery, why the difference? 
3. The acid pulses here showed no effect on proliferation, which is in contrast to earlier work. This 
inconsistency is not discussed and perhaps should be. 
4. Why were 3 measures of proliferation shown for acid, but only 1 for bile? Is the MTS and cell count data 
available for bile treated cells? If so, does it show the same thing as the thymidine data? 
 Accept after minor essential revisions What next?: 
 An article whose findings are important to those with closely related research interests Level of interest: 
 Acceptable Quality of written English: 
 No, the manuscript does not need to be seen by a statistician. Statistical review: 
Declaration of competing interests: 
I declare that I have no competing interests 
assistant