Reviewer's report
Title:The overmethylated genes in Helicobacter pylori-infected gastric mucosa
are demethylated in gastric cancers
Version: 1Date:25 July 2010
Reviewer: Rommel Burbano
Reviewer's report:
Major Compulsory Revisions:
-The authors should clarify the number of gastric cancer samples used on the
paper. In Methods section, they mention n=70 (48 males and 22 females).
However, in page 9 of the manuscript they cited “40 duplicated DNAs of the
same tissue, 48 pairs of 1-cm-adjacente tissues...”
-There is no information regarding the histological type of the gastric cancer
samples used in the manuscript. Is there any difference in the methylation status
according to the histopathological type?
-In pages 10 and 11, the authors classified on or no chromosome lost in
diffuse-type of gastric cancer as LOH-B (baseline level) and as LOH-L (low level)
in intestinal and mixed type. Why?
-The authors concluded that “concurrent methylation of multiple CpG-island
genes initiates and sustains the adaptive differentiation of newly fixed stem cell in
the gastric mucosa infected with H. pylori”. However, no comment about stem
cells is made in the methods or results sections. How the authors conclude such
information about stem cells? Is there any marker that was used to check if the
cells used in DNA extraction were newly fixed stem cells?
Minor Essentials Revisions:
-The authors checked for H. pylori status of non-cancerous tissue samples. How
is the H. pylori status of the gastric cancer tissue samples? Is there any
difference in the methylation status between gastric cancer tissue samples H.
pylori positive and H. pylori negative?
-The authors should explain the 5-level and 10-level classification (including the
intermediary status) of methylation status. In a previous paper (Hong et al.,
2009), they explain the 5-level. I believe that a better explanation should improve
the manuscript;
-The first paragraph of the Results section is about results of a previous paper.
Please, transfer it to the Discussion section. However, if they are results of the
current manuscript (although similar of the obtained previously), please cite the
methodology used in the Methods section;
-The last paragraph of page 13 should be transferred to Methods section;
-In page 13, 1st and 2nd lines, the authors can substitute 20 percent for 20%;
-In page 14, lines 14-17: The authors say that PGC and TFF1 are
stomach-specific genes weakly active when compared with the two master
stomach-specific genes. In which tissue? The authors also say that those genes
are densely methylated in bone marrow. And in the stomach?
-Is there any microsatellite in which the authors observed LOH more frequently?
And how about LOH and histologic type?
-In page 18, please change H202 for H2O2 (there is a zero instead of an “O”).
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Reviewer's report
Title:The overmethylated genes in Helicobacter pylori-infected gastric mucosa
are demethylated in gastric cancers
Version: 1Date:25 July 2010
Reviewer: Rommel Burbano
Reviewer's report:
Major Compulsory Revisions:
-The authors should clarify the number of gastric cancer samples used on the
paper. In Methods section, they mention n=70 (48 males and 22 females).
However, in page 9 of the manuscript they cited “40 duplicated DNAs of the
same tissue, 48 pairs of 1-cm-adjacente tissues...”
-There is no information regarding the histological type of the gastric cancer
samples used in the manuscript. Is there any difference in the methylation status
according to the histopathological type?
-In pages 10 and 11, the authors classified on or no chromosome lost in
diffuse-type of gastric cancer as LOH-B (baseline level) and as LOH-L (low level)
in intestinal and mixed type. Why?
-The authors concluded that “concurrent methylation of multiple CpG-island
genes initiates and sustains the adaptive differentiation of newly fixed stem cell in
the gastric mucosa infected with H. pylori”. However, no comment about stem
cells is made in the methods or results sections. How the authors conclude such
information about stem cells? Is there any marker that was used to check if the
cells used in DNA extraction were newly fixed stem cells?
Minor Essentials Revisions:
-The authors checked for H. pylori status of non-cancerous tissue samples. How
is the H. pylori status of the gastric cancer tissue samples? Is there any
difference in the methylation status between gastric cancer tissue samples H.
pylori positive and H. pylori negative?
-The authors should explain the 5-level and 10-level classification (including the
intermediary status) of methylation status. In a previous paper (Hong et al.,
2009), they explain the 5-level. I believe that a better explanation should improve
the manuscript;
-The first paragraph of the Results section is about results of a previous paper.
Please, transfer it to the Discussion section. However, if they are results of the
current manuscript (although similar of the obtained previously), please cite the
methodology used in the Methods section;
-The last paragraph of page 13 should be transferred to Methods section;
-In page 13, 1st and 2nd lines, the authors can substitute 20 percent for 20%;
-In page 14, lines 14-17: The authors say that PGC and TFF1 are
stomach-specific genes weakly active when compared with the two master
stomach-specific genes. In which tissue? The authors also say that those genes
are densely methylated in bone marrow. And in the stomach?
-Is there any microsatellite in which the authors observed LOH more frequently?
And how about LOH and histologic type?
-In page 18, please change H202 for H2O2 (there is a zero instead of an “O”).
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
Please review this paper.
user
Reviewer's report
Title:The overmethylated genes in Helicobacter pylori-infected gastric mucosa
are demethylated in gastric cancers
Version: 1Date:25 July 2010
Reviewer: Rommel Burbano
Reviewer's report:
Major Compulsory Revisions:
-The authors should clarify the number of gastric cancer samples used on the
paper. In Methods section, they mention n=70 (48 males and 22 females).
However, in page 9 of the manuscript they cited “40 duplicated DNAs of the
same tissue, 48 pairs of 1-cm-adjacente tissues...”
-There is no information regarding the histological type of the gastric cancer
samples used in the manuscript. Is there any difference in the methylation status
according to the histopathological type?
-In pages 10 and 11, the authors classified on or no chromosome lost in
diffuse-type of gastric cancer as LOH-B (baseline level) and as LOH-L (low level)
in intestinal and mixed type. Why?
-The authors concluded that “concurrent methylation of multiple CpG-island
genes initiates and sustains the adaptive differentiation of newly fixed stem cell in
the gastric mucosa infected with H. pylori”. However, no comment about stem
cells is made in the methods or results sections. How the authors conclude such
information about stem cells? Is there any marker that was used to check if the
cells used in DNA extraction were newly fixed stem cells?
Minor Essentials Revisions:
-The authors checked for H. pylori status of non-cancerous tissue samples. How
is the H. pylori status of the gastric cancer tissue samples? Is there any
difference in the methylation status between gastric cancer tissue samples H.
pylori positive and H. pylori negative?
-The authors should explain the 5-level and 10-level classification (including the
intermediary status) of methylation status. In a previous paper (Hong et al.,
2009), they explain the 5-level. I believe that a better explanation should improve
the manuscript;
-The first paragraph of the Results section is about results of a previous paper.
Please, transfer it to the Discussion section. However, if they are results of the
current manuscript (although similar of the obtained previously), please cite the
methodology used in the Methods section;
-The last paragraph of page 13 should be transferred to Methods section;
-In page 13, 1st and 2nd lines, the authors can substitute 20 percent for 20%;
-In page 14, lines 14-17: The authors say that PGC and TFF1 are
stomach-specific genes weakly active when compared with the two master
stomach-specific genes. In which tissue? The authors also say that those genes
are densely methylated in bone marrow. And in the stomach?
-Is there any microsatellite in which the authors observed LOH more frequently?
And how about LOH and histologic type?
-In page 18, please change H202 for H2O2 (there is a zero instead of an “O”).
Level of interest: An article of importance in its field
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests
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