Title: Comprehensive analysis of glycometabolism-related genes reveals PLOD2 as a
prognostic biomarker and therapeutic target in gastric cancer
Version: 1 Date: 18 Feb 2025
Reviewer:  Shuguang Zhou
Reviewer's report:
1. The specific screening criteria for TCGA and GEO data (e.g., sample exclusion conditions,
batch effect correction methods) are not clearly stated in the paper. Additional details are
recommended to enhance reproducibility.
2. In consensus cluster analysis, the basis for selecting k=2 (such as CDF curve and contour
coefficient) needs to be further explained to avoid subjectivity.
3. While integrating 10 algorithms, there is no explicit mention of the cross-validation process
for model performance (e.g., whether the calculation of the C-index is based on an independent
test set or cross-validation). It is recommended to supplement the verification details to avoid
the risk of overfitting.
4. The RSF model should be clearly demonstrated as the statistical basis of the optimal model
(e.g., significant differences with other models) (e.g., through Delong's test).
5. In Western blot experiments, it is not mentioned whether the loading amount of the reference
protein (such as ACTIN) is homogeneous, and quantitative analysis (such as gray value
comparison) needs to be supplemented.
6. In immunofluorescence experiments, the quantitative analysis of PLOD2 and mTOR
colocalization (such as Pearson correlation coefficient) should be supplemented to avoid
subjective judgment.
7. IT IS MENTIONED THAT HIGH EXPRESSION OF PLOD2 IS ASSOCIATED WITH
M2 MACROPHAGE INFILTRATION, BUT IT ONLY RELIES ON THE RESULTS OF
ALGORITHMS SUCH AS CIBERSORT, AND LACKS EXPERIMENTAL VALIDATION
(SUCH AS FLOW CYTOMETRY OR IMMUNOHISTOCHEMISTRY). It is recommended to
supplement the experimental data to enhance persuasiveness.
8. In the association analysis between immunosuppressive phenotype and ICB efficacy, the ROC
curve did not show the AUC value, and the specific value and confidence interval should be
supplemented.
9. The interaction between PLOD2 and mTOR has only been verified by Co-IP, and it is
recommended to supplement functional recovery experiments (such as whether the effect of
combining mTOR inhibitors after overexpression of PLOD2 is reversible).
10. The ratio of phosphorylated protein to total protein (e.g., p-AKT/AKT) that has not
been quantified in the pathway-activated Western blot results should be supplemented with
quantitative analysis.
11. Explicit mention of the bias that may result from small sample sizes (e.g., only 34 cases of
TCGA normal tissue) and the inherent limitations of retrospective studies.
12. The discussion of clinical translational potential (e.g., PLOD2 inhibitor development)
is weak, and it is recommended to combine existing drugs targeting the PI3K/AKT/mTOR
pathway (e.g., everolimus).
13. The content of Reference 46 is a guideline for the diagnosis and treatment of myocarditis in
children, which has nothing to do with gastric cancer, and is suspected of being miscited, and
needs to be checked and corrected.
14. The research innovation is clear (the first construction of a four-gene model related to glucose
metabolism and the unfolding role of PLOD2 in immune regulation), but it is necessary to
highlight its differences from existing studies (such as the advantages of single-gene biomarkers)
in the discussion.
15. The clinical translational part can further explore the potential of PLOD2 as a combination
therapy target (e.g., in combination with immune checkpoint inhibitors).
Title: Comprehensive analysis of glycometabolism-related genes reveals PLOD2 as a
prognostic biomarker and therapeutic target in gastric cancer
Version: 1 Date: 18 Feb 2025
Reviewer:  Shuguang Zhou
Reviewer's report:
1. The specific screening criteria for TCGA and GEO data (e.g., sample exclusion conditions,
batch effect correction methods) are not clearly stated in the paper. Additional details are
recommended to enhance reproducibility.
2. In consensus cluster analysis, the basis for selecting k=2 (such as CDF curve and contour
coefficient) needs to be further explained to avoid subjectivity.
3. While integrating 10 algorithms, there is no explicit mention of the cross-validation process
for model performance (e.g., whether the calculation of the C-index is based on an independent
test set or cross-validation). It is recommended to supplement the verification details to avoid
the risk of overfitting.
4. The RSF model should be clearly demonstrated as the statistical basis of the optimal model
(e.g., significant differences with other models) (e.g., through Delong's test).
5. In Western blot experiments, it is not mentioned whether the loading amount of the reference
protein (such as ACTIN) is homogeneous, and quantitative analysis (such as gray value
comparison) needs to be supplemented.
6. In immunofluorescence experiments, the quantitative analysis of PLOD2 and mTOR
colocalization (such as Pearson correlation coefficient) should be supplemented to avoid
subjective judgment.
7. IT IS MENTIONED THAT HIGH EXPRESSION OF PLOD2 IS ASSOCIATED WITH
M2 MACROPHAGE INFILTRATION, BUT IT ONLY RELIES ON THE RESULTS OF
ALGORITHMS SUCH AS CIBERSORT, AND LACKS EXPERIMENTAL VALIDATION
(SUCH AS FLOW CYTOMETRY OR IMMUNOHISTOCHEMISTRY). It is recommended to
supplement the experimental data to enhance persuasiveness.
8. In the association analysis between immunosuppressive phenotype and ICB efficacy, the ROC
curve did not show the AUC value, and the specific value and confidence interval should be
supplemented.
9. The interaction between PLOD2 and mTOR has only been verified by Co-IP, and it is
recommended to supplement functional recovery experiments (such as whether the effect of
combining mTOR inhibitors after overexpression of PLOD2 is reversible).
10. The ratio of phosphorylated protein to total protein (e.g., p-AKT/AKT) that has not
been quantified in the pathway-activated Western blot results should be supplemented with
quantitative analysis.
11. Explicit mention of the bias that may result from small sample sizes (e.g., only 34 cases of
TCGA normal tissue) and the inherent limitations of retrospective studies.
12. The discussion of clinical translational potential (e.g., PLOD2 inhibitor development)
is weak, and it is recommended to combine existing drugs targeting the PI3K/AKT/mTOR
pathway (e.g., everolimus).
13. The content of Reference 46 is a guideline for the diagnosis and treatment of myocarditis in
children, which has nothing to do with gastric cancer, and is suspected of being miscited, and
needs to be checked and corrected.
14. The research innovation is clear (the first construction of a four-gene model related to glucose
metabolism and the unfolding role of PLOD2 in immune regulation), but it is necessary to
highlight its differences from existing studies (such as the advantages of single-gene biomarkers)
in the discussion.
15. The clinical translational part can further explore the potential of PLOD2 as a combination
therapy target (e.g., in combination with immune checkpoint inhibitors).
Please review this paper.
user
Title: Comprehensive analysis of glycometabolism-related genes reveals PLOD2 as a
prognostic biomarker and therapeutic target in gastric cancer
Version: 1 Date: 18 Feb 2025
Reviewer:  Shuguang Zhou
Reviewer's report:
1. The specific screening criteria for TCGA and GEO data (e.g., sample exclusion conditions,
batch effect correction methods) are not clearly stated in the paper. Additional details are
recommended to enhance reproducibility.
2. In consensus cluster analysis, the basis for selecting k=2 (such as CDF curve and contour
coefficient) needs to be further explained to avoid subjectivity.
3. While integrating 10 algorithms, there is no explicit mention of the cross-validation process
for model performance (e.g., whether the calculation of the C-index is based on an independent
test set or cross-validation). It is recommended to supplement the verification details to avoid
the risk of overfitting.
4. The RSF model should be clearly demonstrated as the statistical basis of the optimal model
(e.g., significant differences with other models) (e.g., through Delong's test).
5. In Western blot experiments, it is not mentioned whether the loading amount of the reference
protein (such as ACTIN) is homogeneous, and quantitative analysis (such as gray value
comparison) needs to be supplemented.
6. In immunofluorescence experiments, the quantitative analysis of PLOD2 and mTOR
colocalization (such as Pearson correlation coefficient) should be supplemented to avoid
subjective judgment.
7. IT IS MENTIONED THAT HIGH EXPRESSION OF PLOD2 IS ASSOCIATED WITH
M2 MACROPHAGE INFILTRATION, BUT IT ONLY RELIES ON THE RESULTS OF
ALGORITHMS SUCH AS CIBERSORT, AND LACKS EXPERIMENTAL VALIDATION
(SUCH AS FLOW CYTOMETRY OR IMMUNOHISTOCHEMISTRY). It is recommended to
supplement the experimental data to enhance persuasiveness.
8. In the association analysis between immunosuppressive phenotype and ICB efficacy, the ROC
curve did not show the AUC value, and the specific value and confidence interval should be
supplemented.
9. The interaction between PLOD2 and mTOR has only been verified by Co-IP, and it is
recommended to supplement functional recovery experiments (such as whether the effect of
combining mTOR inhibitors after overexpression of PLOD2 is reversible).
10. The ratio of phosphorylated protein to total protein (e.g., p-AKT/AKT) that has not
been quantified in the pathway-activated Western blot results should be supplemented with
quantitative analysis.
11. Explicit mention of the bias that may result from small sample sizes (e.g., only 34 cases of
TCGA normal tissue) and the inherent limitations of retrospective studies.
12. The discussion of clinical translational potential (e.g., PLOD2 inhibitor development)
is weak, and it is recommended to combine existing drugs targeting the PI3K/AKT/mTOR
pathway (e.g., everolimus).
13. The content of Reference 46 is a guideline for the diagnosis and treatment of myocarditis in
children, which has nothing to do with gastric cancer, and is suspected of being miscited, and
needs to be checked and corrected.
14. The research innovation is clear (the first construction of a four-gene model related to glucose
metabolism and the unfolding role of PLOD2 in immune regulation), but it is necessary to
highlight its differences from existing studies (such as the advantages of single-gene biomarkers)
in the discussion.
15. The clinical translational part can further explore the potential of PLOD2 as a combination
therapy target (e.g., in combination with immune checkpoint inhibitors).
assistant