Title: Deciphering the Integrated Immunogenomic Landscape of Colorectal Cancer: Insights
from Mendelian Randomization and Immune-Stratified Molecular Subtyping
Version: 4 Date: 11 Jan 2025
Reviewer's report:
1, Figure 3C, how can we see that the best clustering is 2, these two figures do not seem to prove
that the best clustering is 2, please explain in detail
2, Figure 5G, not clear, I hope the authors upload the original figure, and use at least two cell lines
3# Please list the data used by TCGA-CRC, including survival time, survival status, risk score,
etc. in an excel sheet to make the data transparent.
4. Please keep 3 decimals in the OR (95% Cl) and P-value columns in Fig. 1/2, especially the
P-value, which is a very bad scientific attitude, and 4 decimals in Fig. 3B, please standardize
the whole text.
5. The data in Fig. 5A is in PFKM standardized format, and B is in TPM format, so it is
recommended that the same full text analyze the standardization of the data.
6. You wrote (g) Colony formation assays demonstrated proliferation decreases with GPD1L
inhibition, while the experimental result was that proliferation increased after GPD1L inhibition.
The two conclusions are opposite, please explain in detail.
7, WB experiment validation, only one group was done, it is recommended to repeat the
experiment three times and validate it in two cell lines. GPD1L is already low expression in
tumors, why continue to knock down, if increase its overexpression and observe its proliferation
phenotype, it will be more convincing!
Title: Deciphering the Integrated Immunogenomic Landscape of Colorectal Cancer: Insights
from Mendelian Randomization and Immune-Stratified Molecular Subtyping
Version: 4 Date: 11 Jan 2025
Reviewer's report:
1, Figure 3C, how can we see that the best clustering is 2, these two figures do not seem to prove
that the best clustering is 2, please explain in detail
2, Figure 5G, not clear, I hope the authors upload the original figure, and use at least two cell lines
3# Please list the data used by TCGA-CRC, including survival time, survival status, risk score,
etc. in an excel sheet to make the data transparent.
4. Please keep 3 decimals in the OR (95% Cl) and P-value columns in Fig. 1/2, especially the
P-value, which is a very bad scientific attitude, and 4 decimals in Fig. 3B, please standardize
the whole text.
5. The data in Fig. 5A is in PFKM standardized format, and B is in TPM format, so it is
recommended that the same full text analyze the standardization of the data.
6. You wrote (g) Colony formation assays demonstrated proliferation decreases with GPD1L
inhibition, while the experimental result was that proliferation increased after GPD1L inhibition.
The two conclusions are opposite, please explain in detail.
7, WB experiment validation, only one group was done, it is recommended to repeat the
experiment three times and validate it in two cell lines. GPD1L is already low expression in
tumors, why continue to knock down, if increase its overexpression and observe its proliferation
phenotype, it will be more convincing!
Please review this paper.
user
Title: Deciphering the Integrated Immunogenomic Landscape of Colorectal Cancer: Insights
from Mendelian Randomization and Immune-Stratified Molecular Subtyping
Version: 4 Date: 11 Jan 2025
Reviewer's report:
1, Figure 3C, how can we see that the best clustering is 2, these two figures do not seem to prove
that the best clustering is 2, please explain in detail
2, Figure 5G, not clear, I hope the authors upload the original figure, and use at least two cell lines
3# Please list the data used by TCGA-CRC, including survival time, survival status, risk score,
etc. in an excel sheet to make the data transparent.
4. Please keep 3 decimals in the OR (95% Cl) and P-value columns in Fig. 1/2, especially the
P-value, which is a very bad scientific attitude, and 4 decimals in Fig. 3B, please standardize
the whole text.
5. The data in Fig. 5A is in PFKM standardized format, and B is in TPM format, so it is
recommended that the same full text analyze the standardization of the data.
6. You wrote (g) Colony formation assays demonstrated proliferation decreases with GPD1L
inhibition, while the experimental result was that proliferation increased after GPD1L inhibition.
The two conclusions are opposite, please explain in detail.
7, WB experiment validation, only one group was done, it is recommended to repeat the
experiment three times and validate it in two cell lines. GPD1L is already low expression in
tumors, why continue to knock down, if increase its overexpression and observe its proliferation
phenotype, it will be more convincing!
assistant