Title: PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant
chemotherapy for colorectal cancer: a retrospective study
Version: 1 Date: 08 Aug 2023
Reviewer's report:
Mihara et al. has described the association of SNVs identified in the mitophagy-related
gene, PINK1, with the risk of recurrence in patients who received postoperative adjuvant
chemotherapy. Recurrence colorectal cancer and postoperative adjuvant chemotherapy are
undoubtedly the current research hotspots in cancer pathology, I must say that the article looks
very interesting at first glance, but a more detailed reading shows an obvious superficiality in
certain parts of the text. A fundamental shortcoming of the whole research is innovation. Since
it is an interesting topic, I recommend this article for publication after major revisions in the
BMC Gastroenterology.
Major Comments
1. Consider rephrasing the sentence in line 37. A recurrence-prevention biomarker of
adjuvant….to… Novel molecular biomarkers of postoperative adjuvant chemotherapy to
identify patients at increased risk of recurrence colorectal cancer is warranted.
2. Line 44: Consider rewriting the aim of the study in the abstract to make it clearer.
3. Several other prognostic/predictive biomarkers of postoperative adjuvant chemotherapy
include mismatch repair gene, MSI, EGFR Expression, PIK3CA, CIMP, DCC, ERCC1,
circulating tumour cell and circulating tumour DNA. A brief discussion can be added on top of
BRAF and KRAS mutations.
4. The advantage of autophagy-related biomarkers compared to other biomarkers should be
highlighted briefly in the introduction.
5. Line 117: What do you mean by tumour area? Is it the size of the tumour or percentage of
the tumour cells? Did you perform H&E staining on the tissue to confirm the presence of tumor
cells? If yes, please indicate it in the method section.
6. What is the function of the p-value in Table 1? I think it is unnecessary to include statistical
analysis between clinical characteristics in Table 1 because the study aims to see the association
between the identified SNV and the risk of recurrence of CRC.
7. TNM staging is the most common type of staging used in CRC. I strongly suggest using TNM
Staging compared to Tub1, Tub2, and Pap. Are these gastric cancer classifications?
8. The study tried to look at the correlation between pathogenic/likely pathogenic variants,
based on ClinVar, with the recurrence and nonrecurrence group. I suggest including the variant
prioritization strategy in the method section.
9. What you mean by “the original target enrichment sequencing” in the figure legend of Figure
1 is unclear.
10. CRC patients with high microsatellite instability usually have a higher mutation rate, leading
to many identified variants. Microsatellite status is also known as a predictive biomarker for the
recurrence of CRC. I wonder if the author checked on the microsatellite status of the recruited
patients. This is important to ensure that the
11. Line 531: Kindly specify what the criteria for the sample marked as yellow are.
12. It would be good to access the expression level of PINK1 in the patients with PINK1 SNVs
and compare it with wild-type patients to check if the SNVs affect the gene expression and the
mitophagy activity.
Minor comments
1. Words like lack of sufficient can change to insufficient, not satisfactory, change to
unsatisfactory. Not significant to insignificant. Not expected to unexpected. Several other wordy
terms can also be changed to simpler ones.
2. Please consider using consistent between the terms SNV and SNP, relapse and recurrence
3. The samples are from surgical and biopsy specimens. Is it a fresh tissue or FFPE? The kit
used for the extraction is for the FFPE sample. Kindly specify clearly what is the sample type.
4. Line 141 what type of Qubit dsDNA kit did you use? Is it High sensitivity or Broad range?
Please specify.
5. Line 196: Replace the term electrophoresis with sequencing
6. Line 200: Replace targeted sequences with target genes. The same goes with those in Table S1
13. Figure 1(b) has two violin plots in one graph. Kindly provide a legend for individual plots
(green and red)
14. Line 241: Tables 3 and 4 replace with Table 3 and 4 (no S)
15. Line 249: please specify which SNV showed significant differences
16. Line 252: Revise the sentence; two SNVs in the PINK1 gene were found to be significantly
identified in the non-recurrence group compared to the recurrence group.
17. Please include sample ID in Figure 3b
18. In Figure 3C, please specify which sample to use to view the IGV
19. Figure 3a shows only 4 SNVs in the kinase domain, not five, as mentioned in line 246
20. Please rewrite the sentence in lines 257 to 264 to make them more understandable
21. Line 299, 301: Italic BNIP3
22. Line 314, 215: Italic PINK1
23. It is noted that your manuscript needs careful editing by someone with expertise in technical
English editing paying particular attention to English grammar and sentence structure so that
the goals and results are clear to the reader.
Title: PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant
chemotherapy for colorectal cancer: a retrospective study
Version: 1 Date: 08 Aug 2023
Reviewer's report:
Mihara et al. has described the association of SNVs identified in the mitophagy-related
gene, PINK1, with the risk of recurrence in patients who received postoperative adjuvant
chemotherapy. Recurrence colorectal cancer and postoperative adjuvant chemotherapy are
undoubtedly the current research hotspots in cancer pathology, I must say that the article looks
very interesting at first glance, but a more detailed reading shows an obvious superficiality in
certain parts of the text. A fundamental shortcoming of the whole research is innovation. Since
it is an interesting topic, I recommend this article for publication after major revisions in the
BMC Gastroenterology.
Major Comments
1. Consider rephrasing the sentence in line 37. A recurrence-prevention biomarker of
adjuvant….to… Novel molecular biomarkers of postoperative adjuvant chemotherapy to
identify patients at increased risk of recurrence colorectal cancer is warranted.
2. Line 44: Consider rewriting the aim of the study in the abstract to make it clearer.
3. Several other prognostic/predictive biomarkers of postoperative adjuvant chemotherapy
include mismatch repair gene, MSI, EGFR Expression, PIK3CA, CIMP, DCC, ERCC1,
circulating tumour cell and circulating tumour DNA. A brief discussion can be added on top of
BRAF and KRAS mutations.
4. The advantage of autophagy-related biomarkers compared to other biomarkers should be
highlighted briefly in the introduction.
5. Line 117: What do you mean by tumour area? Is it the size of the tumour or percentage of
the tumour cells? Did you perform H&E staining on the tissue to confirm the presence of tumor
cells? If yes, please indicate it in the method section.
6. What is the function of the p-value in Table 1? I think it is unnecessary to include statistical
analysis between clinical characteristics in Table 1 because the study aims to see the association
between the identified SNV and the risk of recurrence of CRC.
7. TNM staging is the most common type of staging used in CRC. I strongly suggest using TNM
Staging compared to Tub1, Tub2, and Pap. Are these gastric cancer classifications?
8. The study tried to look at the correlation between pathogenic/likely pathogenic variants,
based on ClinVar, with the recurrence and nonrecurrence group. I suggest including the variant
prioritization strategy in the method section.
9. What you mean by “the original target enrichment sequencing” in the figure legend of Figure
1 is unclear.
10. CRC patients with high microsatellite instability usually have a higher mutation rate, leading
to many identified variants. Microsatellite status is also known as a predictive biomarker for the
recurrence of CRC. I wonder if the author checked on the microsatellite status of the recruited
patients. This is important to ensure that the
11. Line 531: Kindly specify what the criteria for the sample marked as yellow are.
12. It would be good to access the expression level of PINK1 in the patients with PINK1 SNVs
and compare it with wild-type patients to check if the SNVs affect the gene expression and the
mitophagy activity.
Minor comments
1. Words like lack of sufficient can change to insufficient, not satisfactory, change to
unsatisfactory. Not significant to insignificant. Not expected to unexpected. Several other wordy
terms can also be changed to simpler ones.
2. Please consider using consistent between the terms SNV and SNP, relapse and recurrence
3. The samples are from surgical and biopsy specimens. Is it a fresh tissue or FFPE? The kit
used for the extraction is for the FFPE sample. Kindly specify clearly what is the sample type.
4. Line 141 what type of Qubit dsDNA kit did you use? Is it High sensitivity or Broad range?
Please specify.
5. Line 196: Replace the term electrophoresis with sequencing
6. Line 200: Replace targeted sequences with target genes. The same goes with those in Table S1
13. Figure 1(b) has two violin plots in one graph. Kindly provide a legend for individual plots
(green and red)
14. Line 241: Tables 3 and 4 replace with Table 3 and 4 (no S)
15. Line 249: please specify which SNV showed significant differences
16. Line 252: Revise the sentence; two SNVs in the PINK1 gene were found to be significantly
identified in the non-recurrence group compared to the recurrence group.
17. Please include sample ID in Figure 3b
18. In Figure 3C, please specify which sample to use to view the IGV
19. Figure 3a shows only 4 SNVs in the kinase domain, not five, as mentioned in line 246
20. Please rewrite the sentence in lines 257 to 264 to make them more understandable
21. Line 299, 301: Italic BNIP3
22. Line 314, 215: Italic PINK1
23. It is noted that your manuscript needs careful editing by someone with expertise in technical
English editing paying particular attention to English grammar and sentence structure so that
the goals and results are clear to the reader.
Please review this paper.
user
Title: PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant
chemotherapy for colorectal cancer: a retrospective study
Version: 1 Date: 08 Aug 2023
Reviewer's report:
Mihara et al. has described the association of SNVs identified in the mitophagy-related
gene, PINK1, with the risk of recurrence in patients who received postoperative adjuvant
chemotherapy. Recurrence colorectal cancer and postoperative adjuvant chemotherapy are
undoubtedly the current research hotspots in cancer pathology, I must say that the article looks
very interesting at first glance, but a more detailed reading shows an obvious superficiality in
certain parts of the text. A fundamental shortcoming of the whole research is innovation. Since
it is an interesting topic, I recommend this article for publication after major revisions in the
BMC Gastroenterology.
Major Comments
1. Consider rephrasing the sentence in line 37. A recurrence-prevention biomarker of
adjuvant….to… Novel molecular biomarkers of postoperative adjuvant chemotherapy to
identify patients at increased risk of recurrence colorectal cancer is warranted.
2. Line 44: Consider rewriting the aim of the study in the abstract to make it clearer.
3. Several other prognostic/predictive biomarkers of postoperative adjuvant chemotherapy
include mismatch repair gene, MSI, EGFR Expression, PIK3CA, CIMP, DCC, ERCC1,
circulating tumour cell and circulating tumour DNA. A brief discussion can be added on top of
BRAF and KRAS mutations.
4. The advantage of autophagy-related biomarkers compared to other biomarkers should be
highlighted briefly in the introduction.
5. Line 117: What do you mean by tumour area? Is it the size of the tumour or percentage of
the tumour cells? Did you perform H&E staining on the tissue to confirm the presence of tumor
cells? If yes, please indicate it in the method section.
6. What is the function of the p-value in Table 1? I think it is unnecessary to include statistical
analysis between clinical characteristics in Table 1 because the study aims to see the association
between the identified SNV and the risk of recurrence of CRC.
7. TNM staging is the most common type of staging used in CRC. I strongly suggest using TNM
Staging compared to Tub1, Tub2, and Pap. Are these gastric cancer classifications?
8. The study tried to look at the correlation between pathogenic/likely pathogenic variants,
based on ClinVar, with the recurrence and nonrecurrence group. I suggest including the variant
prioritization strategy in the method section.
9. What you mean by “the original target enrichment sequencing” in the figure legend of Figure
1 is unclear.
10. CRC patients with high microsatellite instability usually have a higher mutation rate, leading
to many identified variants. Microsatellite status is also known as a predictive biomarker for the
recurrence of CRC. I wonder if the author checked on the microsatellite status of the recruited
patients. This is important to ensure that the
11. Line 531: Kindly specify what the criteria for the sample marked as yellow are.
12. It would be good to access the expression level of PINK1 in the patients with PINK1 SNVs
and compare it with wild-type patients to check if the SNVs affect the gene expression and the
mitophagy activity.
Minor comments
1. Words like lack of sufficient can change to insufficient, not satisfactory, change to
unsatisfactory. Not significant to insignificant. Not expected to unexpected. Several other wordy
terms can also be changed to simpler ones.
2. Please consider using consistent between the terms SNV and SNP, relapse and recurrence
3. The samples are from surgical and biopsy specimens. Is it a fresh tissue or FFPE? The kit
used for the extraction is for the FFPE sample. Kindly specify clearly what is the sample type.
4. Line 141 what type of Qubit dsDNA kit did you use? Is it High sensitivity or Broad range?
Please specify.
5. Line 196: Replace the term electrophoresis with sequencing
6. Line 200: Replace targeted sequences with target genes. The same goes with those in Table S1
13. Figure 1(b) has two violin plots in one graph. Kindly provide a legend for individual plots
(green and red)
14. Line 241: Tables 3 and 4 replace with Table 3 and 4 (no S)
15. Line 249: please specify which SNV showed significant differences
16. Line 252: Revise the sentence; two SNVs in the PINK1 gene were found to be significantly
identified in the non-recurrence group compared to the recurrence group.
17. Please include sample ID in Figure 3b
18. In Figure 3C, please specify which sample to use to view the IGV
19. Figure 3a shows only 4 SNVs in the kinase domain, not five, as mentioned in line 246
20. Please rewrite the sentence in lines 257 to 264 to make them more understandable
21. Line 299, 301: Italic BNIP3
22. Line 314, 215: Italic PINK1
23. It is noted that your manuscript needs careful editing by someone with expertise in technical
English editing paying particular attention to English grammar and sentence structure so that
the goals and results are clear to the reader.
assistant