Molecular Analysis of High-Grade Serous Ovarian Carcinoma Exhibiting Low-Grade Serous Carcinoma and Serous Borderline Tumor

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Thank you for the opportunity to review the manuscript submitted by Kasuke Kanno to Current issues in molecular biology. The authors are reporting pathohistological, genetic and epigenetic characteristics of a case of high-grade serous ovarian cancer with tumor, containing serous borderline or low-grade serous carcinoma lesions. The topic is worth investigation, since such cases with HGSOC coexisting with LGSOC and serous borderline lesions are rare. However, some comments and questions should be addressed.

Comment 1:

Under the Introduction section, in the first paragraph some referral to and additional  citation of some internationally recognized classification system of ovarian cancer would be recommended, where low-grade and high-grade ovarian cancer were defined (WHO?).

Comment 2:

Line 53 – “ and other mutations occur in no>5% of HGSC” – this part is unclear, can the authors rephrase the sentence.

Lines 58-59: The sentence is not clear: “Gene expression is not only genetic mechanism but also epigenetic mechanism such as DNA methylation.”, please rephrase.

Comment 3:

Under the section “ 2.3. DNA Extraction and Whole Exome Sequence (WES)”

The methods describing NGS sequencing should be more extensively explained. In the subtitle WES is mentioned, but in the following text 160-cancer related genes are mentioned. It should be clearly stated which kit/reagent was used (with manufacturer mentioned) and if the whole exome sequencing or joust panel sequencing was performed. If WES was performed, but only 160 genes were detailly analyzed, this should be clearly stated. The mean coverage of analyzed NGS data for 160 gene panel should be mentioned.

The performance of the test should be mentioned - limit of detection if possible?  How is the copy number alteration assessed? If author had already published this information in some previous article, they can add the citation.

Were only exome regions analyzed, or also intron-exon boundaries?- this should be explained in the text.

Comment 4:

Line 117-120:  - should probably be deleted.

Comment 5:

Under each Figure and Table abbreviations should be explained.

Comment 6:

Under the section 3.2. Genomic Analysis,

For genes where variants were detected, the authors should state the reference sequence. HGVS nomenclature should be used for variant description (cDNA, protein)

Comment 7:

Line 144-145: - in the sentence “…MDM2 is amplified, while EP300, MEN1, and 144 NF1 mutations were absent in HGSC compared with LGSC and SBT (Table 3, Supplementary Table S2).”

What kind of mutations? Amplifications?  In the Supplementary Table S2 only CAN are listed – the sentence should be rephrased.

Comment 8:

Under the section 3.3. Epigenetic Analysis, authors should explain abbreviation OGs and TGSs (line 155 and 158).

 

Comment 9:

Lines 190-191: The sentence “These studies suggest RAS/MAPK signaling activation or TP53-wild type are characteris-190 tics of mixed type serous carcinoma.” – would suggest to move the sentence after explaining the results of Chui et all,-  in line 194.

Author Response

August 21^st, 2024

 

Prof. Madhav Bhatia

Editor-in-Chief

Current Issues in Molecular Biology

 

Dear Editor

 

Resubmission of manuscript ID cimb-3154051.

Thank you for reviewing our manuscript entitled, “Molecular Analysis of High-grade Serous Ovarian Carcinoma Exhibiting Low-grade Serous Carcinoma and Serous Borderline Tumor.” to the Current Issues in Molecular Biology, and providing us detailed and insightful feedback on ways to strengthen our paper. I am ashamed that my manuscript has quite a lot of basic immature points, and grateful to have an opportunity to be kindly reviewed by you and receiving indication of those immature points.

 

We greatly thank you and the reviewers for their thoughtful suggestions and insights, by which, we believe, the manuscript has apparently been improved, and hopefully being acceptable for publication in the Current Issues in Molecular Biology.

 

The manuscript has been rechecked, and the changes have been made in accordance with the reviewers’ suggestions. The responses to all comments have been indicated in red text as attached below and reflected in the revised version of the manuscript shown in red text using track changes.

 

Responses to reviewer 1 comments

Comment 1:

Under the Introduction section, in the first paragraph some referral to and additional  citation of some internationally recognized classification system of ovarian cancer would be recommended, where low-grade and high-grade ovarian cancer were defined (WHO?).

Thank you for this suggestion. We added citation of WHO Classification of tumors of the ovary 2020 on line 42-43 and modified the name of tumors.

 

Comment 2:

Line 53 – “ and other mutations occur in no>5% of HGSC” – this part is unclear, can the authors rephrase the sentence.

Thank you for this suggestion. We rephrased the sentence as following; “and other mutations occur in less than no >5% of the HGSC” on line 54.

 

Lines 58-59: The sentence is not clear: “Gene expression is not only genetic mechanism but also epigenetic mechanism such as DNA methylation.”, please rephrase.

Thank you for this suggestion. As you indicated, the word “regulated” is missed and this sentence made no sense. We rephrased the sentence as following; “Gene expression is regulated by not only genetic mechanism but also epigenetic mechanism such as DNA methylation” on line 60.

 

Comment 3:

Under the section “ 2.3. DNA Extraction and Whole Exome Sequence (WES)”

The methods describing NGS sequencing should be more extensively explained. In the subtitle WES is mentioned, but in the following text 160-cancer related genes are mentioned. It should be clearly stated which kit/reagent was used (with manufacturer mentioned) and if the whole exome sequencing or joust panel sequencing was performed. If WES was performed, but only 160 genes were detailly analyzed, this should be clearly stated. The mean coverage of analyzed NGS data for 160 gene panel should be mentioned.

The performance of the test should be mentioned - limit of detection if possible?  How is the copy number alteration assessed? If author had already published this information in some previous article, they can add the citation.

Were only exome regions analyzed, or also intron-exon boundaries?- this should be explained in the text.

Thank you for those indication. As you mentioned, the sequence we conducted was NGS, not WES. We apologize that we confused you, and we are appreciated that you indicated our mistake. We changed the all term “WES” or “Whole Exome Sequence” to “NGS” and “Next Generation Sequence”.

The mean depth was depth of SBT, LGSC and HGSC were 620.1, 589.3 and 719.2, respectively. We added the description on line 165.

We are afraid but we don’t have data of limit of detection of PleSSision Panel test.

We added the explanation of copy number alteration and PleSSision Panel test on line 112 to 117.

Only exome regions were analyzed. We added the description on line 113.

 

Comment 4:

Line 117-120:  - should probably be deleted.

Thank you for this indication. I carelessly didn’t delete the template sentence.

 

Comment 5:

Under each Figure and Table abbreviations should be explained.

Thank you for this indication. We added explanation.

 

Comment 6:

Under the section 3.2. Genomic Analysis,

For genes where variants were detected, the authors should state the reference sequence. HGVS nomenclature should be used for variant description (cDNA, protein)

Thank you for this indication. Reference sequence is peripheral blood. We added the description on line 116. We added HGVS nomenclature description on line 168 to 170.

 

Comment 7:

Line 144-145: - in the sentence “…MDM2 is amplified, while EP300, MEN1, and 144 NF1 mutations were absent in HGSC compared with LGSC and SBT (Table 3, Supplementary Table S2).”

What kind of mutations? Amplifications?  In the Supplementary Table S2 only CAN are listed – the sentence should be rephrased.

Thank you for this indication. CN loss was proper expression. We modified the expression from “mutations were absent” to “CNs are less” on line 165.

 

Comment 8:

Under the section 3.3. Epigenetic Analysis, authors should explain abbreviation OGs and TGSs (line 155 and 158).

Thank you for this indication. We added abbreviations on line 181 to 182.

 

Comment 9:

Lines 190-191: The sentence “These studies suggest RAS/MAPK signaling activation or TP53-wild type are characteris-190 tics of mixed type serous carcinoma.” – would suggest to move the sentence after explaining the results of Chui et all,-  in line 194.

Thank you for this indication. We moved the sentence after explanation of the results of Chui et al.

 

Again, thank you for giving us the opportunity to improve our manuscript with your valuable comments and queries.

 

Sincerely,

Kosuke Kanno, MD

Department of Obstetrics and Gynecology, Shimane University Faculty of Medicine

Enyacho 89-1, Izumo, Shimane, Japan 693-8501

Phone: 81-853-20-2268

Email: [email protected]

 

Kentaro Nakayama, MD, PhD

Nagoya City University East Medical Center

Chikusaku Wakamizu 1-2-23, Nagoya, Aichi, Japan 4648547

Phone: 81-52-721-7171

Fax: 81-52-721-1308 (fax)

E-mail: [email protected]

 

Satoru Kyo, MD, PhD

Department of Obstetrics and Gynecology, Shimane University Faculty of Medicine

Enyacho 89-1, Izumo, Shimane, Japan 693-8501

Phone: 81-853-20-2268

Email: [email protected]

 

 

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The paper is well written. However, I have the following concerns.

High grade serous carcinoma and borderline Serous tumours could be present in one case- it's not so uncommon: PMID: 31149473, 30023420 . Therefore, there isn't much novelty here.

Also PMID: 26166714 shows P53 and discusses MDM2. 

 

So perhaps the authors could write how it is novel before resubmitting.

The authors also did not provide criteria for IHC markers.

Not sure what difference there is between Low and Little expression (table 1)

 

 

Comments on the Quality of English Language

Language is ok, with minor proofreading.

Author Response

August 21^st, 2024

 

Prof. Madhav Bhatia

Editor-in-Chief

Current Issues in Molecular Biology

 

Dear Editor

 

Resubmission of manuscript ID cimb-3154051.

Thank you for reviewing our manuscript entitled, “Molecular Analysis of High-grade Serous Ovarian Carcinoma Exhibiting Low-grade Serous Carcinoma and Serous Borderline Tumor.” to the Current Issues in Molecular Biology, and providing us detailed and insightful feedback on ways to strengthen our paper.

 

We greatly thank you and the reviewers for their thoughtful suggestions and insights, by which, we believe, the manuscript has apparently been improved, and hopefully being acceptable for publication in the Current Issues in Molecular Biology.

 

The manuscript has been rechecked, and the changes have been made in accordance with the reviewers’ suggestions. The responses to all comments have been indicated in red text as attached below and reflected in the revised version of the manuscript shown in red text using track changes.

 

Responses to reviewer 2 comments

The paper is well written. However, I have the following concerns.

High grade serous carcinoma and borderline Serous tumours could be present in one case- it's not so uncommon: PMID: 31149473, 30023420 . Therefore, there isn't much novelty here.

Also PMID: 26166714 shows P53 and discusses MDM2. 

 

So perhaps the authors could write how it is novel before resubmitting.

The authors also did not provide criteria for IHC markers.

Not sure what difference there is between Low and Little expression (table 1)

 

1. Novel points of our report

Thank you for this indication.

PMID 31149473 is a case report of a patient who was diagnosed HGSC when she was undergone partial omentectomy as primary surgery, whereas SBT component was found in the second surgery after 6-cycle of combined chemotherapy. We added description about this case report in discussion part, on line 143 to 148.

PMID 30023420 is about a case with SBT with micropapillary pattern, which suggest SBT with LGSC. It is quite interesting report, however, our report is focusing on crosstalk between type 1 and type 2 serous tumors. Thus, we didn’t mention it in our report. Those two case reports didn’t focus on genetic nor epigenetic mechanisms, whereas we conducted genetic and epigenetic sequence. In terms of genetic and epigenetic sequence, our research has novelty compared to them.

PMID 26166714 is an interesting report which uses TCGA study samples and reviewed 14 cases with wild-type TP53 sequences and they found that only one case was HGSC with LGSC. They mentioned MDM2 in their discussion, but it seems there’s no results of MDM2 mutations or copy number alterations in their results. Our result may support their hypothesis, but we believe that it doesn’t mean our study lost novelty. We added description of this report in the discussion part, on line 219 to 221. As we mentioned in our manuscript, there are other studies mentioned MDM2 alterations in TP53 wild-type HGSC, but our report is focusing on not only TP53 wild type HGSC but also mixed type serous carcinoma which show possible crosstalk of type 1 and type 2 serous carcinomas.

 

2. Criteria for IHC markers

Thank you for this indication. We added the clinical roles of IHC we used in our research on line 201 to 205.

 

3. The differences between low and little expression

Thank you for this indication. You may indicate IHC of Ki67. As you mentioned, SBT and LGSC were both low. I wanted to express that in SBT, Ki67 expression is relatively lower than LGSC. As you mentioned, our expression is not proper. We changed the expression “little” to “low” in Table 1.

 

Again, thank you for giving us the opportunity to improve our manuscript with your valuable comments and queries.

 

Sincerely,

Kosuke Kanno, MD

Department of Obstetrics and Gynecology, Shimane University Faculty of Medicine

Enyacho 89-1, Izumo, Shimane, Japan 693-8501

Phone: 81-853-20-2268

Email: [email protected]

 

Kentaro Nakayama, MD, PhD

Nagoya City University East Medical Center

Chikusaku Wakamizu 1-2-23, Nagoya, Aichi, Japan 4648547

Phone: 81-52-721-7171

Fax: 81-52-721-1308 (fax)

E-mail: [email protected]

 

Satoru Kyo, MD, PhD

Department of Obstetrics and Gynecology, Shimane University Faculty of Medicine

Enyacho 89-1, Izumo, Shimane, Japan 693-8501

Phone: 81-853-20-2268

Email: [email protected]

 

 

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

Thanks for providing the response.