Association between SMAD4 Mutations and GATA6 Expression in Paired Pancreatic Ductal Adenocarcinoma Tumor Specimens: Data from Two Independent Molecularly-Characterized Cohorts
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe study aimed to explore the relationship between two molecular biomarkers, SMAD4 mutations and GATA6 expression, in localized pancreatic ductal adenocarcinoma (PDAC) tumors. To achieve this, molecular data from 321 patients across two datasets, TCGA (n=180) and CPTAC (n=141), were analyzed. The study concludes that since there was no observed association between SMAD4 mutations and GATA6 expression or between SMAD4 mutations and Moffitt subtype, further targeted research might be needed to understand the distinct mechanisms and implications of each biomarker in PDAC.
In the abstract, the authors should clearly describe the objective and provide background on the role of these two genes in pancreatic cancer and their influence on treatment outcomes. Was there a significant correlation found between SMAD4 mutations and GATA6 expression in these two cohorts? A mention of the established relationship between SMAD4 and GATA6 in pancreatic cancer treatments would elucidate the existing knowledge gap. While the study concludes that no observed association exists between the biomarkers, the authors should delve into the potential therapeutic or clinical implications based on their findings.
The potential molecular mechanisms or pathways responsible for the observed findings should be further elucidated, as such insights have vital therapeutic implications. The apparent lack of correlation between SMAD4 and the basal-like subtype in PDAC, although of potential significance, requires further validation through more stringent statistical analyses, such as Cox proportional-hazards regression models, multivariate regression analysis, etc.
Author Response
Manuscript ID: biomedicines-2676432
Association Between SMAD4 Mutations and GATA6 Expression in Paired Pancreatic Ductal Adenocarcinoma Tumor Specimens
Dear Dr. Mousa,
Thank you for the opportunity to submit our revised manuscript entitled “Association Between SMAD4 Mutations and GATA6 Expression in Paired Pancreatic Ductal Adenocarcinoma Tumor Specimens” to Biomedicines. We thank the reviewer for their critical appraisal of our manuscript. We now present a revised manuscript, incorporating the reviewer’s suggestions. All changes have been highlighted in this revision. A detailed response to reviewer comments follows. We hope that our revisions will resolve their concerns and questions.
Sincerely,
Brett L. Ecker, MD
Rutgers Cancer Institute of New Jersey
Rutgers Robert Wood Johnson Medical School
Cooperman Barnabas Medical Center
94 Old Short Hills Road | Suite 1172 | Livingston | NJ 07039
(P) 973.322.5195 | (F) 973-322-2471
Reviewer #1:
1. The study aimed to explore the relationship between two molecular biomarkers, SMAD4 mutations and GATA6 expression, in localized pancreatic ductal adenocarcinoma (PDAC) tumors. To achieve this, molecular data from 321 patients across two datasets, TCGA (n=180) and CPTAC (n=141), were analyzed. The study concludes that since there was no observed association between SMAD4 mutations and GATA6 expression or between SMAD4 mutations and Moffitt subtype, further targeted research might be needed to understand the distinct mechanisms and implications of each biomarker in PDAC.
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Response: Thank you for your thorough review of our manuscript.
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2. In the abstract, the authors should clearly describe the objective and provide background on the role of these two genes in pancreatic cancer and their influence on treatment outcomes. Was there a significant correlation found between SMAD4 mutations and GATA6 expression in these two cohorts? A mention of the established relationship between SMAD4 and GATA6 in pancreatic cancer treatments would elucidate the existing knowledge gap. While the study concludes that no observed association exists between the biomarkers, the authors should delve into the potential therapeutic or clinical implications based on their findings.
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Response: Thank you for your feedback. We agree and have added to the abstract to provide further background information, namely that each has been associated with inferior survival uniquely for patients receiving 5-FU-based therapies, and that SMAD4 may directly regulate the expression of GATA6 in PDAC, pointing to a common predictive biomarker. Contrary to hypothesis, there was a lack of association between these two biomarkers in either cohort in our study. We have updated the abstract to reflect the clinical implications of these data, namely that distinct biomarker-defined clinical trials are necessary.
3. The potential molecular mechanisms or pathways responsible for the observed findings should be further elucidated, as such insights have vital therapeutic implications. The apparent lack of correlation between SMAD4 and the basal-like subtype in PDAC, although of potential significance, requires further validation through more stringent statistical analyses, such as Cox proportional-hazards regression models, multivariate regression analysis, etc.
Response: We agree and have added a multivariable Cox regression model adjusting for known prognostic variables that were significantly associated with survival in each cohort (i.e., AJCC stage, N stage and Grade for the TCGA cohort; and AJCC stage for the CPTAC Cohort). SMAD4 was not independently associated with survival in these models. The adjusted hazard ratios have been added to the manuscript. |
Reviewer 2 Report
Comments and Suggestions for AuthorsJoshua D. Greendyk BA et al showed that SMAD4 mutations and GATA6 expression in paired pancreatic ductal adenocarcinoma tumor specimens.
The manuscript is interesting. However, there are many shortcomings to explain the whole of the paper.
It would have been easier to understand if it was written in a graph rather than in a table (Table 1 and Table 2). For example, if authors show a graph that can be compared by age group or race type, I think it will be effectively compared.
Based on the information of a large number of patients, I think this is a useful paper that shows the relationship between SMAD4 and GATA6 in the pancreatic ductal adenocarcinoma tumor.
Comments on the Quality of English LanguageMinor editing of English language required
Author Response
Reviewer #2:
4. Joshua D. Greendyk BA et al showed that SMAD4 mutations and GATA6 expression in paired pancreatic ductal adenocarcinoma tumor specimens. The manuscript is interesting. Based on the information of a large number of patients, I think this is a useful paper that shows the relationship between SMAD4 and GATA6 in the pancreatic ductal adenocarcinoma tumor. However, there are many shortcomings to explain the whole of the paper. It would have been easier to understand if it was written in a graph rather than in a table (Table 1 and Table 2). For example, if authors show a graph that can be compared by age group or race type, I think it will be effectively compared. Based on the information of a large number of patients, I think this is a useful paper that shows the relationship between SMAD4 and GATA6 in the pancreatic ductal adenocarcinoma tumor.
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Response: Thank you for your feedback. We have provided the clinicodemographic data, stratified by the presence versus absence of SMAD4 alterations, in the standard fashion of a “Table 1”. We have provided figures for the display of survival curves. We hope you agree that this is the standard scientific reporting of clinical data. In distinction, the data of Table 3, which represents the primary analysis of this manuscript, could be presented as either a figure (e.g., bar graph) or table. We would be happy to update the display of this analysis at your request. |
Reviewer 3 Report
Comments and Suggestions for AuthorsThe rationale for studying SMAD4 variants versus GATA6 expression is not well explained. Is there any molecular link on for example transcriptional level? Thu study subject does not make a coherent story.
Some % did not add up to 100% in the Tables.
The authors should present some of their own data e.g. tissue microarray versusus variants. This is just a relatively low-dimensional analysis of publically available data with mostly negative results. This is too little work to make proper publication.
The study must be enhanced with a cohort based on another approach.
This is more like preliminary data or a poster.
Is GATA6 mutated in pancreatic cancer?
What about multivariate survival analysis with all relevant data?
Author Response
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Reviewer 4 Report
Comments and Suggestions for AuthorsWith pleasure, I read the paper titled “Association Between SMAD4 Mutations and GATA6 Expression in Paired Pancreatic Ductal Adenocarcinoma Tumor Specimens”. The topic is clinically relevant to practice, and of importance to the readers of Biomedicine journal. Overall, the manuscript reads well and has good flow of ideas, up-to-date citations, and proper summary of data using tables and figures. A MAJOR strength of the article is being—according to authors, the most comprehensive exploration of SMAD4 and GATA6 in PDAC. The research is well-articulated to encourage more research in the field. The introduction section was detailed enough to provide the reader with the needful background information. The methods section was detailed too, however, some edits are needed for complete reporting. The discussion section comprised elaborations from clinical and biological aspects, adding intellectual curiosity. The research had some unavoidable limitations, all of which had been explicitly acknowledged. The conclusion is line with the presented results. All in all, this manuscript is clinically significant and is very likely to be cited extensively in the future. I strongly recommend the manuscript to be accepted—however, prior to that, some combinatorial minor and major changes are required as indicated below:
TITLE
— I recommend changing title to: “Association Between SMAD4 Mutations and GATA6 Expression in Paired Pancreatic Ductal Adenocarcinoma Tumor (PDAC) Specimens: Data from two independent molecularly-characterized PDAC cohorts”
ABSTRACT
— It is important to mention that SMAD4-mutation did not appear to associate with poor clinico-pathological features, such as poor tumor grade, advanced tumor stage, positive LVSI, and positive PNI compared with SMAD4-wildtype.
INTRODUCTION
— Please clarify the nature of SMAD4 alterations associated with unfavorable clinical outcomes. Are they loss-of-function or gain-of-function mutations?
— You mentioned that “SMAD4 may directly regulate the expression of GATA6”. Is it true for the opposite; does GATA6 directly regulate SMAD4?
— Please clearly highlight the significance of your research. Is this the first-ever study to investigate the relationship between SMAD4 and GATA6 in PDAC? If not, please mention how does your research enriches existing literature.
— Please conclude the section with some proposed hypotheses.
METHODS
— Please mention how the tertiles for GATA6 into low, medium, and high were established?
— It would be interesting to investigate also the rates of GATA6 mutations (WT versus MUT), if any, and investigate its impact on clinicopathological features and overall survival.
— You investigated the GATA6 expression at the mRNA level. I wonder if the proteomic data are available and whether the mRNA and protein levels are matched in the samples.
— You explored the outcome of overall survival, and I wonder if it is possible to enrich the manuscript by investigating also the disease-free survival or recurrence-free survival?
RESULTS
— In Table 1 and Table 2, the percentages were calculated according to rows. However, this is not right. The percentages should be calculated according to columns. Considering the data in Table 1 and Table 2, does it mean that SMAD4-mutation does not appear to associate with poor clinico-pathological features, as there was no difference in tumor grade, tumor stage, LVSI, and PNI between SMAD4-WT and SMAD4-MUT?
— In Table 3, the percentages were calculated according to rows. However, this is not right. The percentages should be calculated according to columns. The data from TCGA and CPTAC showed no impact of SMAD4-mutation on GATA6 expression and Moffitt subtype—were these observations predicted, and what are your thoughts?
— The TCGA data showed no difference in OS based on histological subtypes. However, the CPTAC data showed worse overall survival for basal-like type compared with the classical type. Why was there a discrepancy in findings between the two datasets?
— It is possible to mention the type of chemotherapeutic regimens received by the patients in TCGA and CPTAC datasets?
DISCUSSION
— Please provide some biological discussion on the role of GATA6 and how its low expression negatively influences the phenotype and prognosis of PDAC.
— Are there any in-vitro studies that examined the relationship between SMAD4 and GATA6 in PDAC? If so, please briefly summarize their findings to enrich the discussion section from a biological perspective.
OVERALL
— The manuscript requires editing for English language.
Comments on the Quality of English LanguageMinor English editing is needed
Author Response
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Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsI have no further questions about this version.
Reviewer 3 Report
Comments and Suggestions for AuthorsI have the same general reservations as in the first review i.e. the study is generally little work. A few more studies like that could be generated by 1-2 people over a short period.
Still, the authors generally added the formally requested point to the manuscript and there are no major flaws.
Comments on the Quality of English LanguageEnglish is fine.
Reviewer 4 Report
Comments and Suggestions for AuthorsThe authors did a wonderful job by addressed all the comments adequately. The manuscript now reads well and is scientifically valid, methodologically robust, and intellectually interesting. The limitations have been properly acknowledged. All in all, I congratulate the authors on a well-done revision and the manuscript can be accepted in its current stage.
Comments on the Quality of English LanguageMinor editing my be required