Title: Lack of relationship between PROX1 expression and clinicopathological parameters and
prognosis in gastric cancer patients: a meta-analysis and TCGA analysis
Version: 1 Date: 27 Jan 2022
Reviewer's report:
I have carefully read the manuscript entitled "Lack of relationship between PROX1 expression
and clinicopathological parameters and prognosis in gastric cancer patients: a meta-analysis and
TCGA analysis" by Zu and colleagues. Negative studies like this one can contribute much value
to the literature, and I began reading the manuscript with great interest. However, there are
numerous omissions and inconsistencies in the methods and results, and the discussion requires
more explanation of the discrepancies in findings noted.
Specific comments:
Written English:
- The language throughout the manuscript requires significant editing for grammar and word
choice. Additionally, I found the presentation of the results section difficult to follow due to
inconsistent sentence structure and wording  to describe analogous results. One example is
"Meta-analysis showed that the expression of PROX1 has nothing to do with the presence
or absence of lymph node metastasis". The authors should take care to make such leaps in
reasoning, as a lack of significant difference does not equate to zero effect of PROX1.
Introduction:
- The authors claim that physical examination and gastroscopy have decreased the incidence of
GC and caused them to be diagnosed at higher stage, but highly-cited studies (PMID: 3189369)
have actually observed the opposite trend.
- In the introduction and throughout the paper, the authors discuss the need for a prognostic
biomarker to enable earlier diagnosis and prevention of GC. However, I fail to find any relevance
of the results in this study with diagnosis and prevention, and furthermore the analyses in this
study are not thorough enough to make any conclusions on the role of PROX1 as a biomarker.
Methods:
- Please clarify how many authors performed the search and from what year studies were
screened.
- Please define what constitutes a "major article" for manually searching the reference lists.
- Why were studies only included if they showed a relationship between PROX1,
clinicopathologic characteristics, AND prognosis? Studies showing a relationship between
PROX1 and only clinicopathologic characteristics or only prognosis would also provide
valuable sample sizes to the analyses.
- Why were studies excluded if patients received adjuvant chemoradiation? This potentially
decreases clinical relevance and creates bias in patient selection, as chemoradiation is the
standard of care for GC across all stages.
- The authors mention the use of R software, then state that Stata was used for all analyses.
Please clarify, and also include the R version.
- The authors must describe the statistical method used to compare PROX1 expression in the
TCGA cohort, and whether the RNA-seq data was normalized. For reference, please see the
DESeq2 package in the Bioconductor software in R.
Results:
- Please include the supplement, I had a hard time judging some results without it. Additionally,
the authors should present a main table with each study's clinicopathologic variables summarized
in addition to gender (i.e. age, TNM stage) to be transparent of the homogeneity or heterogeneity
among the studies.
- The authors must describe how each study, including their own TCGA analysis, defined high/
low PROX1 expression. High heterogeneity in this definition may preclude the study's ability
to compare each study's results in meta-analysis. Although the authors correctly identify this
as a limitation in the discussion, they should transparently present the degree of heterogeneity
in the results.
- The authors should not suggest that individuals with high PROX1 expression had a shorter
OS as it was not significant.
- Please specify which sub-figure (a,c,e) corresponds to OS at 1,3,5 years
Discussion:
- As described above, the authors should not make any conclusions as to the relevance of PROX1
as a diagnostic or prognostic biomarker. On the contrary, the authors' own finding that PROX1
expression was highly associated with GC would support further investigation of PROX1 as a
biomarker.
- Several of the statements made about the findings or conclusions of the cited studies are
incorrect. For example, the statement "Laitinen A et al. reported 273 patients in total to indicate
the expression of PROX1 is negatively correlated with the depth of invasion, lymph node
metastasis and cancer stage by their study" is not supported by the figures (Fig 3, 4, 5). Also, the
authors write that Ueta and colleagues found that "PROX1 expression acts as a good prognostic
predictor for GC patients" in one sentence, then that Ueta and colleagues found that "PROX1
may be a bad promising prognostic biomarker" in the next sentence. I read the article cited and
failed to see where Ueta and colleagues thought PROX1 may be a bad prognostic biomarker.
- The authors claim that their meta-analysis reveals that PROX1 is not associated with overall
survival. However, almost all the studies included in their meta-analysis showed either a positive
or negative association with survival that was significant (Fig 8c, e). Further, a look at the
corresponding funnel plots (Fig 8d, f) reveals asymmetry. Therefore, I find it difficult to
believe that PROX1 has no association with survival, and the authors should attempt to explain
methodological differences between their included studies that give rise to opposite survival
associations.
- The authors should describe how and which data were derived from estimates of survival
curves.
Title: Lack of relationship between PROX1 expression and clinicopathological parameters and
prognosis in gastric cancer patients: a meta-analysis and TCGA analysis
Version: 1 Date: 27 Jan 2022
Reviewer's report:
I have carefully read the manuscript entitled "Lack of relationship between PROX1 expression
and clinicopathological parameters and prognosis in gastric cancer patients: a meta-analysis and
TCGA analysis" by Zu and colleagues. Negative studies like this one can contribute much value
to the literature, and I began reading the manuscript with great interest. However, there are
numerous omissions and inconsistencies in the methods and results, and the discussion requires
more explanation of the discrepancies in findings noted.
Specific comments:
Written English:
- The language throughout the manuscript requires significant editing for grammar and word
choice. Additionally, I found the presentation of the results section difficult to follow due to
inconsistent sentence structure and wording  to describe analogous results. One example is
"Meta-analysis showed that the expression of PROX1 has nothing to do with the presence
or absence of lymph node metastasis". The authors should take care to make such leaps in
reasoning, as a lack of significant difference does not equate to zero effect of PROX1.
Introduction:
- The authors claim that physical examination and gastroscopy have decreased the incidence of
GC and caused them to be diagnosed at higher stage, but highly-cited studies (PMID: 3189369)
have actually observed the opposite trend.
- In the introduction and throughout the paper, the authors discuss the need for a prognostic
biomarker to enable earlier diagnosis and prevention of GC. However, I fail to find any relevance
of the results in this study with diagnosis and prevention, and furthermore the analyses in this
study are not thorough enough to make any conclusions on the role of PROX1 as a biomarker.
Methods:
- Please clarify how many authors performed the search and from what year studies were
screened.
- Please define what constitutes a "major article" for manually searching the reference lists.
- Why were studies only included if they showed a relationship between PROX1,
clinicopathologic characteristics, AND prognosis? Studies showing a relationship between
PROX1 and only clinicopathologic characteristics or only prognosis would also provide
valuable sample sizes to the analyses.
- Why were studies excluded if patients received adjuvant chemoradiation? This potentially
decreases clinical relevance and creates bias in patient selection, as chemoradiation is the
standard of care for GC across all stages.
- The authors mention the use of R software, then state that Stata was used for all analyses.
Please clarify, and also include the R version.
- The authors must describe the statistical method used to compare PROX1 expression in the
TCGA cohort, and whether the RNA-seq data was normalized. For reference, please see the
DESeq2 package in the Bioconductor software in R.
Results:
- Please include the supplement, I had a hard time judging some results without it. Additionally,
the authors should present a main table with each study's clinicopathologic variables summarized
in addition to gender (i.e. age, TNM stage) to be transparent of the homogeneity or heterogeneity
among the studies.
- The authors must describe how each study, including their own TCGA analysis, defined high/
low PROX1 expression. High heterogeneity in this definition may preclude the study's ability
to compare each study's results in meta-analysis. Although the authors correctly identify this
as a limitation in the discussion, they should transparently present the degree of heterogeneity
in the results.
- The authors should not suggest that individuals with high PROX1 expression had a shorter
OS as it was not significant.
- Please specify which sub-figure (a,c,e) corresponds to OS at 1,3,5 years
Discussion:
- As described above, the authors should not make any conclusions as to the relevance of PROX1
as a diagnostic or prognostic biomarker. On the contrary, the authors' own finding that PROX1
expression was highly associated with GC would support further investigation of PROX1 as a
biomarker.
- Several of the statements made about the findings or conclusions of the cited studies are
incorrect. For example, the statement "Laitinen A et al. reported 273 patients in total to indicate
the expression of PROX1 is negatively correlated with the depth of invasion, lymph node
metastasis and cancer stage by their study" is not supported by the figures (Fig 3, 4, 5). Also, the
authors write that Ueta and colleagues found that "PROX1 expression acts as a good prognostic
predictor for GC patients" in one sentence, then that Ueta and colleagues found that "PROX1
may be a bad promising prognostic biomarker" in the next sentence. I read the article cited and
failed to see where Ueta and colleagues thought PROX1 may be a bad prognostic biomarker.
- The authors claim that their meta-analysis reveals that PROX1 is not associated with overall
survival. However, almost all the studies included in their meta-analysis showed either a positive
or negative association with survival that was significant (Fig 8c, e). Further, a look at the
corresponding funnel plots (Fig 8d, f) reveals asymmetry. Therefore, I find it difficult to
believe that PROX1 has no association with survival, and the authors should attempt to explain
methodological differences between their included studies that give rise to opposite survival
associations.
- The authors should describe how and which data were derived from estimates of survival
curves.
Please review this paper.
user
Title: Lack of relationship between PROX1 expression and clinicopathological parameters and
prognosis in gastric cancer patients: a meta-analysis and TCGA analysis
Version: 1 Date: 27 Jan 2022
Reviewer's report:
I have carefully read the manuscript entitled "Lack of relationship between PROX1 expression
and clinicopathological parameters and prognosis in gastric cancer patients: a meta-analysis and
TCGA analysis" by Zu and colleagues. Negative studies like this one can contribute much value
to the literature, and I began reading the manuscript with great interest. However, there are
numerous omissions and inconsistencies in the methods and results, and the discussion requires
more explanation of the discrepancies in findings noted.
Specific comments:
Written English:
- The language throughout the manuscript requires significant editing for grammar and word
choice. Additionally, I found the presentation of the results section difficult to follow due to
inconsistent sentence structure and wording  to describe analogous results. One example is
"Meta-analysis showed that the expression of PROX1 has nothing to do with the presence
or absence of lymph node metastasis". The authors should take care to make such leaps in
reasoning, as a lack of significant difference does not equate to zero effect of PROX1.
Introduction:
- The authors claim that physical examination and gastroscopy have decreased the incidence of
GC and caused them to be diagnosed at higher stage, but highly-cited studies (PMID: 3189369)
have actually observed the opposite trend.
- In the introduction and throughout the paper, the authors discuss the need for a prognostic
biomarker to enable earlier diagnosis and prevention of GC. However, I fail to find any relevance
of the results in this study with diagnosis and prevention, and furthermore the analyses in this
study are not thorough enough to make any conclusions on the role of PROX1 as a biomarker.
Methods:
- Please clarify how many authors performed the search and from what year studies were
screened.
- Please define what constitutes a "major article" for manually searching the reference lists.
- Why were studies only included if they showed a relationship between PROX1,
clinicopathologic characteristics, AND prognosis? Studies showing a relationship between
PROX1 and only clinicopathologic characteristics or only prognosis would also provide
valuable sample sizes to the analyses.
- Why were studies excluded if patients received adjuvant chemoradiation? This potentially
decreases clinical relevance and creates bias in patient selection, as chemoradiation is the
standard of care for GC across all stages.
- The authors mention the use of R software, then state that Stata was used for all analyses.
Please clarify, and also include the R version.
- The authors must describe the statistical method used to compare PROX1 expression in the
TCGA cohort, and whether the RNA-seq data was normalized. For reference, please see the
DESeq2 package in the Bioconductor software in R.
Results:
- Please include the supplement, I had a hard time judging some results without it. Additionally,
the authors should present a main table with each study's clinicopathologic variables summarized
in addition to gender (i.e. age, TNM stage) to be transparent of the homogeneity or heterogeneity
among the studies.
- The authors must describe how each study, including their own TCGA analysis, defined high/
low PROX1 expression. High heterogeneity in this definition may preclude the study's ability
to compare each study's results in meta-analysis. Although the authors correctly identify this
as a limitation in the discussion, they should transparently present the degree of heterogeneity
in the results.
- The authors should not suggest that individuals with high PROX1 expression had a shorter
OS as it was not significant.
- Please specify which sub-figure (a,c,e) corresponds to OS at 1,3,5 years
Discussion:
- As described above, the authors should not make any conclusions as to the relevance of PROX1
as a diagnostic or prognostic biomarker. On the contrary, the authors' own finding that PROX1
expression was highly associated with GC would support further investigation of PROX1 as a
biomarker.
- Several of the statements made about the findings or conclusions of the cited studies are
incorrect. For example, the statement "Laitinen A et al. reported 273 patients in total to indicate
the expression of PROX1 is negatively correlated with the depth of invasion, lymph node
metastasis and cancer stage by their study" is not supported by the figures (Fig 3, 4, 5). Also, the
authors write that Ueta and colleagues found that "PROX1 expression acts as a good prognostic
predictor for GC patients" in one sentence, then that Ueta and colleagues found that "PROX1
may be a bad promising prognostic biomarker" in the next sentence. I read the article cited and
failed to see where Ueta and colleagues thought PROX1 may be a bad prognostic biomarker.
- The authors claim that their meta-analysis reveals that PROX1 is not associated with overall
survival. However, almost all the studies included in their meta-analysis showed either a positive
or negative association with survival that was significant (Fig 8c, e). Further, a look at the
corresponding funnel plots (Fig 8d, f) reveals asymmetry. Therefore, I find it difficult to
believe that PROX1 has no association with survival, and the authors should attempt to explain
methodological differences between their included studies that give rise to opposite survival
associations.
- The authors should describe how and which data were derived from estimates of survival
curves.
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