Title: Establishment and validation of a hypoxia-related signature predicting prognosis in
hepatocellular carcinoma
Version: 0 Date: 07 Oct 2021
Reviewer's report:
Cai et al. presented an interesting manuscript, elucidating the possible role of hypoxia in
HCC development and its prognosis. The most innovative and important result showed is the
establishment of a risk prognostic model for HCC, which could be used in the practice of
immunotherapy.
However, some concerns have to be addressed to be considered for publication.
1- The training and validation cohorts are significantly different for age and tumor stage. This
could affect the results of their association analyses between hypoxia and clinical information (in
particular stage stratification) and the K-M survival curves. Similarly, the association between
the 3 hypoxia genes’ expression level and stage stratification is weak and showing a different
trend between the two databases (fig. 4), especially for UGP2.
2- In the “Background” section, the Authors have probably erroneously indicated reference 9
since the cited review on HCC biomarkers does not consider the hypoxia topic.
3- Could the Authors explain how the 50 genes with the higher degree of interaction have been
identified to have an important role in hypoxia process of HCC or reported references for this
statement?
4- How were selected the 3 genes (ENO1, UGP2, TPI1) for the construction of the prognostic
model? Two of them were not even among the 8 genes analyzed in LASSO by the Authors.
5- The Confidence Interval (CI) of UGP2 showed in the forest plot cross the HR of 1. If the IC
includes 1, then the hazard ratio is not significant.
6- In Chapter 2.7 of “Results”, in contrast to what the Authors affirm, T cells regulatory are not
suppressed in patients with higher hypoxia in both groups.
7- Among the popular immune checkpoint genes (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC7284108/) why and how the Authors selected CTLA-4, TIM-3,
and LAG-3? Why they did not analyze PD1/PD-L1 which is reported in the
latest phase I/II studies (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821931/ https://
www.frontiersin.org/articles/10.3389/fonc.2020.601240/full)?
Minor revision:
1- Please check the gene nomenclature of TPI1. In “Result” section is called TPL1, while in
“Discussion” is TPI1.
2- In the “Results” section, the Authors refer to Data S1 for hypoxia-related genes’ details, but
it is only a list of the 200 gene names.
3- AUC curves 0.7-0.8 can be considered acceptable not good predictive. The AUC for
3- and 5- years OS in the verification cohort is <0.7, which is considered poor (https://
doi.org/10.1002/9781118548387.ch5).
4- In the “Discussion” section, the Authors could consider to use other references than 19. (doi:
10.2147/CMAR.S182183  DOI: 10.18632/oncotarget.7649).
5- To explain the TPI1 paradox the Authors could compare their data with more studies (such
as https://doi.org/10.3892/ijo_00000058).
Title: Establishment and validation of a hypoxia-related signature predicting prognosis in
hepatocellular carcinoma
Version: 0 Date: 07 Oct 2021
Reviewer's report:
Cai et al. presented an interesting manuscript, elucidating the possible role of hypoxia in
HCC development and its prognosis. The most innovative and important result showed is the
establishment of a risk prognostic model for HCC, which could be used in the practice of
immunotherapy.
However, some concerns have to be addressed to be considered for publication.
1- The training and validation cohorts are significantly different for age and tumor stage. This
could affect the results of their association analyses between hypoxia and clinical information (in
particular stage stratification) and the K-M survival curves. Similarly, the association between
the 3 hypoxia genes’ expression level and stage stratification is weak and showing a different
trend between the two databases (fig. 4), especially for UGP2.
2- In the “Background” section, the Authors have probably erroneously indicated reference 9
since the cited review on HCC biomarkers does not consider the hypoxia topic.
3- Could the Authors explain how the 50 genes with the higher degree of interaction have been
identified to have an important role in hypoxia process of HCC or reported references for this
statement?
4- How were selected the 3 genes (ENO1, UGP2, TPI1) for the construction of the prognostic
model? Two of them were not even among the 8 genes analyzed in LASSO by the Authors.
5- The Confidence Interval (CI) of UGP2 showed in the forest plot cross the HR of 1. If the IC
includes 1, then the hazard ratio is not significant.
6- In Chapter 2.7 of “Results”, in contrast to what the Authors affirm, T cells regulatory are not
suppressed in patients with higher hypoxia in both groups.
7- Among the popular immune checkpoint genes (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC7284108/) why and how the Authors selected CTLA-4, TIM-3,
and LAG-3? Why they did not analyze PD1/PD-L1 which is reported in the
latest phase I/II studies (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821931/ https://
www.frontiersin.org/articles/10.3389/fonc.2020.601240/full)?
Minor revision:
1- Please check the gene nomenclature of TPI1. In “Result” section is called TPL1, while in
“Discussion” is TPI1.
2- In the “Results” section, the Authors refer to Data S1 for hypoxia-related genes’ details, but
it is only a list of the 200 gene names.
3- AUC curves 0.7-0.8 can be considered acceptable not good predictive. The AUC for
3- and 5- years OS in the verification cohort is <0.7, which is considered poor (https://
doi.org/10.1002/9781118548387.ch5).
4- In the “Discussion” section, the Authors could consider to use other references than 19. (doi:
10.2147/CMAR.S182183  DOI: 10.18632/oncotarget.7649).
5- To explain the TPI1 paradox the Authors could compare their data with more studies (such
as https://doi.org/10.3892/ijo_00000058).
Please review this paper.
user
Title: Establishment and validation of a hypoxia-related signature predicting prognosis in
hepatocellular carcinoma
Version: 0 Date: 07 Oct 2021
Reviewer's report:
Cai et al. presented an interesting manuscript, elucidating the possible role of hypoxia in
HCC development and its prognosis. The most innovative and important result showed is the
establishment of a risk prognostic model for HCC, which could be used in the practice of
immunotherapy.
However, some concerns have to be addressed to be considered for publication.
1- The training and validation cohorts are significantly different for age and tumor stage. This
could affect the results of their association analyses between hypoxia and clinical information (in
particular stage stratification) and the K-M survival curves. Similarly, the association between
the 3 hypoxia genes’ expression level and stage stratification is weak and showing a different
trend between the two databases (fig. 4), especially for UGP2.
2- In the “Background” section, the Authors have probably erroneously indicated reference 9
since the cited review on HCC biomarkers does not consider the hypoxia topic.
3- Could the Authors explain how the 50 genes with the higher degree of interaction have been
identified to have an important role in hypoxia process of HCC or reported references for this
statement?
4- How were selected the 3 genes (ENO1, UGP2, TPI1) for the construction of the prognostic
model? Two of them were not even among the 8 genes analyzed in LASSO by the Authors.
5- The Confidence Interval (CI) of UGP2 showed in the forest plot cross the HR of 1. If the IC
includes 1, then the hazard ratio is not significant.
6- In Chapter 2.7 of “Results”, in contrast to what the Authors affirm, T cells regulatory are not
suppressed in patients with higher hypoxia in both groups.
7- Among the popular immune checkpoint genes (https://www.ncbi.nlm.nih.gov/
pmc/articles/PMC7284108/) why and how the Authors selected CTLA-4, TIM-3,
and LAG-3? Why they did not analyze PD1/PD-L1 which is reported in the
latest phase I/II studies (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821931/ https://
www.frontiersin.org/articles/10.3389/fonc.2020.601240/full)?
Minor revision:
1- Please check the gene nomenclature of TPI1. In “Result” section is called TPL1, while in
“Discussion” is TPI1.
2- In the “Results” section, the Authors refer to Data S1 for hypoxia-related genes’ details, but
it is only a list of the 200 gene names.
3- AUC curves 0.7-0.8 can be considered acceptable not good predictive. The AUC for
3- and 5- years OS in the verification cohort is <0.7, which is considered poor (https://
doi.org/10.1002/9781118548387.ch5).
4- In the “Discussion” section, the Authors could consider to use other references than 19. (doi:
10.2147/CMAR.S182183  DOI: 10.18632/oncotarget.7649).
5- To explain the TPI1 paradox the Authors could compare their data with more studies (such
as https://doi.org/10.3892/ijo_00000058).
assistant