Title: Molecular subtyping based on TRP family and prognostic assessment for TRP-associated
lncRNAs in pancreatic adenocarcinoma
Version: 2 Date: 23 Aug 2022
Reviewer's report:
The manuscript entitled “TRP-associated lncRNAs exert crucial functions in prognosis and
immune microenvironment of pancreatic cancer: a bioinformatic analysis and experimental
verification” addresses bioinformatic methods of analyzing the implications of TRP-related
lncRNAs to pancreatic cancer prognosis. The objective of the study is original and important
for the field, however I found that some important issues have to be addressed.
Major comments:
1. The introduction should be related to pancreatic cancer, as several groups reported results
about the expression and the function of TRP channels, including bioinformatic tools used for
analysis. Please provide information about these papers and critically discuss their results in the
discussion section.
2. The manuscript lacks precision in describing the results. When TRP-associated lncRNAs are
mentioned, it is not clear which lNcRNAs with which TRP channels are associated. Specific
TRP genes should me mentioned at least for the most important results.  If there are 28 TRP
genes and 345 TRP-associated lncRNAs there must be some TRP genes that are associated with
more than one lnc-RNA. Please provide the information about these genes.
3. Please name at least the most important TRP genes in each of the clusters (A, B, C) and how
they are linked to the tumorigenic process.
3. It is not clear whether the indicated lncRNAs overexpressed in PC cell lines are related to
TRP genes. Please provide information about TRP genes expressed in these cell lines. Can you
prove that in cell cultures those TRP channels are related to these specific lncRNAs?
4. The title states that some TRP-associated lncRNAs exert crucial function in immune
microenviroment. I think that this relation is overestimated and should not be mentioned in
the title. While correlation between tumor-infiltrating immune cells to clinical outcomes in
pancreatic cancer is already reported in other studies, the present analysis fails to present a direct
relationship between these items: immune cells, PC, lncRNs and TRP channels.
Minor comments:
1. Number of samples (PATIENTS) extracted from TCGA with TRP expression.
2. The cell lines should be grown in the same culture media (RPMI or DMEM) because the
expression of TRP proteins depend on these growing conditions.
3. CNV should be defined.
4. It is not clear from the results whether the PC prognosis is correlated with mutation in TRP
genes or the expression of TRP genes. Please clarify.
5. The resolution of figures should be improved.
Title: Molecular subtyping based on TRP family and prognostic assessment for TRP-associated
lncRNAs in pancreatic adenocarcinoma
Version: 2 Date: 23 Aug 2022
Reviewer's report:
The manuscript entitled “TRP-associated lncRNAs exert crucial functions in prognosis and
immune microenvironment of pancreatic cancer: a bioinformatic analysis and experimental
verification” addresses bioinformatic methods of analyzing the implications of TRP-related
lncRNAs to pancreatic cancer prognosis. The objective of the study is original and important
for the field, however I found that some important issues have to be addressed.
Major comments:
1. The introduction should be related to pancreatic cancer, as several groups reported results
about the expression and the function of TRP channels, including bioinformatic tools used for
analysis. Please provide information about these papers and critically discuss their results in the
discussion section.
2. The manuscript lacks precision in describing the results. When TRP-associated lncRNAs are
mentioned, it is not clear which lNcRNAs with which TRP channels are associated. Specific
TRP genes should me mentioned at least for the most important results.  If there are 28 TRP
genes and 345 TRP-associated lncRNAs there must be some TRP genes that are associated with
more than one lnc-RNA. Please provide the information about these genes.
3. Please name at least the most important TRP genes in each of the clusters (A, B, C) and how
they are linked to the tumorigenic process.
3. It is not clear whether the indicated lncRNAs overexpressed in PC cell lines are related to
TRP genes. Please provide information about TRP genes expressed in these cell lines. Can you
prove that in cell cultures those TRP channels are related to these specific lncRNAs?
4. The title states that some TRP-associated lncRNAs exert crucial function in immune
microenviroment. I think that this relation is overestimated and should not be mentioned in
the title. While correlation between tumor-infiltrating immune cells to clinical outcomes in
pancreatic cancer is already reported in other studies, the present analysis fails to present a direct
relationship between these items: immune cells, PC, lncRNs and TRP channels.
Minor comments:
1. Number of samples (PATIENTS) extracted from TCGA with TRP expression.
2. The cell lines should be grown in the same culture media (RPMI or DMEM) because the
expression of TRP proteins depend on these growing conditions.
3. CNV should be defined.
4. It is not clear from the results whether the PC prognosis is correlated with mutation in TRP
genes or the expression of TRP genes. Please clarify.
5. The resolution of figures should be improved.
Please review this paper.
user
Title: Molecular subtyping based on TRP family and prognostic assessment for TRP-associated
lncRNAs in pancreatic adenocarcinoma
Version: 2 Date: 23 Aug 2022
Reviewer's report:
The manuscript entitled “TRP-associated lncRNAs exert crucial functions in prognosis and
immune microenvironment of pancreatic cancer: a bioinformatic analysis and experimental
verification” addresses bioinformatic methods of analyzing the implications of TRP-related
lncRNAs to pancreatic cancer prognosis. The objective of the study is original and important
for the field, however I found that some important issues have to be addressed.
Major comments:
1. The introduction should be related to pancreatic cancer, as several groups reported results
about the expression and the function of TRP channels, including bioinformatic tools used for
analysis. Please provide information about these papers and critically discuss their results in the
discussion section.
2. The manuscript lacks precision in describing the results. When TRP-associated lncRNAs are
mentioned, it is not clear which lNcRNAs with which TRP channels are associated. Specific
TRP genes should me mentioned at least for the most important results.  If there are 28 TRP
genes and 345 TRP-associated lncRNAs there must be some TRP genes that are associated with
more than one lnc-RNA. Please provide the information about these genes.
3. Please name at least the most important TRP genes in each of the clusters (A, B, C) and how
they are linked to the tumorigenic process.
3. It is not clear whether the indicated lncRNAs overexpressed in PC cell lines are related to
TRP genes. Please provide information about TRP genes expressed in these cell lines. Can you
prove that in cell cultures those TRP channels are related to these specific lncRNAs?
4. The title states that some TRP-associated lncRNAs exert crucial function in immune
microenviroment. I think that this relation is overestimated and should not be mentioned in
the title. While correlation between tumor-infiltrating immune cells to clinical outcomes in
pancreatic cancer is already reported in other studies, the present analysis fails to present a direct
relationship between these items: immune cells, PC, lncRNs and TRP channels.
Minor comments:
1. Number of samples (PATIENTS) extracted from TCGA with TRP expression.
2. The cell lines should be grown in the same culture media (RPMI or DMEM) because the
expression of TRP proteins depend on these growing conditions.
3. CNV should be defined.
4. It is not clear from the results whether the PC prognosis is correlated with mutation in TRP
genes or the expression of TRP genes. Please clarify.
5. The resolution of figures should be improved.
assistant