Title: ncRNA-mediated SOX4 overexpression correlates with unfavorable outcomes and
immune infiltration in hepatocellular carcinoma
Version: 2 Date: 03 Oct 2023
Reviewer's report:
In their article, Li and colleagues analysed the correlation between SOX4 expression in HCC
and tumor immunity using data from The Cancer Genome Atlas and UALCAN databases.
Additionally, the authors correlate SOX4 expression, cancer immune characteristics, and
infiltrated immune cell gene marker sets in patients with HCC using data from the Tumor
Immune Estimation Resource, Gene Expression Profiling Interactive Analysis, and Tumor-
Immune System Interactions databases, together with an evaluation of SOX4 expression in HCC
tissues and the correlation of SOX4 expression with survival rate. Then, the authors identified
the MCM3AP-AS1/hsa-miR-204-5p axis as the most likely upstream ncRNA-related pathway
for SOX4 in HCC.
Despite it would be a quite interesting work that could possibly point out that ncRNA-mediated
upregulation of SOX4  correlates with the immune infiltration level and poor prognosis in HCC,
there several crucial points that need to be addressed and some clarified before the manuscript
can be further considered for publication.
- A first general concern focuses on the fact that there is no experimental validation for the
findings emerging from the in-silico bioinformatics analyses reported along the manuscript.
- Starting from Fig. 1, in particular panel B-F, it is clear that there is a difference in SOX4 mRNA
expression level between normal and tumor specimens. But what about protein expression level
in the same experimental condition?
- In Fig. 2 the authors confirm at gene expression level the over expression of SOX4, however
any experimental validation using SOX4 over expression or silencing has been conducted in the
cellular models available in the manuscript to further validate the in-silico findings. This is a
crucial aspect that need to be addressed.
- The same applies for the upstream regulation analyses showed in Fig. 7, that identified
mir-204-5p as the most regulatory SOX4 miRNA. Mimics and Antagomir experiments are
needed here before the authors could sustain their hypothesis. A similar experimental approach
is needed for the MCM3AP-AS1.
-  There are some typos within the text that need to be corrected.
Title: ncRNA-mediated SOX4 overexpression correlates with unfavorable outcomes and
immune infiltration in hepatocellular carcinoma
Version: 2 Date: 03 Oct 2023
Reviewer's report:
In their article, Li and colleagues analysed the correlation between SOX4 expression in HCC
and tumor immunity using data from The Cancer Genome Atlas and UALCAN databases.
Additionally, the authors correlate SOX4 expression, cancer immune characteristics, and
infiltrated immune cell gene marker sets in patients with HCC using data from the Tumor
Immune Estimation Resource, Gene Expression Profiling Interactive Analysis, and Tumor-
Immune System Interactions databases, together with an evaluation of SOX4 expression in HCC
tissues and the correlation of SOX4 expression with survival rate. Then, the authors identified
the MCM3AP-AS1/hsa-miR-204-5p axis as the most likely upstream ncRNA-related pathway
for SOX4 in HCC.
Despite it would be a quite interesting work that could possibly point out that ncRNA-mediated
upregulation of SOX4  correlates with the immune infiltration level and poor prognosis in HCC,
there several crucial points that need to be addressed and some clarified before the manuscript
can be further considered for publication.
- A first general concern focuses on the fact that there is no experimental validation for the
findings emerging from the in-silico bioinformatics analyses reported along the manuscript.
- Starting from Fig. 1, in particular panel B-F, it is clear that there is a difference in SOX4 mRNA
expression level between normal and tumor specimens. But what about protein expression level
in the same experimental condition?
- In Fig. 2 the authors confirm at gene expression level the over expression of SOX4, however
any experimental validation using SOX4 over expression or silencing has been conducted in the
cellular models available in the manuscript to further validate the in-silico findings. This is a
crucial aspect that need to be addressed.
- The same applies for the upstream regulation analyses showed in Fig. 7, that identified
mir-204-5p as the most regulatory SOX4 miRNA. Mimics and Antagomir experiments are
needed here before the authors could sustain their hypothesis. A similar experimental approach
is needed for the MCM3AP-AS1.
-  There are some typos within the text that need to be corrected.
Please review this paper.
user
Title: ncRNA-mediated SOX4 overexpression correlates with unfavorable outcomes and
immune infiltration in hepatocellular carcinoma
Version: 2 Date: 03 Oct 2023
Reviewer's report:
In their article, Li and colleagues analysed the correlation between SOX4 expression in HCC
and tumor immunity using data from The Cancer Genome Atlas and UALCAN databases.
Additionally, the authors correlate SOX4 expression, cancer immune characteristics, and
infiltrated immune cell gene marker sets in patients with HCC using data from the Tumor
Immune Estimation Resource, Gene Expression Profiling Interactive Analysis, and Tumor-
Immune System Interactions databases, together with an evaluation of SOX4 expression in HCC
tissues and the correlation of SOX4 expression with survival rate. Then, the authors identified
the MCM3AP-AS1/hsa-miR-204-5p axis as the most likely upstream ncRNA-related pathway
for SOX4 in HCC.
Despite it would be a quite interesting work that could possibly point out that ncRNA-mediated
upregulation of SOX4  correlates with the immune infiltration level and poor prognosis in HCC,
there several crucial points that need to be addressed and some clarified before the manuscript
can be further considered for publication.
- A first general concern focuses on the fact that there is no experimental validation for the
findings emerging from the in-silico bioinformatics analyses reported along the manuscript.
- Starting from Fig. 1, in particular panel B-F, it is clear that there is a difference in SOX4 mRNA
expression level between normal and tumor specimens. But what about protein expression level
in the same experimental condition?
- In Fig. 2 the authors confirm at gene expression level the over expression of SOX4, however
any experimental validation using SOX4 over expression or silencing has been conducted in the
cellular models available in the manuscript to further validate the in-silico findings. This is a
crucial aspect that need to be addressed.
- The same applies for the upstream regulation analyses showed in Fig. 7, that identified
mir-204-5p as the most regulatory SOX4 miRNA. Mimics and Antagomir experiments are
needed here before the authors could sustain their hypothesis. A similar experimental approach
is needed for the MCM3AP-AS1.
-  There are some typos within the text that need to be corrected.
assistant