Title: Metabolism-associated molecular classification of cervical cancer
Version: 1 Date: 15 Jul 2023
Reviewer's report:
Ref. to: Metabolism-associated molecular classi#cation of cervical cancer
In this study, Zhao et al identified metabolism-related genes in cervical squamous cell carcinoma
and endocervical adenocarcinoma (CESC) samples, which most of them contained related
mutations. Authors planned to evaluate a relationship between those mutations and prognosis
of CESC patients, which metabolic pathways were affected and how those genes’ expression
was regulated.
The manuscript contains interesting results but some details about the procedures and the
reasoning behind the experiment are missing. Also, there are some mistakes in text and figures
and the subtitles of the tables and figures were missing, making it harder to understand. In view
of this, I cannot draw any conclusions about the acceptance of the article yet.
Major issues:
(1) The main issue is that Figure titles and subtitles were missing. This impaired the
comprehension of the manuscript substantially.
(2) Some figures do not show what is reported in the text or they show it incompletely. It made
it confusing and harder to follow.
Also, some specific topics may be addressed:
(3) The manuscript reported 3620 genes related to metabolism in CESC, from which 2493 genes
harbored CESC-related mutations. Then, it is shown in Figure 1A, the top three genes with the
highest mutation frequency among other 10 genes.
I. How many CESC samples were analyzed in order to get those data?
II. What does the sentence “Altered in 202 (69.9%) of 289 samples” written above the Figure
1A mean? Is it related to the results presented? Subtitles would be very useful here.
(4) L134 – It was “analyzed the number of mutations in more than five samples”. How much is
“more than” five samples? Which criteria was used t define this amount of samples?
(5) L136 – Fifteen genes were found to be closely related to prognosis in patients with CESC.
Among them, four genes: KALRN, SLC18A2, ABCA8, and STK11.
I. It is not clear what is special about those genes. Why they were selected to be mentioned in
the text and showed in the Figure 1C.
II. Also, it is not clear, neither in the text nor in the figures (maybe because subtitles were
missing) which parameters were used for assessing CESC prognosis.
(6) It was reported three gene pairs were related to the prognosis of CESC as shown is Supp.
Table 2. But figure 1E shows an association of ABAC8 vs KALRN genes, which is confusing.
(7) Clinical stage was associated with metabolism-related TMB in endocervical
adenocarcinoma, but there were no association between TMB scores and CESC clinical stage
in general.
I. Considering that the number of samples for this type of tumor is smaller than the others, it is
important to mention how statistics were performed in those analysis.
II. Also, it was reported that FGL differed among various histological types, but figure 2B shows
data related to recurrence.
(8) L167 – “Additional analyses showed that 374 of these genes were significant for the
prognosis of patients with CESC”. Which analysis were those? How were they performed?
(9) It was reported that the expression levels of six genes were affected by their mutations (Figure
4B, Supplementary Table 9). However, figure 4B shows data of three genes only and the table
does not show gene expression data at all.
(10) For validation of those genes, it was performed an assay to evaluate the proliferative
capacity after KALRN-knockdown. Which type of proliferative assay was used? It could be
explained in Methods section. Also, which statistical analysis was performed and what is the
p value for these assays?
Minor issues
(1) The manuscript should be revised for an English native speaker.