FYB2 Is a Potential Prognostic Biomarker for Hepatocellular Carcinoma

Round 1

Reviewer 1 Report

It is a well organised study and I have no major comments.

I would suggest to the authors to explain better the reasons for choosing this biomarker (C1orf168) in hepatocellular carcinoma and their pathway-relationship.  

Author Response

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Reviewer 2 Report

 

Yifan Qu et al. investigates C1orf168 as a potential prognostic biomarker for liver hepatocellular carcinoma. Although the topic is very interesting and we need biomarkers for liver cancer, there are some concerns regarding the quality of the manuscript:

Introduction

In general, the Introduction is not well structured, but it does not provide a clearly defined AIM and the authors do not sufficiently explain the background for investigating C1orf168 in association with liver cancer.

The introduction should only contain background and study aims. However, study results are presented in the introduction.

Materials and Methods

The authors do not give a general presentation of the study design, setting, population and selection of samples. It is not clear how and where samples are selected and retrieved for the current study.

The authors provide an analysis plan, but they do not provide background and quality on the databases and datasets used. One example is data from the NCBI-GEO database (section 2.3). However, the database is not described for the readers. Other examples are GEPIA results (section 2.4, line 71) and “GSE115469 was used to retrieve the RDS dataset” (section 2.5, line 76). There is no description of the datasets mentioned.

In the “Discussion” the authors state that data was mainly retrieved from the GEO and TCGA databases. However, the TCGA database was not mentioned in “Materials and Methods”.

Results

Results are described without presenting the specific differences or significance levels. One example is section 3.1.

“It shows that C1orf168 is downregulated in tumor tissues when com-97 pared with normal tissues. Next, we specifically compared C1orf168 expression in 50 pairs 98 of LIHC tumor tissues and adjacent normal tissues. In addition, the lines between left and 99 right data points are drawn from the same case (Figure 2).”

They found a difference in expression levels, however, the difference measured and the significance level is not presented.

In general, figures should be described in further detail, including units, to enable interpretation of the results.

Discussion

The authors summarize their results with clear discussion of the findings. They do not discus their hypothesis on why C1orf168 is associated with impaired prognosis. And they do not discuss their resulst compared to other biomarkers.

Author Response

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Reviewer 3 Report

In this paper, the authors explored the hypothetical role of FYB2 in the prognosis of hepatocellular carcinoma (HCC). They observed that FYB2 was downregulated in HCC when compared to normal livers. Low expression of FYB2 was associated with poor prognosis and partially with the TNM staging system. By univariate and multivariate analysis the authors observed that FYB2 expression was associated with overall survival. GSEA analysis revealed that low FYB2 expression  was associated with enrichment of DNA replication genes, Hedgehog metabolism and ribosomes. Single cell and spatial transcriptomics confirmed that FYB2 is primarily expressed in normal hepatocytes although it can be found in other cell types in case of tumor.

This work is studded with multiple and crippling problems.

First, English is insufficient and it should be reviewed throughout.

Secondly, and more importantly the rationale of this study is difficult to grasp. There are 30 000 genes in human genome, several thousands of them are dysregulated in HCC either because they are instrumental or simply as innocent bystanders mapping in regions submitted to copy number variations. The choice of FYB2 as a candidate tumor suppressor is poorly supported by the explanations given by the authors.

FYB2 is located in 1p32 a region commonly affected by loss of material in HCC. The down regulation of FYB2 is most probably linked to such phenomenon also correlated with a more general genome instability usually associated with poor prognosis. In addition, according to GTex the first territory of expression is the liver. In case of tumor, several thousand of genes are downregulated in HCC simply because liver cancer cells get rid of gene expression useless for growth.

Major problems:

Title: Why using C1ORF168 while FYB2 is now the official name?

“Liver hepatocellular carcinoma” is pleonastic

Abstract:

What are hypertropia and syringomyelia?  What is the event that associates FYB2 and these diseases? Germline mutations?

What is the meaning of “genetic materials metabolism”? it is particularly vague and not quite supported later on in the text.

Material and methods:

What  is the meaning of “multiple mutation 1.5”? FYB2 is rarely mutated in HCC (3.8% in HCC according to COSMIC database)

The site used for prognosis analysis http://abren.net is a site using Mandarin ideograms. It is absolutely inacceptable as a source of information outside China.

Table 1: The 95%CI interval of FYB2 are not blindingly supporting its role as a prognostic marker in HCC. Especially multivariate analysis includes 1.0. meaning that in reality it is not significant.

Page 6: “Furthermore, we discovered…” This sentence is particularly meaningless. The upregulation in HCC is defined by comparison with healthy liver. By definition, there are no upregulated genes in healthy livers. It is the physiological levels.

Spatial transcriptomics observed that there is a higher expression of FYB2 in non-tumor tissue. This fact was already exposed earlier in the manuscript.

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Round 2

Reviewer 2 Report

The authors have done a major revision that has improved the quality of the manuscript.

I have a few comments:

Why do the authors abbreviate hepaticellular carcinome LIHC when usually it is abbreviated HCC?

In the 'Intrduction' section:

I suggest line 53-63 is removed to 'Methods' as the 'Introduction' should not contain description of the methods used in the study, but only background and aim.

In the 'Discussion' section:

I suggest the paragraph with 'Limitations' lines 287-293: 'Nevertheless....' to come after the paragraph with 'In addition...' lines 296-302.

References: Please revise so all references are citated with three authors and 'et al' 

At present references 11,14,16,18,21,24,25 and 26 mention more than three authors.

 

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Reviewer 3 Report

The authors modified extensively their manuscript to take into account my remarks.

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