In Silico Bioinformatics Analysis on the Role of Long Non-Coding RNAs as Drivers and Gatekeepers of Androgen-Independent Prostate Cancer Using LNCaP and PC-3 Cells

Round 1

Reviewer 1 Report

The authors study long non-coding RNA sequences in cellular models.

The manuscript has many criticisms that suggest immediate rejection.

Here are some key points:

1) It is not clear what "in silico" in the title refers to. The reported study appears to be an "in vitro" study. Where is the computational analysis?

2) The authors study lncRNAs in cellular models purchased from ATCC. Why is this? These cell lines are immortalized, it is not serious to use these cell lines for oncological studies. It would have been more correct to isolate primary cells from patients and characterize lncRNAs in these cellular models.

3) The figures are unclear. In Figure 1, the authors report "fold change" but neither SD (standard deviation) nor SEM (standard error of the mean). It is also not clear whether these different fold changes are significant. What data are shown in Figure 2? To whom do the different fold changes refer? Is it a repeat of the data shown in Figure 1?

4) The statistical analysis is missing or not very detailed.

5) Finally, the whole manuscript is descriptive. No hypothesis about the mechanism of action or possible therapeutic strategies is discussed.

Minor editing of English language required

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

This study aimed to profile the aberrantly expressed lncRNAs in androgen-dependent (LNCaP) PCa compared to androgen-independent (PC-3) PCa cells.

Understanding lncRNAs as competitive endogenous RNA molecules and their interactions with miRNAs may aid in the identification of novel prognostic PCa biomarkers and therapeutic targets. Therefore, the research topic is undoubtedly relevant.

There is little material in this area of research, so any research complements the information field. In particular, the authors using bioinformatics analysis showed the involvement of differentially expressed lncRNAs in oncogenic pathways. Some lncRNAs undergo hypermethylation, others are encapsulated by exosomes while others interact with several microRNAs (miRNAs), favoring tumorigenic pathways. Notably, TERC lncRNA was shown to sponge tumour-suppressor miRNAs hsa-miR-4429 and hsa-miR-320b. This interaction in turn activates TGF-β-signalling and ECM-receptor interaction pathways, favoring the progression of PCa.

The drawings are of very poor quality, I noted this in my review in detail.

In general, I liked the article, the material is logically and consistently presented, but there are many minor comments on the drawings:

1. In figure 1a, KRT81 and all other lncRNAs should be followed separately, since the scale varies greatly and the figure is not informative. Similar to Figure 1b - the first three lncRNAs should be a separate pattern.

2. The color scale in Figure 2 is not informative, the differences in this quality are not visible, it needs to be redone.

3. The inscriptions in Figure 3a, b are unreadable, very small, you need to change the font size.

4. In figure 4, it is also necessary to separate diagrams with different scales and make fig. 4a, b, c, etc.

5. In figure 5, even at high magnification, it is not possible to read the inscriptions.

6. On the bar charts, except for Figure 7, there are no "whisker" variation intervals to be added.

Author Response

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Reviewer 3 Report

Dear authors,

After the review process, I have several comments: part of the figure should be as a supplementary file, like figure 6; in discussions, you should include more comments related to the applications of computational procedures such as molecular docking, virtual high-throughput screening, molecular dynamic (MD) simulation, quantum-mechanical methods for drug design. 

Best regards!

Author Response

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Author Response File: Author Response.pdf

Reviewer 4 Report

An attractive, well-prepared, and carefully prepared manuscript on the role of lncRNA in prostate cancer.

Below are some minor comments:

1. I ask authors to check that all abbreviations are explained when they are first used,

2. the introduction, materials, and methods are clearly described - I have no criticisms here.

3. results - I have only a minor remark: the figures are of poor quality.

4. Discussion:

a. please describe the limitations of the study,

b. please briefly describe the future directions of research - I propose to describe the role of TERC lncRNAs exposed by EVs in the modulation of carcinogenesis using these publications:

doi: 10.3390/cells11182913.

doi: 10.3390/ijms22042227.

Author Response

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Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

I'm sorry, but the authors have not responded to the criticisms raised. In fact, the answers given are incomplete and meaningless. Of course, everyone knows that ATCC is an authoritative source of cell lines, but in my opinion, other types of cell lines should be used for their study. Also, since I didn't change the title, I think the authors don't understand the meaning of the word "in silico". I confirm my previous verdict, rejection!

Minor editing of English language required

Reviewer 4 Report

The authors have addressed all my questions and concerns.