Review Reports - Integrative Analyses of Mitophagy-Related Genes and Mechanisms Associated with Type 2 Diabetes in Muscle Tissue

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

I could not find any tables or supplementary data in the attached file (only one PDF was provided). As a result, I was unable to conduct a comprehensive review of the article. However, I believe this study is crucial for understanding the impact of mitophagy on Type 2 Diabetes. I have provided some comments to the best of my ability, and I strongly request the authors to revise their manuscript in accordance with these comments and include the necessary tables and supplementary data in the revised submission.

Major comments:

1. Include the necessary tables and supplementary data in the revised submission.

2. In the introduction, the authors state, “Glucose homeostasis depends on mitochondria (MT), suggesting that MT is involved in DM[5].” However, this explanation lacks sufficient detail. It is necessary to provide a more comprehensive overview of the established knowledge regarding glucose homeostasis and mitochondrial function.

3. The author should provide an explanation of mitophagy in the introduction to fit the title. This would help clarify the focus on mitophagy, as it may be challenging for readers to understand the reason for this emphasis.

4. It unusual that many cited results do not include references as follow. Please ensure that all necessary references are included throughout the article.

In the introduction:

Mitochondria are essential double-membrane cellular organelles involved in multiple important processes, including energy supply, metabolism, redox homeostasis, cell differentiation, and ion homeostasis, and they are thus the main regulators of both the life and death of cells. They constantly generate reactive oxygen species (ROS), highly reactive derivatives of molecular oxygen that act as cell signaling molecules in multiple regulatory processes involved in cell survival, mitochondrial function, and insulin sensitivity.

In the discussion:

a) Interferon-gamma (IFN)-γ is a multifunctional cytokine, which can regulate the balance between T helper 1 and T helper 2 cells, and regulate cell proliferation and apoptosis. IFN-γ is produced by T cells, natural killer cells, natural killer T cells, and antigen-presenting cells such as macrophages, den-dritic cells, and the Be-1 and CD11ahiFcγRIIIhi subsets of B cells.

b) Previous studies have shown that NF-κB, MAPK, STAT these pathways could lead to islet β-cell apoptosis which accelerating the development of T2D.

c) Signal transduction initiated by Toll-like receptor-4 ( TLR4 ) and tumor necrosis factor-α ( TNF-α) receptors leads to activation of the NFkB pathway, which is associated with reduced mitochondrial respiration and inhibition of activation of transcription regulators that pro-mote mitochondrial biosynthesis. The others, have also previously demonstrated that obesity in rodents and chronic oversupply of metabolic fuel to skeletal muscle cells in vitro is associated with an increase in proinflammatory NFkB signalling and insulin resistance.

5. This article examines mitophagy-related genes in the muscle tissue of T2D pt. It is recommended that the author include this specific focus in the title.

Minor comments:

1. In the abstract, “IR” should be written in full name rather than as an abbreviation. On page 2, “GEO” should be written in full name at the first time.

2. Please correct the font in the figure legend.

Author Response

Comments and Suggestions for Authors

We greatly appreciate your help and concerning improvement to this paper. Supplementary data has been uploaded this time.

Major comments:

Include the necessary tables and supplementary data in the revised submission.

Thanks a lot.It has been revised.

In the introduction, the authors state, “Glucose homeostasis depends on mitochondria (MT), suggesting that MT is involved in DM[5].” However, this explanation lacks sufficient detail. It is necessary to provide a more comprehensive overview of the established knowledge regarding glucose homeostasis and mitochondrial function.

We appreciate your attention to this part. A more comprehensive overview of the established knowledge regarding glucose homeostasis and mitochondrial function have been added in references 7.

The author should provide an explanation of mitophagy in the introduction to fit the title. This would help clarify the focus on mitophagy, as it may be challenging for readers to understand the reason for this emphasis.

Thank you for your positive comments. It has been added in references 8.

It unusual that many cited results do not include references as follow. Please ensure that all necessary references are included throughout the article.

In the introduction:

In the discussion:

a) Interferon-gamma (IFN)-γ is a multifunctional cytokine, which can regulate the balance between T helper 1 and T helper 2 cells, and regulate cell proliferation and apoptosis.IFN-γ is produced by T cells, natural killer cells, natural killer T cells, and antigen-presenting cells such as macrophages, den-dritic cells, and the Be-1 and CD11ahiFcγRIIIhi subsets of B cells.
b) Previous studies have shown that NF-κB, MAPK, STAT these pathways could lead to islet β-cell apoptosis which accelerating the development of T2D.
c) Signal transduction initiated by Toll-like receptor-4 ( TLR4 ) and tumor necrosis factor-α ( TNF-α) receptors leads to activation of the NFkB pathway, which is associated with reduced mitochondrial respiration and inhibition of activation of transcription regulators that pro-mote mitochondrial biosynthesis. The others, have also previously demonstrated that obesity in rodents and chronic oversupply of metabolic fuel to skeletal muscle cells in vitro is associated with an increase in proinflammatory NFkB signalling and insulin resistance.

All of these references have been added.

5.This article examines mitophagy-related genes in the muscle tissue of T2D pt. It is recommended that the author include this specific focus in the title.

We appreciate your attention to the mistake. I have changed the title for "Integrative analyses of mitophagy-related genes and mechanisms associated with type 2 diabetes in the muscle tissue" to suit this article.

Minor comments:

In the abstract, “IR” should be written in full name rather than as an abbreviation. On page 2, “GEO” should be written in full name at the first time.
Please correct the font in the figure legend.

All of these have been revised. Thanks.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The research article by Wangjia Mao et al. discussed about the role of mitochondrial damage and autophagy-related genes in T2D. Using enriched bioinformatic tools (GO, KEGG, and GSE, etc.,) the author demonstrated how the expression of mitophagy-related genes changes in the T2D diagnostic model. There are a couple of minor comments that need to be addressed. Some of the individual issues are listed below.

Comments:

Abstract- missing information about the MRHGs genes. Needs to be clearer.

Discussion- It’s difficult to follow the interpretation, so please be more specific and clearer. For a better understanding of the journal's larger audience

Missing supplementary information in the manuscript file.

Line numbers are missing throughout the manuscript.

Author Response

Comments and Suggestions for Authors

Comments:

Abstract- missing information about the MRHGs genes. Needs to be clearer.

Discussion- It’s difficult to follow the interpretation, so please be more specific and clearer. For a better understanding of the journal's larger audience

Missing supplementary information in the manuscript file.

Line numbers are missing throughout the manuscript.

We greatly appreciate your help and concerning improvement to this paper and we have corrected.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

Please refer to the comments below:

1. Please include the data from following supplementary figures into the main manuscript:

Study design (Supp. 1)

Merger of T2D datasets (Supp. 2)

Differential expression of 10 pathways between T2D and control groups from GSVA study (Supp. 3B)

Supp. Fig 5A and 5B

Supp. Fig. 6A and 6B

2. In materials and methods, subsection 1, the authors refer to "Table 1", but there is no table 1 in the manuscript. If it is supplementary table 1, please include it in the main manuscript since it is important to know the information about the datasets.

3. In results, subsection 1, the authors are requested to change the description from "27 downregulated genes" to "27 upregulated genes", since the parentheses say "logFC > 0".

4. For fig.1, panel A and fig. 5, panel A, could the authors highlight the MRDEGs on the volcano plot?

5. Figure legend for fig. 1 says Wayne diagram. Please correct it to Venn diagram.

6. Figure 6, panel B is not readable. Please make the figure bigger.

The authors have correctly addressed the limitations of this study. This reviewer would like to congratulate the authors for the work in this manuscript while being aware of the shortcomings of the study.

Author Response

Comments and Suggestions for Authors

Please refer to the comments below:

1. Please include the data from following supplementary figures into the main manuscript:

Study design (Supp. 1)

Merger of T2D datasets (Supp. 2)

Differential expression of 10 pathways between T2D and control groups from GSVA study (Supp. 3B)

Supp. Fig 5A and 5B

Supp. Fig. 6A and 6B

We appreciate your attention to the mistake.New supplementary figures haved been uploaded.

3. In results, subsection 1, the authors are requested to change the description from "27 downregulated genes" to "27 upregulated genes", since the parentheses say "logFC > 0".

Your are right,so it has been changed.

4. For fig.1, panel A and fig. 5, panel A, could the authors highlight the MRDEGs on the volcano plot?

Thank you for your positive comments. We are very sorry that these have been highlight in orange and green.

5. Figure legend for fig. 1 says Wayne diagram. Please correct it to Venn diagram.

Thank you for your positive comments. It has been revised.

6. Figure 6, panel B is not readable. Please make the figure bigger.

I'soory that due to the whole picture is larger, it becomes smaller after shrinking.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

The revised version of the manuscript is significantly improved. The figures are clear, and the results are appropriately discussed. In my opinion, it is now sufficiently convincing.