Palmitoylation in Renal Physiology and Pathology

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Palmitoylation in Renal Physiology and Pathology by Jingru Ma, Zhen Zhang, Jiaqi Guo, Hu Cai, Jian Yao, Dahai Yang, Huiyuan Zhu, Haijing Liu, Changhe Wang and Hongbo Xu.

This review is timely, balanced, and provides important insights.

I ask the authors to collect all therapeutic avenues that involve palmitoylation and all modifications (positive or negative) of other therapies, which are related to palmitoylation in kidney disease, in a table or figure. Right now, they are spread over the text and are not easy to find and evaluate.

Author Response

Comments 1: I ask the authors to collect all therapeutic avenues that involve palmitoylation and all modifications (positive or negative) of other therapies, which are related to palmitoylation in kidney disease, in a table or figure. Right now, they are spread over the text and are not easy to find and evaluate.

Response 1: Thank you for your valuable comments. We have summarized the table 3 related to therapeutic avenues that involve palmitoylation in kidney disease at the end of Section 4, "The Role of Palmitoylation in Renal Pathophysiology," as Table 3 (Line 492-513).

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The review is well structured, comprehensive, and informative. The authors organize the manuscript into clearly defined sections, including Introduction, Reaction and Regulatory Mechanisms of Palmitoylation, Palmitoylated Proteins in the Kidney, The Role of Palmitoylation in Renal Pathophysiology, Techniques for Detecting Protein Palmitoylation, Research Strategies for Palmitoylation, and Conclusion. This logical structure facilitates a clear understanding of the topic, from basic biochemical mechanisms to their physiological and pathological relevance in the kidney. The figures presented in the article are illustrative and well designed, effectively supporting the explanations provided in the text.

I have only minor comments regarding the manuscript. The numbering of the figures in the text appears to be incorrect. Figure 2 is not cited in the text, and the figure referred to as Figure 2 actually corresponds to Figure 3. Figure 3 should be renumbered as Figure 4 and should be appropriately referenced in the text. Therefore, the figure numbering should be carefully revised and adjusted throughout the manuscript.

The phrase “Error! Reference source not found.” (Line 78) appears in the manuscript, indicating a missing or broken reference that should be corrected.

Author Response

Comments 1: The numbering of the figures in the text appears to be incorrect. Figure 2 is not cited in the text, and the figure referred to as Figure 2 actually corresponds to Figure 3. Figure 3 should be renumbered as Figure 4 and should be appropriately referenced in the text. Therefore, the figure numbering should be carefully revised and adjusted throughout the manuscript.

Response 1: Thank you for your valuable comments. We have carefully reviewed the captions of all figures and corrected the figure numbers to ensure they correspond correctly.

Comments 2: The phrase “Error! Reference source not found.” (Line 78) appears in the manuscript, indicating a missing or broken reference that should be corrected.

Response 2: Thank you for your valuable comments. We have recited Figure 2 (Line 81).

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

The review covers the role of palmitoylation in kidney physiology and disease. The manuscript gathers many recent studies and provides a broad overview of enzymes, signaling pathways, specific proteins, and detection methods. The topic is valuable and relevant. The schematic figures are well-designed and usefull. However, the paper needs substantial revision before it is ready for publication. My major comments are as follows:

• The review is too descriptive, but not enough critical analysis. It reads more like a list of studies rather than a critical review. Please consider comparing conflicting findings, discussing limitations of current methods, and explain how different enzymes (e.g., ZDHHC family members) may have overlapping or opposing roles.
• Some sections repeat similar information. For example, CD36 and DKD (L 347-366 and L 445-454); β-catenin and CKD (L 211-216 and L 416-423).
• Correct the numbering in the sections.
• A few statements need clarification or correction, for example:
  • Description of N-palmitoylation is not fully accurate.
  • ABE method specificity is somewhat overstated.
  • 2-bromopalmitate (2-BP) is described too simply as a DHHC inhibitor, but it has broad off-target effects.
• The authors frequently suggest palmitoylation enzymes are promising drug targets. However, most data are preclinical and targeting these enzymes systemically may cause side effects. So, in my view, the discussion should be more cautious.

Author Response

Comments 1: The review is too descriptive, but not enough critical analysis. It reads more like a list of studies rather than a critical review. Please consider comparing conflicting findings, discussing limitations of current methods, and explain how different enzymes (e.g., ZDHHC family members) may have overlapping or opposing roles.

Response 1: We are grateful for your insightful comments. We have carefully revised the entire manuscript to incorporate a more critical analysis, including conflicting findings and the limitations of current methodologies. Additionally, we have reexamined the current understanding of ZDHHC family members and specifically addressed the potentially overlapping or opposing functions (Line 124–149).

Comments 2: Some sections repeat similar information. For example, CD36 and DKD (L 347-366 and L 445-454); β-catenin and CKD (L 211-216 and L 416-423).

Response 2: Thank you for your valuable comments. Since the associations of CD36 with DKD and β-catenin with CKD were derived from two different references, the content may exhibit some structural similarities. However, their emphases are distinct: the parts that discuss CD36 and β-catenin primarily describe the functions of these proteins, while the sections on DKD and CKD address the pathogenic mechanisms of the respective diseases. To avoid any confusion between these two components, we have revised the manuscript accordingly, no issues were found with the logic of the DKD-related section (CD36 and DKD), so it was left unchanged (Lines 343-349 and Lines 428-437); β-catenin and CKD (Lines 199-204 and Lines 401-404)

Comments 3: Correct the numbering in the sections.

Response 3: Thank you for your valuable comments. The numbering in each section has been corrected in the revised manuscript.

Comments 4: A few statements need clarification or correction, for example:

Description of N-palmitoylation is not fully accurate.

Response 4: Thank you for your valuable comments. To ensure the accuracy of the concept, we have reconsulted the relevant literature on N-palmitoylation and provided a more precise description of its definition in the revised manuscript (Lines 43–47).

Comments 5: ABE method specificity is somewhat overstated.

Response 5: Thank you for your valuable comments. We have revised the text accordingly to provide a more objective perspective. (Line 529–540).

Comments 6: 2-bromopalmitate (2-BP) is described too simply as a DHHC inhibitor, but it has broad off-target effects.

Response 6: Thank you for your valuable comments. We revised the Discussion to provide a more detailed explanation of its off-target effects and also introduce its cytotoxicity profile to better clarify the limitations (Line 668–682).

Comments 7: The authors frequently suggest palmitoylation enzymes are promising drug targets. However, most data are preclinical and targeting these enzymes systemically may cause side effects. So, in my view, the discussion should be more cautious.

Response 7: Thank you for your valuable comments. We have carefully revised the entire manuscript to adopt a more balanced tone and to explicitly acknowledge these limitations throughout.

Author Response File: Author Response.pdf

Round 2

Reviewer 3 Report

Comments and Suggestions for Authors

The authors have addressed nearly all of my previous comments. The only remaining issue is the inconsistent numbering in Section 2.