Regulatory-Associated Protein of mTOR-Mediated Signaling: A Nexus Between Tumorigenesis and Disease

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

In the manuscript by Chouhan et al., the authors reviewed the structure of RAPTOR, its post-translational modifications, and its essential role within the mTORC1 complex, focusing on its regulatory functions.

The review is very nicely written.

I have a few major/minor suggestions for polishing the manuscript.

Major Comments:

1. The authors should cite some recent research articles that highlight the roles of RAPTOR.
2. The authors should add a figure highlighting various PTMs associated with RAPTOR, along with their corresponding functions.
3. The authors should add a section highlighting the cross-talk of RAPTOR and cancer stem cells.

Author Response

In the manuscript by Chouhan et al., the authors reviewed the structure of RAPTOR, its post-translational modifications, and its essential role within the mTORC1 complex, focusing on its regulatory functions. The review is very nicely written. I have a few major/minor suggestions for polishing the manuscript.

Author’s reply- Thank you for your feedback. We're glad to hear that you found the review well-written. Your insights are valuable for refinement of our manuscript.

Major Comments:

1. The authors should cite some recent research articles that highlight the roles of RAPTOR.

Author’s reply to comment 1- Thank you for this suggestion. We have now incorporated more recent articles that highlight the roles of RAPTOR in various contexts, particularly focusing on its latest research in RAPTOR mediated mTORC1 regulation and disease implications. We hope that these new edits throughout manuscript will now satisfy reviewer’s concern.

2. The authors should add a figure highlighting various PTMs associated with RAPTOR, along with their corresponding functions.

Author’s reply to comment 2- We agree that a figure would enhance the manuscript. We have now included Figure 3 (Line 232) which summarizes the various PTMs of RAPTOR and their respective functions, including phosphorylation, acetylation, ubiquitination, and O-GlcNAcylation.

3. The authors should add a section highlighting the cross-talk of RAPTOR and cancer stem cells.

Author’s reply to comment 3- Thank you for this valuable suggestion. We have now introduced a new section 4.5 discussing the interplay between RAPTOR and cancer stem cells, emphasizing the role of RAPTOR in regulating the tumorigenic potential of these cells.

(Highlighted section: 4.5. Interplay between RAPTOR and Cancer Stem Cells in Tumorigenesis, Line 833)

Reviewer 2 Report

Comments and Suggestions for Authors

1.      Authors should discuss about the clinical implications to develop therapeutic drugs/inhibitors by targeting RAPTOR-mTOR signalling factors. I would recommend adding another section that discuss about the potential therapeutic strategies against RAPTOR mTOR signalling pathways. Add a table with Drug name, target, mechanism of action and ref.

2.      Figure 3 summarizes the functional role of RAPTOR. Figures related to each section would be helpful to readers to understand the signalling pathway effectively. Figures for immune cells (monocytes, NK, T and B cells), Metabolism, Autophagy would be getting more attention than elaborated text.

3.      Overall, the manuscript is too lengthy and hard to follow. I would ask the authors to remove unrelated text and make it clearer.

4.      Some of the sentences in the manuscript are very long, so it would be good for the reader’s understanding if the authors re-write some of the manuscript to make their point clearer.

5.      Minor: Page 4: typos. RAPTOR

Comments on the Quality of English Language

Grammatical errors are there. Minor to moderate editing is required.

Author Response

1. Authors should discuss about the clinical implications to develop therapeutic drugs/inhibitors by targeting RAPTOR-mTOR signalling factors. I would recommend adding another section that discuss about the potential therapeutic strategies against RAPTOR mTOR signalling pathways. Add a table with Drug name, target, mechanism of action and ref.

Author’s reply to comment 1- Thank you for the valuable comment. We have now included Table 2 (Line 1022), which summarizes various drugs, their targets, mechanisms of action, and corresponding references. Given the limited research on the development of direct RAPTOR inhibitors and the relatively new and evolving nature of this field, the table is focused on drugs, modulators and inhibitors that have been reported to influence RAPTOR as part of their mode of action.

2. Figure 3 summarizes the functional role of RAPTOR. Figures related to each section would be helpful to readers to understand the signaling pathway effectively. Figures for immune cells (monocytes, NK, T and B cells), Metabolism, Autophagy would be getting more attention than elaborated text.

Author’s reply to comment 2- We acknowledge the need for more figures to clarify the text. In response, we have now added four new figures, Figure 5 (Lines 573), 6 (Lines 644), 7 (Lines 823) and 8 (Lines 903), illustrating the roles of RAPTOR in cellular metabolism, regulation of angiogenesis, autophagy and cell survival, immune modulation and its crosstalk with cancer stem cells (CSC) & other signaling cascades to facilitate a better understanding of these pathways.

3. Overall, the manuscript is too lengthy and hard to follow. I would ask the authors to remove unrelated text and make it clearer.

Author’s reply to comment 3- We appreciate your feedback regarding the manuscript’s length. We have now streamlined the manuscript text by removing unrelated sections to enhance readability and focus. We hope that these new edits throughout manuscript will now satisfy reviewer’s concern.

 

4. Some of the sentences in the manuscript are very long, so it would be good for the reader’s understanding if the authors re-write some of the manuscript to make their point clearer.

Author’s reply to comment 4- Thank you for highlighting this concern. We have carefully revised the manuscript to make the sentences more concise, ensuring clarity without compromising scientific rigor. We hope that the updated manuscript will address the reviewer’s concerns satisfactorily.

5. Minor: Page 4: typos. RAPTOR

Author’s reply to comment 5- Thank you for pointing this out. We apologize for the error. We have now corrected the typo on page 4 as noted.

Reviewer 3 Report

Comments and Suggestions for Authors

The paper titled "RAPTOR Mediated Signaling: A Nexus Between Tumorigenesis and Disease," authored by Surbhi Chouhan and colleagues under the supervision of Abdul Khalique, presents the RAPTOR protein, a pivotal component of the mammalian target of rapamycin complex 1 (mTORC1). The authors effectively highlight the potential of targeting RAPTOR-mediated mTORC1 signaling to revolutionize cancer treatment. The paper is well-written and demonstrates a solid foundation, but I would like to offer several essential suggestions to further improve the manuscript.

1. There are various pathways involved in cell signaling. Please elaborate further on why mTOR complex-related pathways are particularly valuable in this context.

2. The structural information in Figure 2 is relatively insufficient. Please supplement and improve this figure.

3. Provide a brief explanation of the general concept of post-translational modification (PTM) processes.

4. Can you explain the mechanism by which hydrophobic interactions between amino acid residues at key PTM sites influence the function of the protein?

5. Minor: Would it be more appropriate to italicize the term "in vivo" throughout the text? I leave this to the discretion of the authors

Author Response

The paper titled "RAPTOR Mediated Signaling: A Nexus Between Tumorigenesis and Disease," authored by Surbhi Chouhan and colleagues under the supervision of Abdul Khalique, presents the RAPTOR protein, a pivotal component of the mammalian target of rapamycin complex 1 (mTORC1). The authors effectively highlight the potential of targeting RAPTOR-mediated mTORC1 signaling to revolutionize cancer treatment. The paper is well-written and demonstrates a solid foundation, but I would like to offer several essential suggestions to further improve the manuscript.

Author’s reply- Thank you for your feedback. We're pleased to hear that you found the review well-written. Your insights are greatly appreciated and will help us further refine the manuscript. Additionally, I would like to make a minor correction to the above comment: Abdul Khalique is one of the coauthors and the manuscript is supervised by Surbhi Chouhan. We appreciate your understanding and thank you again for your valuable feedback.

1. There are various pathways involved in cell signaling. Please elaborate further on why mTOR complex-related pathways are particularly valuable in this context.

Author’s reply to comment 1- Thank you for this important point. We have now expanded our discussion on why mTORC1-related pathways are especially valuable in the context of tumorigenesis and disease, focusing on their roles in regulating growth, metabolism, and survival. The new edits are now incorporated both in introduction section and in section 4. (Highlighted section: 4. Hyperactivation of mTORC1 in cancer and disease and the central role of RAPTOR, Line 477)

2. The structural information in Figure 2 is relatively insufficient. Please supplement and improve this figure.

Author’s reply to comment 2- We appreciate this suggestion. We have now improved the structural details in Figure 2 (Line 179), adding more specific information on RAPTOR’s domains. We hope that these new edits throughout manuscript will now satisfy reviewer’s concern.

3. Provide a brief explanation of the general concept of post-translational modification (PTM) processes.

Author’s reply to comment 3- Thank you for the valuable suggestion. We have now added a brief explanation in section 3 (Highlighted section: 3. Post-Translational Modifications on RAPTOR and their role in mTOC1 activity, Line 187) on the general concept of PTMs, detailing how these modifications influence protein function and cellular signaling, particularly within the mTORC1 pathway.

4. Can you explain the mechanism by which hydrophobic interactions between amino acid residues at key PTM sites influence the function of the protein?

Author’s reply to comment 4- Thank you for the valuable comment. In section 3 (Line 196), we have now elaborated on the mechanisms by which hydrophobic interactions at key PTM sites influence protein function, providing examples of how these interactions regulate protein stability and activity. We hope that the new edits will address the reviewer’s concerns satisfactorily.

5. Minor: Would it be more appropriate to italicize the term "in vivo" throughout the text? I leave this to the discretion of the authors.

Author’s reply to comment 5- Thank you for pointing this out. In the updated manuscript we have now ensured that "in vivo" is italicized consistently throughout the manuscript where appropriate.

 

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

In the manuscript by Chouhan et al., the authors reviewed the structure of RAPTOR, its post-translational modifications, and its essential role within the mTORC1 complex, focusing on its regulatory functions.

The authors have addressed all the previous comments. Thus, the manuscript can be accepted in its present form.

Author Response

Author’s reply to comment- Thank you for your thorough review and for the positive feedback regarding our manuscript. We are delighted to hear that our revisions have adequately addressed all prior comments, particularly concerning the structural and regulatory insights on RAPTOR within the mTORC1 complex. We appreciate the opportunity to share our findings and look optimistically forward to the manuscript’s consideration for acceptance for publication.

Reviewer 2 Report

Comments and Suggestions for Authors

While the review contains valuable information and is well-researched, it requires minor revisions to address the following minor issues. Upon addressing these points, it would be suitable for publication. Therefore, minor revisions are recommended for conditional acceptance.

1.    Inconsistent Terminology Usage: The term “post-translational modifications” is abbreviated as “PTMs,” but later, the full term is used without abbreviation. This inconsistency in terminology can confuse readers and detracts from the clarity of the text. 

2. Lack of Novelty in Therapeutic Discussion: lines 1023-1038, the review discusses the role of RAPTOR inhibitors like AZD8055, cardamonin, 1c and dual inhibitors 1 like BEZ235 and GDC-0980. However, the therapeutic insights presented here are not novel and mostly reiterate well-established findings from earlier studies without offering new perspectives or future directions

Author Response

While the review contains valuable information and is well-researched, it requires minor revisions to address the following minor issues. Upon addressing these points, it would be suitable for publication. Therefore, minor revisions are recommended for conditional acceptance.

Author’s reply to comment- Thank you for the thoughtful feedback and recommendation for minor revisions. We have now revised the highlighted sections promptly to meet publication standards and ensure the content's accuracy and coherence.

1. Inconsistent Terminology Usage: The term “post-translational modifications” is abbreviated as “PTMs,” but later, the full term is used without abbreviation. This inconsistency in terminology can confuse readers and detracts from the clarity of the text.

Author’s reply to comment 1-We have now revised the manuscript to ensure consistent terminology throughout, specifically using the abbreviation “PTMs” consistently after its initial full-term introduction (Highlighted throughout the updated manuscript).

 

2. Lack of Novelty in Therapeutic Discussion: lines 1023-1038, the review discusses the role of RAPTOR inhibitors like AZD8055, cardamonin, 1c and dual inhibitors 1 like BEZ235 and GDC-0980. However, the therapeutic insights presented here are not novel and mostly reiterate well-established findings from earlier studies without offering new perspectives or future directions.

Author’s reply to comment 2- In response to the reviewer’s concern, we would like to emphasize that although RAPTOR is a key regulatory component of mTORC1, however, its druggable potential remains underexplored, primarily due to the absence of a specific inhibitor (Also highlighted in lines 960-962). Only recently has the first RAPTOR-specific small molecule inhibitor, compound 1c (a daphnane diterpenoid derivative), been identified as a highly selective inhibitor, capable of blocking RAPTOR’s integration into mTORC1 (XL Yan et al., 2023). While numerous studies have underscored RAPTOR’s regulatory role in mTORC1 across various physiological and pathological contexts including cancer, metabolic and neurodegenerative disorders the absence of potent, selective inhibitors has limited further exploration of RAPTOR’s potential as a therapeutic target. Now with the identification of compound 1c, we anticipate that this will catalyze a new direction in RAPTOR-based drug discovery. Meanwhile, we also want to highlight the strong evidence supporting the indirect modulation of RAPTOR’s function by the current pool of mTORC1 inhibitors such as rapalogs, AZD8055, cardamonin and dual mTOR inhibitors like BEZ235 and GDC-0980. These drugs have shown to affect mTOC1 activity by either modulating RAPTOR’s upstream regulators or its PTMs which ultimately influence RAPTOR’s incorporation into mTORC1. Thus, in Section 5 of this review manuscript, we aim to comprehensively examine the mechanisms of only those mTORC1 inhibitors that have been reported to influence RAPTOR’s stability by upstream regulation or PTMs, ultimately affecting its regulatory role in mTORC1 activity.

In lines 1023-1033, we have now expanded this discussion of RAPTOR inhibitors to incorporate recent developments and emerging insights. Also, in section 6. Conclusions and Perspectives (Highlighted lines 1048-1067), we have now specifically proposed the need for novel RAPTOR-based inhibitors and discussed potential future research directions to enhance therapeutic targeting of RAPTOR. We appreciate your careful review and we believe these changes enhance the manuscript's clarity and scientific value. Thank you once again for your insightful suggestions.