PONE-D-24-15467Development of innovative multi-epitope mRNA vaccine against central nervous system tuberculosis using in silico approachesPLOS ONE

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PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: No

Reviewer #5: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: N/A

Reviewer #3: Yes

Reviewer #4: N/A

Reviewer #5: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

Reviewer #5: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

Reviewer #5: No

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: This insilico approach of developing a multiepitope vaccine for CNS TB is an innovative and thoroughly carried out study. The comprehensive bioinformatics analyses, including sequence homology, antigenicity prediction, and epitope mapping, contribute to a comprehensive understanding of the vaccine candidates' immunogenic potential. Additionally, the incorporation of immunoinformatic tools facilitates the prediction of T-cell and B-cell epitopes, further enhancing the vaccine's efficacy and specificity. Despite the remarkable accomplishments of this study, I have few questions and minor concerns that needs to be addressed.

Please provide clarifications on the following questions:

2. Line 229: Claim “the two proteins are highly homologous, suggesting that they may be derived from the same gene and have similar roles in the immune response”. Did you find any link between the two genes in the previous literatures or perform any additional study to investigate the same other than sequence homology?

3. Did you check similarity between analyzed bacterial proteins and host proteome?

4. Did you by any chance used another software such as Signal BLAST to predict signal peptide?

5. Would you have any other already tested CTL and HTL epitope from previous CNS TB studies / published literature which can be used as comparison with your selected epitope candidates to validate how selected epitope candidates stand out or performing better.

Major concern:

1: Most of the figures are hard to read and see. Image quality is poor and written text is unclear. Please replace with good quality images.

Minor concern:

1. There are various formatting errors like invalid spacing between words in headings and paragraphs. Please check thoroughly.

2. Line 40: Rephrase. Why would TB report 2022 will predict cases in 2021. Prediction happens for future.

3. Line 260: “Docking result between CTLs and HLA-A*02:01 seems confusing. Please rephrase this. Does this mean CTL epitope and HLA-A*02:01?

4. Line 261: Similarly, “Docking result between HTLs and HLA-DRB1*07:01” seems confusing.

5. Section 3.8: Please make a table for MEV properties instead of writing the properties in sentences.

6. Section 9.3: Would it be possible to extrapolate dose and time intervals of injection during simulation of immune response?

7. 3.12 and 3.13 heading both has prediction of secondary structure. Why?

8. Table 4 does not have heading for characteristics measured. No row to define which column represents which characteristics. Include antigenicity values in table 5

Reviewer #2: Following are the comments for the authors to improve on the manuscript -

1. Please use a correct font, font size and text settings for the manuscript

2. Define all the abbreviations in the manuscript for the words where they are used for the first time.

3. Please use the correct style for the citations in the manuscript.

4. The quality and resolution of the images needs to be improved, the aspect ratio for some of the images is incorrect.

5. Please remove the characters from the other languages from the manuscript.

6. please try to reduce the number of images from manuscript, possibly by merging them together.

Reviewer #3: Decision: Minor revision.

General comments:

The authors of this study aimed to develop an innovative mRNA therapeutic vaccine targeting a protein associated with central nervous system tuberculosis, addressing the pressing need for effective treatments for this debilitating condition. Employing in silico techniques such as IEDB, NetCTLpan1.1, NetMHCIIpan-4.0, and SVMtrip, they analyzed the antigen epitopes of PknD and Rv0986. Additionally, CTL, HTL, and B cell epitopes were linked together using AAY, GPGPG, and KK linkers. This research was spurred by the lack of therapeutic options for central nervous system tuberculosis, underscoring its urgency.

The utilization of in silico methods paved the way for designing an mRNA therapeutic vaccine targeting central nervous system tuberculosis, offering a foundation for potential future experimental investigations. The outcomes of these assessments yielded promising observations, indicating the potential efficacy of the developed vaccine.

The authors have presented promising results in the manuscript. However, to optimize its effectiveness for our readers, it would be beneficial to address the following comments for streamlining and enhancement. While the manuscript exhibits good writing and organization, improvements in overall English language usage, particularly in grammar, punctuation, and clarity, would enhance engagement for general readers. Please consider revising the language to maximize effectiveness.

Comments:

1. Line 26: Define ‘BCG’ or provide more descriptive information as it appears first time here in this manuscript. Applicable for all abbreviations throughout the manuscript.

2. Line 33-34: please revise this sentence for effectiveness: ‘The results indicate that the vaccine structure shows promise’.

3. Line 40-41: The tense of the following sentence needs to be revised. If updated and most recent data is available, please provide that. ‘The World Health Organization (WHO) Global TB Report 2022 predicts that 41 10.6 million people will be diagnosed with TB in 2021, with 1.6 million fatalities.’

4. Line 42: Consider defining as this term is used many times in the manuscript ‘Central nervous system tuberculosis’.

5. Line 42: ‘TB’ is not defined, please define it.

6. Line 44: If authors could provide specifics in terms of specific mortality rate from the cited article, that would be helpful for readers.

7. Line 77 to 83: This paragraph has three references cited. This is confusing. Have these previous studies been conducted already? if they are, how they are related to the current study is not clear? please revise the language for clarity. If the intention is to cite for the part of the study, please make it clear.

8. Please revise the whole manuscript for formatting, such as: provide space between the last word in the sentence and the reference parenthesis. Applicable throughout the manuscript.

9. Line 87: link for the database should be before full stop. Please check the formatting throughout the manuscript.

10. 1All figures: Presently, all figures appear distorted and oddly stretched. Please recreate them with appropriate resolution and dimensions to ensure clarity. Additionally, consider increasing the font size on the figures for improved legibility. Some content on certain figures is currently illegible due to distortion. This feedback applies to all figures.

11. All section titles: provide a space between the number and section title, applicable for all section titles.

12. Validation of Models: It is advisable to elaborate on the validation process of the models utilized in this study to assess their reliability. Please address any limitations associated with validating these models to provide insight for readers or researchers interested in utilizing them in the future.

Reviewer #4: The study investigates the innovative epitopes mRNA vaccine by in silico approach. They have utilized bioinformatics tools to justify the epitopes could be the potential candidates for mRNA vaccine. Overall paper makes contribution in finding the novel vaccines for CNS TB. Recommendations for improvements are included in the attachment.

Reviewer #5: In this review, Shi et al, explained a in silico approach for the treatment of CNS Tuberculosis. The authors have explained a detail approach from the selection of the target sequences to codon optimization probabilities to ensure it’s translation in Human host. The authors needs to address some of the queries

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

Reviewer #4: No

Reviewer #5: Yes: Pallapati Anusha Rani

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Attachments

Attachment

Submitted filename: Reviewer comments.docx

Attachment

Submitted filename: Comments_PONE-D-24-15467.docx

Attachment

Submitted filename: Reviewer Comments _05-14-2024.docx

Development of innovative multi-epitope mRNA vaccine against central nervous system tuberculosis using in silico approaches

PONE-D-24-15467R1

Dear Dr. Zhang,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Satish Rojekar, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The author must check image quality and formatting, which can be improved and replaced during manuscript proofing.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #3: All comments have been addressed

Reviewer #4: All comments have been addressed

Reviewer #5: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #3: Yes

Reviewer #4: Yes

Reviewer #5: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #3: Yes

Reviewer #4: Yes

Reviewer #5: Yes

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #3: Yes

Reviewer #4: Yes

Reviewer #5: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #3: Yes

Reviewer #4: Yes

Reviewer #5: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The review still need minor revision for formatting errors to enhance the readability of the article. Some of the images are still not clear and needs replacement.

Reviewer #3: Thank you for your prompt and comprehensive responses to my critical questions regarding your manuscript. I appreciate the rigor and thoroughness with which you addressed each point. Your detailed explanations have satisfactorily clarified my concerns, and I am now confident in the validity and robustness of your work.

Based on your responses and the thorough explanations provided, I am pleased to accept your manuscript for publication.

Reviewer #4: I think that the authors have adequately addressed the comments made in the

revised version of the manuscript. Therefore, I have no further comments.

Reviewer #5: In this review, Shi et al, explained a in silico approach for the treatment of CNS Tuberculosis. The authors have explained a detail approach from the selection of the target sequences to codon optimization probabilities to ensure it’s translation in Human host.

Authors addressed all of the major concerns mentioned in the previous report.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #3: No

Reviewer #4: No

Reviewer #5: Yes: PALLAPATI ANUSHA RANI

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