PONE-D-23-33311Understanding the Relationship between Cerebellum and the Frontal-Cortex region of c9orf72-Related Amyotrophic Lateral Sclerosis: A Comparative Analysis of Genetic FeaturesPLOS ONE

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 [INDIA - IN].  

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Reviewers' comments:

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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

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

Reviewer #1: Yes

Reviewer #2: 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

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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: No

Reviewer #2: Yes

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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 manuscript reports the results of a study assessing transcriptomic features of biological samples obtained from biobank of brain cortical tissue of 25 C9-ALS patients and healthy controls. Gene expression analysis and biological characterization of identified genes of interest were performed, as well as screening of possible miRNAs to interact with such genes.

Although the study is of interest, and methodology seems overall adequate, I have important concerns regarding the clarity of the manuscript in its present form, which looks partially incomplete, disorganized and slightly out of focus as regards the clinical relevance of the authors' findings.

-Introduction reports several details about FTD, but here the authors included only patients with ALS. I would limit mentioning FTD.

- The authors state that "frozen human post-mortem tissue was obtained from motor cortex (medial and lateral)", but the manuscript only reports data from frontal and cerebellar tissue.

-The authors state that data were obtained from "25 C9-ALS patients and control patients", but it is unclear how many were C9 and how many were controls. Moreover, what do the authors mean as "control patients"? Were they healthy individuals or patients with different diseases? This should be clearly specified.

-In some paragraphs of the methods section the authors use the future tense (e-g., "the count data will then further be used"). This should be corrected.

-Some paragraphs of the results section actually report details to be reported in the methods. See for example "DESeq2 tool was then used to ...".

- The quality of English should be reviewed carefully. See for example "the current study compared the transcriptome changes in the cerebellum and frontal cortex of C9-ALS cases, with between (?), indicating etc.")

- Why did the authors only select frontal and cerebellar regions? This should be better clarified.

Reviewer #2: The aim of this study was identifying and and spatially determining differential gene expression signature differences between cerebellum and frontal cortex in C9ALS, to study the network properties of these differentially expressed genes, and to identify miRNAs targeting the common differentially expressed genes in both the tissues. The study used data generated by several research groups.

The authors observed that the genes involved in neuron development, protein localization and transcription are mostly enriched in cerebellum of C9ALS patients, while the UPR-related genes are enriched in the frontal cortex. Finally, UPR pathway genes were mostly dysregulated both in the C9ALS cerebellum and frontal cortex.

The study is well performed and highlight a possible role of cerebellum in the neurodegenerative process of C9ALS.

The fina sentence of the paper (Although the cerebellum role in coordination and motor control is well established, its involvement in ALS has been largely unnoticed) is not correct. Just limiting on cases with C9ORF72 expansion, the role of cerebellum has been identified in clinical (PMID: 35189395), neuropathological (PMID 37816685), neuroimaging (PMID: 34168085; PMID: 34544819), machine learning (PMID: 36694130) studies as well as in preclinical models (PMID: 35843530). In addition, the presence of cerebellar functional involvement has been found to be a prognostic predictor in ALS (PMID: 36308536). I suggest commenting these important papers at the light of the findings of the present study.

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Reviewer #1: No

Reviewer #2: No

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Understanding the Relationship between Cerebellum and the Frontal-Cortex region of C9orf72-Related Amyotrophic Lateral Sclerosis: A Comparative Analysis of Genetic Features

PONE-D-23-33311R1

Dear Dr. Kumar,

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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Kind regards,

Massimo Filippi

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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 #2: 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 #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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 #2: 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 #2: 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: I have no further comments. The authors have addressed my previous concerns regarding the rationale of selecting some cortical regions

Reviewer #2: All my comments were adequately addressed. The paper can be published in the current form. Congratulations to the authors for their work.

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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 #2: No

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