Classification of Brainstem Gliomas Based on Tumor Microenvironment Status

Round 1

Reviewer 1 Report

Dear Authors,

I have read the manuscript entitled "Classification of Brainstem Gliomas Based on Tumor Microenvironment Status" with much attention and interest. Following, I report my comments for your convenience.

The manuscript reports of an extension of works published in doi:10.1038/s41467-020-16682-y (genomics) and doi:10.1016/j.radonc.2018.07.011 (imaging).

In section "2.2. TME status estimation and clustering" it is said that the key features of TME was based on single-sample gene set enrichment analysis, and in section "2.5. Multiplex immunofluorescence staining" we learn that just 31 cases were explored by immunofluorescence staining with the purpose of validating the status estimation. 88 cases had MRIs available.
It would be useful to understand how the various groups overlap, and how many complete cases were studied.

Clinical and demographic data should be presented as boundary conditions within which all the variables subject of testing in the manuscript are evaluated, which is currently not the case. Thus it is not possible to exclude that some(?) results about the prognostic value of the proposed clusters results from confounding by known determinants. For example the authors might use the corrected Cox-Kalbfleisch-Prentice regression.

The found differences, if confirmed after correction for baseline demographic determinants, are anyway rather weak, and the sample is small (not to mention it being only an extension of a previously published one, thus not an independent replication but rather a somewhat biased selection, which is unaccounted for e.g. by lack of multiple testing correction of the statistical tests)... the conclusions should thus be much more nuanced, and emphasize the many limitations of the study at hand.

Is Figure S2 A and B a duplication?

I look forward to reading an improved version of the manuscript.

Best regards,

The manuscript may benefit from undergoing a proofreader's care. Some forms (e.g. "Due to vital functions of brainstem they locate" in line #46, or the period "And, Temozolomide (TMZ) based chemotherapy" in line #48, "However, there is no immunotherapeutic approach has proven clinically effective against BSG" in lines #55-56, ...it's beyond the scopes of this review to offer a full list) make the text less than obvious to peruse.

Author Response

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Reviewer 2 Report

Well written paper with an interesting bioinformatics analysis of brain-stem gliomas. Since there is a large, publicly available childhood cancer database from St.Jude for these gliomas, they should be included or compared with the dataset used in the present analysis.

There are some minor issues in grammar and typographical errors. Minor english editing is needed.

Author Response

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Reviewer 3 Report

Authors present a classification model for tumor microenvironment in brainstem gliomas and particularly DIPGs based on clinical and gene expression signatures, also involving MR images.

 

The manuscript is comprehensibly written. The introduction could be extended in view of TME models on the one hand and BSG classification features on the other hand.

 

Results are clearly presented, except the color scheme description is missing in Figure 3 legend.

 

In terms of reproducibility, why are data not made available via a suitable repository? The model itself could also be shared. If necessary, data as pseudoanonymized version! Especially, rare pediatric data are essential to be made open as possible to support the international developments of novel treatments.

Author Response

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Reviewer 4 Report

The manuscript titled "Classification of Brainstem Gliomas Based on Tumor Microenvironment Status" presents a compelling study that explores the relationship between the classification of the Tumor Microenvironment (TME) and its impact on patient prognosis and tumor phenotype in the context of Brainstem Gliomas (BSG). This study utilizes transcriptional data from a cohort of Brainstem Glioma patients and employs established molecular signatures to evaluate the status of the TME, ultimately classifying Brainstem Gliomas based on this classification. While the study's results demonstrate the potential clinical implications for predicting the prognosis of Brainstem Glioma patients, there are areas in the discussion of the findings that could benefit from further elaboration and clarity.

 

1.     Line 198-202, The statement should be rewritten as “The "F" cluster was characterized by the highest expression of genes related to angiogenesis/fibrosis whereas exhibited relatively low activity in immune response (Figure 1b). The "IEF" cluster showed increased activity in angiogenesis/fibrosis and immune response, while the "depleted" cluster displayed the lowest levels of these TME properties (Figure 1b).

2.     Line 236-247, this paragraph looks like repetition on method however, it should be based on interpretation of data from Figure 3 and Table S3.

3.     Section 3.6. must be elaborated based on results. This too looks like repetition of the methods.

4.     Figure 6A and 6B are nor clear.

5.     Line 361-382. This paragraph is repetition of result section. Overall, discussion is shallow and authors are requested to rewrite the discussion section with in-depth discussion on results and related studies.

Author Response

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Round 2

Reviewer 4 Report

The manuscript is revised well based on reviewers' comment. This revised version is recommended for acceptance.