PONE-D-25-29408A multi-omics atlas of CAF subtypes reveals apCAF–M2 macrophage interactions driving immune resistance in gliomaPLOS ONE

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #2: Yes

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Reviewer #1: This study uses a combination of single-cell transcriptome, spatial transcriptome, bulk RNA-seq, and multiple immunofluorescence staining data to systematically reveal the heterogeneity of cancer-associated fibroblasts (CAFs) in glioma and its association with immune escape.

However, some questions need to be addressed

1. When analyzing different data, was the batch effect removed?

2. What is the marker gene set for CAFs? Where was it obtained from?

3. Why were only two patients selected for the immunofluorescence staining experiment? Are there specific values ​​for spatial distance to illustrate the research conclusions? It is recommended to use HALO spatial coordinate analysis software to define the distance between different cell types.

4. How is the spatial co-localization of AQP4 and M2 macrophage markers in the same area in ST defined? Was the spatial co-localization score used?

5. What is the expression pattern of AQP4 in immunofluorescence staining?

Reviewer #2: Ren et al. analyzed publicly available scRNA-seq and bulk RNA sequencing datasets, as well as ST data from glioma patients. They investigated nine distinct CAF subtypes and mostly focused on apCAFs. Their data shows that apCAF2 is co-localized with M2 macrophages and there is a crosstalk between them via the TGF-b pathway. Patients with high apCAFs scores exhibited stronger immune resistance than patients with low apCAFs scores. Furthermore, they found that AQP4 is a specific marker for apCAFs and high expression of AQP4 in the tumor microenvironment indicated the immune resistance as well. Overall, the manuscript is well-written and presents interesting data.

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Reviewer #1: No

Reviewer #2: Yes: Ece Tavukcuoglu

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A multi-omics atlas of CAF subtypes reveals apCAF–M2 macrophage interactions driving immune resistance in glioma

PONE-D-25-29408R1

Dear Dr. Sun,

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Kind regards,

Zeyneb Kurt, PhD

Academic Editor

PLOS ONE

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