PONE-D-21-25753Drug resistance mechanisms create targetable proteostatic vulnerabilities in Her2+ breast cancersPLOS ONE

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Reviewer #1: Yes

Reviewer #2: Partly

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Reviewer #1: N/A

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: No

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: In the era/context of precision medicine, oncogenic kinase inhibitor is the key for drug matching with specific oncogenic mutations but their response often short lived due to development of clinical (ad inito or acquired ) resistance. In this aspect this is an interesting/important article.

Critical comments:

1. This is a question to authors: Can this proteostatic vulnerabilities correlate well with immune vulnerabilities following the treatment of ant-HER2 therapies? Since authors demonstrated some correlation between proteostatic and genomic vulnerabilities.

2. Authors performed some experiments with BT474 cells (along with SRBR3 cells), both cells are HER2 amplified, but SKBR3 is ER negative and BT474 is ER+ cells. In their hands both behave almost similarly following the development of lapatinib resistance. Any comments from authors side about the role of ER in the development of lapatinib-induced metabolic resistance.

3. Authors may provide NRG1 and EGF Western blot expression data.

4. In Figure 4A, please make it bold for UDP-glucose (in the figure).

5 In line 290, where authors mentioned increased citrate expression, here authors failed to mention about the high expression of Creatin Phosphate.

6. Authors may provide qRT-PCR data of GADD34 mRNA expression.

7. Please mentioned number of patients sample for Figure 5H. These patients were exposed with trastuzumab but not lapatinib. Any thoughts from authors side?

Minor comments:

1. Authors failed to mentioned about the phosphorylation sites of AKT following lapatinib treatment. Better to provide both Ser473 and Thr308 phosphorylation expression.

Reviewer #2: The Authors, in their work, using transcriptomic, metabolomic and proteomic analysis, characterized the mechanism of acquisition of drug resistance in Her2+ breast cells. The topic of the manuscript is attractive and very important; however, some points need clarification:

• Transcriptomics and qPCR methods are not described in the material and methods section.

• The raw data of transcriptomic and metabolomic analysis should be registered in the public repository, and the accession ID should be displayed in the main text. Moreover, it would be helpful to include the results of these analyses (lists of genes and metabolites with most altered expression) as tables in supplementary materials.

• The results chapter should be divided into subsections that would make this chapter clearer.

• There are no units in figures 1B, 2C, 2E, 3B, 3C, 4C, 4E, and supplementary results.

• The Authors should explain how the relative viability and growth rate were counted (presented in figures).

• What was the reference gene used to normalize the qPCR results?

• The discussion in this publication is too general. The Authors should discuss their results in the context of other published work instead of just repeating the description of their results.

• There are some grammar and spelling mistakes.

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Reviewer #1: No

Reviewer #2: No

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Drug resistance mechanisms create targetable proteostatic vulnerabilities in Her2+ breast cancers

PONE-D-21-25753R1

Dear Dr. Komurov,

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Academic Editor

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