Molecular architecture of the tumor microenvironment caused by BRCA1 and BRCA2 somatic mutations in lung adenocarcinoma

Reviewer #1 (Public review):

Summary:

Liao et al. performed a large-scale integrative analysis to explore the function of two cancer genes (BRCA1 and BRCA2) in lung cancer, which is one of the cancers with an extremely high mortality rate. The detailed genetic analysis demonstrated new roles of BRCA1/2 in causing the tumor microenvironment in lung cancer. In particular, the discovery of different mechanisms of BRCA1 and BRCA2 provides an essential foundation for developing drugs that target BRCA1 or BRCA2 in lung cancer therapy.

Strengths:

(1) This study leveraged large-scale genomic and transcriptomic datasets to investigate the prognostic implications of BRCA1/2 mutations in LUAD patients (~2,000 samples). The datasets range from genomics to single-cell RNA-seq to scTCR-seq.

(2) In particular, the scTCR-seq offers a powerful approach for understanding T cell diversity, clonal expansion, and antigen-specific immune responses. Leveraging these data, this study found that BRCA1 mutations were associated with CD8+ Trm expansion, whereas BRCA2 mutations were linked to tumor CD4+ Trm expansion and peripheral T/NK cell cytotoxicity.

(3) This study also performed a comprehensive analysis of genomic variation, gene expression, and clinical data from the TCGA program, which provides an independent validation of the findings from LUAD patients newly collected in this study.

(4) This study provides an exemplary integration analysis using both computational biology and wet bench experiments. The experimental testing in the A549 cell line further supports the robustness of the computational analysis.

(5) The findings of this study offer a comprehensive view of the molecular mechanisms underlying BRCA1 and BRCA2 mutations in LUAD. BRCA1 and BRCA2 are two well-known cancer-related genes in multiple cancers. However, their role in shaping the tumor microenvironment, particularly in lung cancer, is largely unknown.

(6) By focusing on PD-L1-negative LUAD patients, this study demonstrated the molecular mechanisms underlying resistance to immune therapy. These new insights highlight new opportunities for personalized therapeutic strategies to BRCA-driven tumors. For example, they found histone deacetylase (HDAC) inhibitors consistently downregulated 4-R genes in A549 cells.

(7) The deposition of raw single-cell sequencing (including scRNA-seq and scTCR-seq) data will provide an essential data resource for further discovery in this field.

Weaknesses:

(1) The finding of histone deacetylase (HDAC) inhibitors suggests the potential roles of epigenetic regulation in lung cancer. It would be interesting to explore epigenetic changes in LUAD patients in the future.

(2) For some methods, more detailed information is needed.

(3) There are grammar issues in the text that need to be fixed.

(2) Some text in the figures is not labeled well.

Reviewer #2 (Public review):

Summary:

This study investigates the impact of BRCA1/2 mutations on immunotherapy in lung adenocarcinoma using multi-omics approaches. The work highlights distinct roles of BRCA1 and BRCA2 mutations in shaping immune-related processes, and is logically structured with clearly presented analyses. However, the conclusions rely primarily on descriptive computational analyses and would benefit from additional immunological validation.

Strengths:

By integrating public datasets with in-house data, this study examines the impact of BRCA1/2 mutations on immunotherapy in lung adenocarcinoma from multiple perspectives using multi-omics approaches. The analyses are diverse in scope, with a clear overall logic and a well-organized structure.

Weaknesses:

The study is largely descriptive and would benefit from additional immunological experiments or validation using in vivo models. The fact that the BRCA1 and BRCA2 samples were each derived from a single patient also limits the robustness of the conclusions.

Author response:

eLife Assessment

This important study investigates the impact of BRCA1/2 mutations on immunotherapy in lung adenocarcinoma using multi-omics approaches. The detailed genetic analysis of two cancer genes (BRCA1 and BRCA2) demonstrated new roles for these genes in causing the tumor microenvironment in lung cancer. Further experimental explorations of the immune-related changes may still be required. The solid findings of this study provide a foundation for further developing drugs targeting BRCA1/2 in lung cancer therapy.

We would like to express our sincere gratitude for your thoughtful and constructive comments on our manuscript. We will carefully consider each comment from these two reviewers and will revise the manuscript accordingly. Below, we provide a point-by-point response to each comment.

Reviewer #1 (Public review):

Summary:

Liao et al. performed a large-scale integrative analysis to explore the function of two cancer genes (BRCA1 and BRCA2) in lung cancer, which is one of the cancers with an extremely high mortality rate. The detailed genetic analysis demonstrated new roles of BRCA1/2 in causing the tumor microenvironment in lung cancer. In particular, the discovery of different mechanisms of BRCA1 and BRCA2 provides an essential foundation for developing drugs that target BRCA1 or BRCA2 in lung cancer therapy.

Strengths:

(1) This study leveraged large-scale genomic and transcriptomic datasets to investigate the prognostic implications of BRCA1/2 mutations in LUAD patients (~2,000 samples). The datasets range from genomics to single-cell RNA-seq to scTCR-seq.

(2) In particular, the scTCR-seq offers a powerful approach for understanding T cell diversity, clonal expansion, and antigen-specific immune responses. Leveraging these data, this study found that BRCA1 mutations were associated with CD8+ Trm expansion, whereas BRCA2 mutations were linked to tumor CD4+ Trm expansion and peripheral T/NK cell cytotoxicity.

(3) This study also performed a comprehensive analysis of genomic variation, gene expression, and clinical data from the TCGA program, which provides an independent validation of the findings from LUAD patients newly collected in this study.

(4) This study provides an exemplary integration analysis using both computational biology and wet bench experiments. The experimental testing in the A549 cell line further supports the robustness of the computational analysis.

(5) The findings of this study offer a comprehensive view of the molecular mechanisms underlying BRCA1 and BRCA2 mutations in LUAD. BRCA1 and BRCA2 are two well-known cancer-related genes in multiple cancers. However, their role in shaping the tumor microenvironment, particularly in lung cancer, is largely unknown.

(6) By focusing on PD-L1-negative LUAD patients, this study demonstrated the molecular mechanisms underlying resistance to immune therapy. These new insights highlight new opportunities for personalized therapeutic strategies to BRCA-driven tumors. For example, they found histone deacetylase (HDAC) inhibitors consistently downregulated 4-R genes in A549 cells.

(7) The deposition of raw single-cell sequencing (including scRNA-seq and scTCR-seq) data will provide an essential data resource for further discovery in this field.

Weaknesses:

(1) The finding of histone deacetylase (HDAC) inhibitors suggests the potential roles of epigenetic regulation in lung cancer. It would be interesting to explore epigenetic changes in LUAD patients in the future.

Thank you for your insightful comment. We fully agree that the specific situation of epigenetic dysregulation in LUAD needs to be explored. We believe that future investigations utilizing clinical specimens and animal models to map histone acetylation patterns and DNA methylation profiles will be crucial for identifying novel biomarkers and therapeutic targets unique to LUAD.

(2) For some methods, more detailed information is needed.

This is a valid point. We agree that additional details regarding are necessary for clarity and reproducibility. We will expand these method details in the revised manuscript.

(3) There are grammar issues in the text that need to be fixed.

We apologize for our irregular use of grammar. In the revised manuscript, we will carefully check the grammar and make corrections.

(4) Some text in the figures is not labeled well.

We appreciate the reviewers' comments. We will add labels to the revised version of the figures.

Reviewer #2 (Public review):

Summary:

This study investigates the impact of BRCA1/2 mutations on immunotherapy in lung adenocarcinoma using multi-omics approaches. The work highlights distinct roles of BRCA1 and BRCA2 mutations in shaping immune-related processes, and is logically structured with clearly presented analyses. However, the conclusions rely primarily on descriptive computational analyses and would benefit from additional immunological validation.

Strengths:

By integrating public datasets with in-house data, this study examines the impact of BRCA1/2 mutations on immunotherapy in lung adenocarcinoma from multiple perspectives using multi-omics approaches. The analyses are diverse in scope, with a clear overall logic and a well-organized structure.

Weaknesses:

The study is largely descriptive and would benefit from additional immunological experiments or validation using in vivo models. The fact that the BRCA1 and BRCA2 samples were each derived from a single patient also limits the robustness of the conclusions.

Thank you for this excellent suggestion. In the revised manuscript, we will supplement the additional immunological experiments or validation using in vivo models. In addition, we will elaborate on the limitations of our study in the Discussion section and provide reasonable explanations.