PONE-D-24-28375Identifying functional roles and pathways of shared mutations in canine solid tumors by Whole-Genome SequencingPLOS ONE

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Reviewers' comments:

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Reviewer #1: No

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

Reviewer #1: Yes

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Reviewer #1: Yes

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Reviewer #1: Yes

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5. Review Comments to the Author

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Reviewer #1: This study investigates commonly mutated genes and altered pathways in canine solid tumors using whole-genome sequencing (WGS). Tumor tissues from four dogs diagnosed with different neoplasias—urothelial carcinoma, adenocarcinoma, rhabdomyosarcoma, and chondrosarcoma—were analyzed and categorized into carcinoma and sarcoma groups. Gene set enrichment analyses identified 43 and 58 mutated genes in the carcinoma and sarcoma groups, respectively. The study found significant mutations in cell adhesion molecules in carcinomas and extracellular matrix-related molecules in sarcomas, highlighting differences in metastatic processes. These findings suggest that distinct therapeutic approaches are necessary for each tumor type, offering insights into potential targeted therapies for canine cancers.

The study could be better if its experimental design could be further considered. Firstly, the sample size is limited, with only four dogs representing two distinct tumor groups (carcinomas and sarcomas). This small sample size restricts the generalizability of the findings and may need to capture the genetic diversity of canine tumors adequately. Additionally, the study lacks a detailed explanation of potential biases introduced by random selection or variation in tumor progression among the dogs. The absence of functional validation for the identified mutations, such as in vitro or in vivo experiments to confirm their roles in tumor development, limits the study’s ability to establish direct causal links between mutations and tumor pathways. Here are several potential research questions that could arise from this study:

There are some questions the reviewer wants to clarify further and might need the authors to carefully validate or discuss them.

1. In addition to CanFam 1.0, other canine genome sequencing references include CanFam 2.0, CanFam 3.1, the Dog10K project, and breed-specific references like Shib 2.0 for Shiba Inu. These updated versions offer improved accuracy, broader genetic data, and tools for studying breed-specific traits and diseases, providing valuable resources for canine genetic research. So, what are the potential limitations of using only a single canine genome reference, such as CanFam 1.0, for analysis in this study, particularly regarding genetic diversity, breed-specific mutations, and the accuracy of variant detection across different tumor types?

2. What are the specific roles of immune-related mutations in the development and metastasis of canine solid tumors, and can these pathways be targeted therapeutically?

3. Can the identified genetic mutations in canine tumors be directly linked to similar mutations in human cancers, providing potential translational insights for both veterinary and human oncology?

4. Would larger-scale studies with more diverse tumor types confirm the findings, or would additional genetic variations and pathways be discovered in a broader canine population?

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Reviewer #1: No

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Identifying functional roles and pathways of shared mutations in canine solid tumors by Whole-Genome Sequencing

PONE-D-24-28375R1

Dear Dr. Yu,

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.

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Kind regards,

Andre van Wijnen

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The authors have adequately revised the paper in response to the previous reviewer.

Reviewers' comments: