PREreview of Circulating tumor extracellular vesicles to monitor metastatic prostate cancer genomics and transcriptomic evolution

This review reflects comments and contributions from Arddey Isaac, Teena Bajaj, Sabareeswaran Krishnan, Arpita Ghosh, Akanksha, Rebecca A Shelley, Ghada Tagorti, Garima Jain, Harini Lakshminarayanan, Adriana Mena & Ruchika Bajaj. Review synthesized by Garima Jain & Arpita Ghosh

The study investigated the potential of analyzing DNA and RNA contained in circulating extracellular vesicles (EVs) secreted by tumor cells to reflect genomic and transcriptomic features of prostate cancer (PC). The researchers developed a method to analyze mRNA expression in circulating EVs (RExCuE) and applied it to clinical samples from patients with metastatic PC. The study aimed to identify clinically relevant transcriptomic signatures associated with resistance to androgen receptor inhibition (AR inhibition) and lineage plasticity.

General Comments:

The study presents a novel approach for analyzing tumor-related genetic and transcriptomic information from circulating EVs in metastatic prostate cancer patients. The findings are promising and have implications for liquid biopsy-based cancer research. However, several methodological and interpretational considerations should be addressed to strengthen the study's conclusions.

Major Comments:

Credit Attribution: The hypothesis that EVs from prostate cancer cells could serve as a source of tumor genomic and transcriptomic characterization is well-supported by existing research. It's important to acknowledge the existing body of work that has contributed to this understanding.

Methodological Clarification: The study discusses the use of DNase digestion to avoid cfDNA contamination in EV-DNA samples, but it's unclear what measures were taken to prevent EV-DNA contamination in cfDNA samples. Additionally, the application of DNase treatment seems to have been introduced only after the initial set of experiments. This methodological detail should be clarified, and evidence of DNA purity from patient plasma samples should be provided.

Calculation of Tumor Fraction: The study lacks an explanation of how the percentage tumor fraction was calculated from the EV-DNA and EV-RNA analyses. Providing a clear description of the calculation method would enhance the transparency of the analysis.

Selection of PC-Associated Transcripts: The rationale behind the selection of specific PC-associated transcripts for analysis needs further elaboration on their biological significance in metastatic prostate cancer contexts. This information should be included in either the Results or Discussion section.

Visualization of Functional Annotations: The functional annotations identified through GO enrichment analysis should be visually represented for better understanding. Consider using dot plots, bar plots, or network graphs to effectively convey the results of the enrichment analysis.

Inclusion of Patient Cohorts: The study could benefit from the inclusion of patients with localized prostate cancer alongside the metastatic cohort and healthy donors. This addition would provide insights into gene expression changes specifically associated with metastasis, compared to localized disease, and further validate the findings.

Additionally, the method's sensitivity and specificity in earlier disease stages should be investigated to assess its broader applicability.

Minor Comments:

Abstract Clarification: Consider adding a brief explanation of the term "RExCuE" in the abstract, especially if it holds a specific meaning or significance in the context of the study.

Transitional Phrases in Introduction: Enhance the flow between introductory paragraphs by incorporating transitional phrases that clearly connect one idea to the next. This will help guide readers through the logical progression of concepts.

Explanation of Liquid Biopsy: Provide a concise explanation of what a liquid biopsy is and why it's relevant to metastatic prostate cancer. This will provide context for the subsequent discussion of liquid biopsy tools like ctDNA and cfRNA.

Stating Existing Research: Instead of claiming that tumor EV potential remains largely unexplored, it might be more accurate to state that ongoing research is actively investigating the potential of tumor EVs as a source of clinically relevant DNA and RNA biomarkers.

Identical Values in Figure 4A: Address the issue of identical values for LNCaP and C4-2 TBx RNA in Figure 4A. An explanation should be provided to ensure the accuracy of the data presentation.

Data Availability: It would be beneficial to clarify the availability of the data generated in this study. Information about data sharing, repositories where the data can be accessed, and any associated metadata would improve the transparency and reproducibility of the study.

Suggestions for Future Studies:

The study could provide suggestions for future research directions based on the limitations and implications discussed. For instance, discussing the potential of combining EV analysis with other liquid biopsy approaches or integrating multi-omics data for a more comprehensive understanding of cancer evolution could provide valuable insights.

Competing interests

The author declares that they have no competing interests.