Introduction: There is an unmet need for liquid biopsy tests to support the management of patients with intermediate and high-risk prostate cancer (PCa). In treatment naïve patients, risk stratification by standard pathology and tissue based genomic testing can be influenced by sampling errors inherent to PCa biopsy. Exosome-based liquid biopsies are emerging as a clinically effective platform for minimally invasive and highly sensitive diagnostics for diverse types of cancer. Exosomes are small double-lipid membrane vesicles that cells shed into various biofluids and that provide packages for RNA, DNA and protein molecules. In this project we undertake the development of a plasma exosome-based liquid biopsy to stratify patients with clinically significant PCa that may circumvent the sampling challenges associated with tissue-based genomic tests.
Methods: Our pilot study included plasma samples from 11 NCCN high-risk and 9 NCCN low-risk, treatment-naïve, biopsy-confirmed PCa patients together with 4 healthy controls. Exosomes were isolated from 1 ml plasma using the ExosomeDx ExoLution platform. A hybrid-capture RNA Next Generation Sequencing analysis was performed to enrich for transcripts of exons, 3’ and 5’ untranslated RNA and long non-coding RNA (lncRNA). Data analysis included identification of differentially expressed RNAs in high-risk vs low-risk vs control samples.
Results: In each plasma exosome sample we detected transcripts of over 10,000 protein coding genes and ~400 lncRNAs using exosomal RNAseq. 273 genes were differentially expressed between high-risk vs control but not between low-risk vs control. We identified four potential plasma exosomal biomarkers of high-risk PCa. These include three protein coding mRNA transcripts that showed > 20-fold lower expression in plasma from high-risk compared to low-risk patients; TCGA data show that two of these transcripts are also downregulated in PCa tissue in patients with worse survival. In addition, we identified one lncRNA that showed > 20-fold higher expression in plasma from high-risk compared to low-risk patients. We also detected multiple alternate androgen receptor transcripts in plasma exosomal RNA from high-risk patients. Together, these represent early data for potentially novel liquid biopsy RNA biomarkers for high-risk PCa.
Conclusions: Here we report results of a liquid biopsy biomarker discovery study to develop an exosome-based RNA test to support the management of patients with intermediate and high-risk PCa. Plasma exosomal RNA provides a rich reservoir of currently untapped biomarkers for high-risk PCa.
Source of Funding: NIH Grants R01CA189295, U01CA239141 and P30CA240139
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