Abstract
Genomic classification (GC) in prostate cancer has demonstrated ability to distinguish patients with favorable disease from those most at risk of metastasis and cancer-related death. GC contributes to personalization of care by identifying subsets of patients for whom treatment intensification with radiation and hormonal therapy may be warranted. In treatment-naïve patients, risk stratification by standard clinical pathologic factors and GC can be influenced by sampling errors inherent to prostate cancer biopsy. There is an unmet need for liquid biopsy tests to support the management of patients with intermediate and high-risk prostate cancer. Exosome-based liquid biopsies are emerging as a clinically effective platform for minimally invasive and highly sensitive diagnostics in diverse types of cancer. The mRNA and long non-coding RNA encapsulated in exosomes are of particular interest since most proven cancer diagnostic markers are long RNA-based. In this project we undertake the development of exosome-based liquid biopsies that may circumvent sampling challenges associated with tissue biopsy-dependent GC to stratify patients with clinically significant prostate cancer.
Our pilot biomarker discovery study compared plasma exosomal RNA profiles from 11 high-risk and 9 low-risk, treatment-naïve, biopsy-confirmed patients together with 4 healthy controls. The high-risk patients are enrolled in a radiotherapy trial and the low-risk patients in an active surveillance trial. Exosomes were isolated from 1 ml plasma samples and exosomal RNA prepared. A hybrid-capture-based Next Generation RNA Sequencing (RNAseq) analysis was performed on enriched transcripts of exons, 3’ and 5’ untranslated RNA and long non-coding RNA (lncRNA) to profile and identify differentially expressed long RNAs in these samples.
We detected over 10,000 protein coding genes and ∼400 lncRNAs in each plasma sample using exosomal RNAseq. 273 genes were differentially expressed between high-risk vs control but not in low-risk vs control. This pilot study identified four potential plasma exosomal biomarkers of high-risk prostate cancer. These include three protein coding mRNA transcripts that showed > 20-fold lower expression in plasma from high-risk in comparison to low-risk patients; TCGA data show that two of these mRNA markers are also downregulated in prostate cancer tissue in patients with worse survival. In addition, one lncRNA was identified that showed > 20-fold higher expression in plasma from high-risk in comparison to low-risk patients. Together, these represent early data for potentially novel liquid biopsy RNA biomarkers for high-risk prostate cancer.
Plasma exosomal long RNA provides a rich reservoir of currently untapped biomarkers for high-risk prostate cancer. Radiotherapy trial: BLaStM NCT02307058; active surveillance trial: MAST NCT02242773.