Clinical Translation of a Large Oncosome-Based Prostate Cancer Blood Test

ABSTRACT - The focus of this proposal is on lethal, metastatic prostate cancer (PC). The aim of this study is to develop an innovative, minimally invasive, liquid biopsy assay that can be used to identify molecular subtypes of lethal prostate cancer PC in patients with a biologically aggressive disease. Phenotyping Large

Oncosomes for Ultimate Evaluation of Patients Status (PLUS) will identify biomarkers of short/long response to treatment, and progressively assess tumor phenotype during PC evolution and under treatment pressure. We propose to focus on extracellular vesicles (EV) known as large oncosomes (LO) that are identified in the plasma

of patients with aggressive cancer. Using gold standard methods, we obtained pure populations of LO and performed extensive mass spectrometry and NGS experiments that identified a set of proteins and RNA markers that have been validated by multiple experiments in vitro and in a few pilot patient cohorts, as explained in

preliminary results. In this application, we will employ innovative technologies to translate our efforts to define LO-based signatures to the CLIA laboratory to determine clinical utility of our liquid biopsy approach in PC patients with lethal disease, both in the castration resistant and hormone sensitive space. We will leverage an

expansive cohort of clinically annotated PC specimens (N=600), both retrospectively and prospectively collected from 2 independent sites. In Aim 1, we will perform analytical validation of LO isolation technologies for clinical use. In Aim 2, we will develop an LO-centered multianalyte assay to detect lethal PC and predict ARSI response.

In Aim 3 we will assess the sensitivity and specificity of PLUS in metastatic hormone-sensitive PC patients to predict lethal outcomes. We will continue to focus on PC because of the significance of PC open clinical questions, of the challenges relative to this tumor-type in liquid biopsy development, and our extensive

experience in the field of PC molecular landscape. Yet, there is great opportunity for our LO-based assay to be expanded to other tumor types in the future. Our study is technologically innovative and will likely result in the identification of new markers and ultimately in the application of a microfluidic device to the CLIA lab. The M-PI

team brings expertise not only on EVs (Di Vizio, Stott, Demichelis), but also on ctDNA (Demichelis) and CTCs (Stott) and propose orthogonal approaches to determine which method, among bead-based and microfluidic capture, which will be benchmarked against density gradients, has the best performance in a complex clinical

lab.