Project 2: Integrating a Novel MiPS-Based Next-Generation Sequencing Urine Assay for the Early Detection of Unfavorable Risk Prostate Cancer

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Project 2 of the Michigan Prostate SPORE seeks to improve the early detection of unfavorable risk prostate cancer (PCa) by employing a novel urine-based next-generation sequencing (NGS) assay. Recent studies have demonstrated that men with certain germline genetic alterations (e.g., BRCA 1/2 and Lynch syndrome) may be at increased risk of potentially aggressive PCa. Men at increased genetic risk represent a newly recognized group in whom early detection is particularly compelling. Generally speaking, a central problem inherent to PCa screening is the profound overdiagnosis of Gleason 6 (low risk) disease. To counterbalance the overtreatment of Gleason 6 PCa, a number of active surveillance (AS) strategies have been introduced. Transition to definitive treatment (e.g., surgery or radiation) can be triggered by evidence of risk reclassification often due to grade progression. Improved early detection of grade progression in men with previously diagnosed Gleason 6 PCa on AS represents a major opportunity to improve and optimize resource utilization (prostate biopsy and MRI) as well as the diagnosis of clinically significant PCa. How to reliably identify potentially aggressive PCa so treatment can be appropriately recommended continues to represent a critical knowledge gap. Building on prior work from a successful SPORE project involving the Mi Prostate Score (MiPS) test (using transcription-mediated amplification quantification of urine KLK3, PCA3, and TMPRSS2:ERG), we have developed a novel urine-based NGS assay (MiPS-NGS) to detect unfavorable risk (≥Gleason 7) PCa. MiPS-NGS is a targeted RNA-seq assay comprised of 83 prostate-, PCa-, and aggressive PCa-specific transcripts (e.g., lncRNAs, ETS genes fusions, HOXB13). We hypothesize that MiPS-NGS can improve the early detection of unfavorable risk PCa and will test this through the following Specific Aims: Aim 1: To assess the utility of MiPS-NGS as a PCa early detection assay in men at high genetic risk. Aim 2: To determine whether MiPS-NGS can predict grade progression in men on AS. Sub-Aim 2.1: To test MiPS-NGS alone for the early detection of grade progression in two prospective AS cohorts. Sub-Aim 2.2: To develop a multi-dimensional clinical tool based on MiPS-NGS to optimize early detection of grade progression in men on AS. Upon successful completion of this project, we will have established a role for our innovative urine NGS assay in the early detection of unfavorable risk PCa in two important contexts: 1) men at high genetic risk and 2) AS. Our interdisciplinary team, comprised of experts in clinical management, genomics, bioinformatics, biostatistics, and cancer genetics, coupled with our unique institutional resources (Michigan Urological Surgery Improvement Collaborative (MUSIC), University of Michigan Prostate Cancer Risk Clinic (PCRC), and the Karmanos Cancer Institute) and collaborations (University of Washington/Fred Hutchinson Cancer Research Center and the National Cancer Institute), is uniquely poised to execute our stated research plan.