Approximately 55% of prostate cancers (PCA) harbor cancer specific gene fusions. This represents an important opportunity to develop a non-invasive highly specific test for the early detection of PCA. Implementation of a urine assay to detect the TMPRSS2-ERG gene fusion is already underway, demonstrating a high specificity. A logical next step in biomarker development is the exploration of novel cancer specific gene fusions and somatic alterations. The overall goal of this proposal is to discover and validate PCA specific biomarkers that can be non- invasively detected in the urine. We have taken a Systems Biology approach integrating state-of-the-art RNA-sequencing (RNA-seq) and DNA 6.0 single nucleotide polymorphism (SNP) arrays with novel computational approaches for analysis.
In Aim 1, we will identify novel gene fusions with RNA-seq and in Aim 2 we will determine somatic copy number alterations (gains and losses) associated with altered gene transcript expression as determined by RNA-seq from Aim 1. We will use 100 frozen PCA samples and 25 paired benign prostate tissues in the discovery step of Phase 1 for initial discovery of PCA specific biomarkers. The PCA samples will be equally divided based Gleason Score (tumor grade), 6 (3+3), 7 (3+4), 7(4+3), and 8-10. We will also attempt to balance for age at time of biopsy, PSA levels, and tumor stage (organ confined (pT2) versus extraprostatic extension (pT3). Tumors will be evaluated for known ETS gene fusions (e.g., TMPRSS2- ERG, SLC45A3-ETV1, etc.). We will also attempt to balance samples based on known fusions versus no fusions based on the current knowledge of gene fusions. The verification step of Phase 1 will occur using FISH for the novel gene fusions and immunohistochemisty (IHC) and/or FISH for somatic alterations to determine PCA specificity on tissue microarrays with over 200 PCA samples and 400 benign tissues. We will also explore PCA specificity in 100 urine samples collected from men with and without PCA using a rigorous EDRN Protocol on local samples. RT-PCR assays for fusion genes and over or under expression of somatically altered genes will be tested using mRNA for PSA as an internal control. The biostatistical group will supervise all steps of the analysis and help prioritize the lead candidates in conjunction with the computational biology group. We anticipate nominating 20 candidates from each biomarker category per year and will hand off 5-10 for formal Phase 2 validation by the EDRN Clinical Validation Center of Harvard/Michigan/Weil Cornel (outside the scope of this application). Discoveries made in this proposal will be strong candidates for clinical validation as part of the Early Detection Research Network PCA program. This study will also generate important insight into the molecular biology of PCA, which has broad implications in understanding disease progression and identifying potential drug targets. Finally, the computational tools and dataset will be important resources for the research community at large.

Public Health Relevance

Prostate Cancer is the most common non-skin cancer and the second leading cause of cancer death in American men. Screening with serum prostate specific antigen (PSA) test for the early detection of prostate cancer is widespread, with approximately half of all 50- to 79-year-old American men having had a PSA test in the past 2 years. However, the PSA test has several severe limitations as a prostate cancer screening test. The PSA test is not specific for prostate cancer, as it is commonly elevated in benign conditions of the prostate gland, and in contemporary series where men most commonly undergo needle biopsy for an elevated PSA level, less than half of biopsies result in a diagnosis of prostate cancer. The PSA test is also not sensitive, as demonstrated by the recent prostate cancer prevention trial (PCPT), which demonstrated that 15% of men with PSA in the normal range (0-4.0ng/ml) have prostate cancer, with 15% of them having high grade disease. Therefore, the PSA screening test leads to a significant number of unnecessary biopsies and simultaneously misses significant cancers. Our research proposes to develop the next generation prostate cancer screening test, a test that is positive in all and only men with prostate cancer. Our approach will be to harness new molecular understanding of prostate cancer biology. The main focus will be to discover molecular alterations that occur only in the cancerous state and not in the benign state. One important finding, discovered in 2005, was that at least half of all prostate cancers have a cancer specific gene rearrangement. This new gene only exists in prostate tumors. Therefore by developing a test to detect these rearrangements, we can already begin to improve on the current PSA test. This grant will expand on this landmark discovery by trying to characterize all prostate cancers either by the presence of a gene rearrangement or another molecular lesion only seen in cancer. The assembled group, expert in prostate cancer test development and computational biology, is well positioned to achieve the important stated goal of developing the first draft a more accurate prostate cancer diagnostic test. As the U.S. population ages, more and more men will need to be screened for prostate cancer. A more accurate test will reduce both the psychological and financial burden of a false positive PSA screening test while not missing treatable prostate cancers.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
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Special Emphasis Panel (ZRG1-OTC-N (02))
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Kagan, Jacob
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Weill Medical College of Cornell University
Schools of Medicine
New York
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