A New Tool for Discovery, Assay and Validation of Biomarkers in Prostate Cancer

DESCRIPTION (provided by applicant): In the United States, the incidence of prostate cancer accounts for approximately 30,000 male deaths annually (1). Prostate-specific antigen screening can detect early-stage prostate cancer, but it is nonspecific and is not recommended by the Centers for Disease Control and Prevention (2). The discovery of new biomarkers for early diagnosis and prognosis of prostate cancer will therefore be important for improvements in the management of the disease and in developing new treatments to increase survival rates. The goal for Phase I of this Project is to optimize a new proteomics technology, Differential Capture Proteomics(tm) (DCP) in human serum. The team of investigators submitting this proposal is at Differential Proteom ics Inc., which has received a patent for the technology. DCP identifies the differences in protein composition between two fluid or tissue samples and also simultaneously creates affinity reagents for each of the identified difference proteins. The DCP pr ocess consists of three major components: DCP Component 1: Affinity binders originating from a display library are selected using an innovative process. The product of the selection is a set of affinity reagents (peptides from phage display libraries in th e current work plan) that recognize just the proteins that are different in amount or type between the two samples (Figure 2, DCP Steps 1-4). DCP Component 2: The phage-displayed peptides are reformatted en masse into a single affinity matrix suitable for purifying all of the detected difference proteins simultaneously (Figure 2, DCP Step 5). DCP Component 3: The specific affinity matrix is used to capture the difference proteins from each of the two samples. These proteins are then identified and quantifie d using mass spectrometry, allowing a direct comparison of their level and type in the two samples (Figure 2, DCP Steps 6-7). Studies to date to optimize the DCP technology have successfully focused on a model system. However, the application of DCP for ca ncer biomarker discovery in patient serum samples has yet to be demonstrated with an optimization study. Such a study is proposed here, in which doped prostate cancer-associated biomarkers (representing a model prostate cancer patient sample) will be teste d for detectability at clinical sample level concentrations. The proposed study will use five specific prostate cancer-associated protein proteins, for which there are commercially available immunoassays. They are Prostate Specific Antigen, Kallikrein 6, P rostate Acid Phosphatase, IGF Binding Protein 3, and TGF Beta 1. The study proposed herein has two specific aims. Specific Aim 1: To ensure that the pooled Random Peptide Phage Display Libraries actually contain binding phage species against each of the fi ve cancer proteins chosen. Specific Aim 2: To determine how well Differential Capture Proteomics(tm) detects the differences between two human serum samples, one of which is doped with the mixture of five cancer-associated proteins, and how specific the af finity capture reagents are that are generated as part of the process. The success of this Phase I study will lead to a Phase II project for testing multiple prostate cancer patient serum samples for novel biomarker discovery, assay generation, and validat ion. PUBLIC HEALTH RELEVANCE:Differential Capture Proteomics will be significantly more cost- and time-effective than current approaches to biomarker discovery. This technology is a breakthrough system for the integrated discovery, verification, and valida tion of biomarkers leading to clinically important assays, including those for biomarkers of prostate cancer.