High-Throughput Epitope Characterization of Cancer-Related Biomarkers.

Ligand-protein interactions are important for molecular event recognition in cancer-based cellular processes and pathways. To understand complicated processes such as these requires primary molecular level information that is gained by studying and identifying the epitopes of proteins recognized by antibodies. Our approach uses high-throughput epitope extraction and epitope excision methods to generate initial candidate epitopes and build peptide libraries. Subsequent peptide binding investigations of these peptide libraries provides us with detailed epitope characterization. In this way we have characterized the epitopes of ten cancer-related proteins. Resultant information can then be utilized in the design of biologic proteins as cancer therapeutics, diagnostics, vaccines and theragnostics. This fusion of therapeutics and diagnostics will place increasing focus on the applications in large sample populations and at point of patient care. To assimilate these applications, and especially theragnostic testing, will require amassed information and integration from analyses of large sample numbers from multiplexed biomarkers. Thus, the focus of this research does not rely on a single marker, but rather on the integration of information from diverse sets of biomarkers and their ligand components. This work is supported by National Institute of Cancer, Contract No: HHSN261200900067C to KT and AB. (poster)