Project 1: Identification and Validation of Panel of Early Cell Surface Gene Targets

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Abstract – This research project falls under genomics of tumor heterogeneity and their impact on the progression toward EAC as one of the possible areas defined in RFA-CA-16-006. We have previously identified EGFR and ErbB2 using gene expression profiles as promising cell surface targets based on high- frequency gene amplification for imaging of EAC, and have developed peptides that are specific for these targets. We now aim to identify early targets that arise in progression of BE to EAC. We expect to find greater variability and lower levels of expression for early compared with late targets, thus have prepared a more rigorous approach. We will use Affymetrix arrays and RNAseq analysis to identify early gene targets that are overexpressed on the cell surface and can be developed for imaging. We will use these sophisticated genomic tools to provide a comprehensive analysis of gene alterations, mutations, and DNA copy number variations in human esophagus specimens to identify a panel of promising candidates. We will rigorously validate candidate targets using quantitative RT-PCR and immunohistochemistry on tissue microarrays prepared from an independent cohort of specimens. This approach requires a large number of HGD that are uniquely available in our large tissue biorepository of n = 780 human esophageal specimens, including n = 560 EAC, collected de novo (no neo-adjuvant chemo or radiation therapy). For each early target validated, we will transfect telomerase-immortalized BE cells to overexpress the target on the cell surface for use in developing the monomer and dimer peptides in Project 2. Successful completion of these aims will result in identification and validation of a panel of early gene targets that arise in progression of BE to EAC that will be used in Project 2 to develop novel peptide imaging agents.