Aptamer-based Proteomic Analysis for Cancer Signatures

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DESCRIPTION (provided by applicant): Cells are comprised of many types of molecules, including small organic and inorganic molecules, carbohydrates, lipids, proteins, and nucleic acids. All of these molecules act in an integrated fashion at the molecular level to result in macroscopic cellular, tissue, and systemic phenotypes. Complete understanding of biological function would require accurate measurement of all of these molecules simultaneously. Vlicroarrays have made it possible to analyze nucleic acids at the genome-scale, but techniques for other cellular molecules currently lag behind. With proteins as another class of molecules prominent in cellular function and communication, intense effort is being invested toward the development and implementation of proteomic strategies for the analysis of clinical and research samples. Current proteomic strategies take many forms but can be grossly categorized as either array-based or not. Multiple array-based strategies nave been developed based on antibody recognition of the proteins of interest. The use of antibodies, however, brings with it issues of reproducible antibody production, target binding affinity, and denaturation. It is proposed to develop a strategy by which cancer signatures can be established by measuring protein concentrations in an array-based proteomic technology using aptamers, protein-binding RNA molecules. To ensure that the method can be expanded to parallel studies, each aptamer will be labeled with a molecular barcode. The protein concentration will then be obtained by measuring the concentration of the barcode on the aptamer that binds specifically to that protein. The method will be tested on a cell-culture model of Type 2 diabetes, providing valuable data for technique development as well as an improved understanding of the response of the liver to inflammatory stresses. Aptamers will be used for solution phase measurement of acute phase proteins as a preliminary demonstration of the possibility of future implementation of the strategy in a microarray format. The specific aims of the proposed work are to: i) generate molecular barcode-containing, structure-switching aptamers by in vitro selection and identify conserved sequence and structural features; ii) quantify the affinities and association kinetics of aptamertarget protein binding interactions; and iii) measure the acute phase protein expression profile of stimulated rat hepatocytes in cell- culture using the molecular barcode-containing aptamer strategy.