title: Facile Discovery of Cell-Surface Protein Targets of Cancer Cell Aptamers.
abstract: Cancer biomarker discovery constitutes a frontier in cancer research. In recent years, cell-binding aptamers have become useful molecular probes for biomarker discovery. However, there are few successful examples, and the critical barrier resides in the identification of the cell-surface protein targets for the aptamers, where only a limited number of aptamer targets have been identified so far. Herein, we developed a universal SILAC-based quantitative proteomic method for target discovery of cell-binding aptamers. The method allowed for distinguishing specific aptamer-binding proteins from nonspecific proteins based on abundance ratios of proteins bound to aptamer-carrying bait and control bait. In addition, we employed fluorescently labeled aptamers for monitoring and optimizing the binding conditions. We were able to identify and validate selectin L and integrin α4 as the protein targets for two previously reported aptamers, Sgc-3b and Sgc-4e, respectively. This strategy should be generally applicable for the discovery of protein targets for other cell-binding aptamers, which will promote the applications of these aptamers.
authors.affiliation: From the ‡Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; §Department of Chemistry, University of California, Riverside, CA92521-0403.
authors.forename: Tao
authors.initials: T
authors.lastname: Bing
authors.affiliation: From the ‡Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; Yinsheng.Wang@ucr.edu sgdh@iccas.ac.cn.
authors.forename: Dihua
authors.initials: D
authors.lastname: Shangguan
authors.affiliation: §Department of Chemistry, University of California, Riverside, CA92521-0403 Yinsheng.Wang@ucr.edu sgdh@iccas.ac.cn.
authors.forename: Yinsheng
authors.initials: Y
authors.lastname: Wang
mesh_terms: D052157:Aptamers, Nucleotide / Q000378:metabolism*; D001120:Arginine; D002247:Carbon Isotopes; D045744:Cell Line, Tumor; D005434:Flow Cytometry; D006801:Humans; D039441:Integrin alpha4 / Q000378:metabolism*; D007553:Isotope Labeling; D019041:L-Selectin / Q000378:metabolism*; D008239:Lysine; D009587:Nitrogen Isotopes; D040901:Proteomics; D021241:Spectrometry, Mass, Electrospray Ionization; D053719:Tandem Mass Spectrometry
chemical_list: D052157:Aptamers, Nucleotide; D002247:Carbon Isotopes; D009587:Nitrogen Isotopes; D019041:L-Selectin; D039441:Integrin alpha4; D001120:Arginine; D008239:Lysine