Generation of an Aptamer Targeting Receptor-Type Tyrosine-Protein Phosphatase F

Abstract

Cell-SELEX is a powerful tool to generate aptamers that specifically bind the native molecules on living cells. Here, we report an aptamer ZAJ4a generated by cell-SELEX. The molecular target of ZAJ4a was pulled down by the enriched cell-SELEX pool and identified to be the receptor-type tyrosine-protein phosphatase F (PTPRF) through a stable isotope labeling using amino acids in cell culture (SILAC)-based quantitative proteomic method. ZAJ4a showed high binding affinity with nanomolar range to cancer cells expressing PTPRF. Meanwhile, PTPRF was proven to highly express on several cancer cell lines using ZAJ4a as a molecular probe and to highly express in many kinds of cancer samples using gene expression profiling interactive analysis (GEPIA2) from the TCGA and GTEx databases. These results indicate that the aptamer generated by cell-SELEX showed good specificity at the molecular level. This cell-SELEX and target identification strategies show great potential for identifying biomarkers on the cell surface.

Aptamer-Based Enforced Phosphatase-Recruiting Chimeras Inhibit Receptor Tyrosine Kinase Signal Transduction

“…31 It features an extracellular region, a single transmembrane region, and intracellular catalytic domains. Therefore, PTPRF-targeted aptamer Zaj4a 32 was utilized as a model to construct aptamer-based RIPR (Apt-RIPR) chimeras to recruit PTPRF to and inhibit RTKs of interest, e.g., c-Met and epidermal growth factor receptor (EGFR). As shown in Scheme 1, multiplex Apt-RIPR chimeras contain a PTPRF-targeted module (aptamer Zaj4a), an RTK-targeted module (for example c-Met-targeted aptamer SL1 33 or EGFR-targeted peptide GE11 34 ), and a linking spacer made from DNA duplex or chemical bridging molecules (Scheme 1a).…”