Abstract 4337: Selection of DNA aptamers for an ovarian cancer cell line using high-throughput sequencing.

The mucin, MUC16, facilitates metastasis and immuneprotection of ovarian tumors. Therefore, agents that effectively target MUC16 expressing ovarian cancer cells will be useful for diagnostic and therapeutic applications. Here, we have utilized the Cell-based Systematic Evolution of Ligands by Exponential Enrichment (cell-SELEX) approach to generate high affinity single-stranded DNA (ssDNA) aptamers as agents for detection and treatment of MUC16-positive ovarian tumors. An ssDNA aptamer library composed of ∼100 trillion sequences was subjected to ten iterative rounds of negative and positive selection using the MUC16-knockdown and MUC16-positive ovarian cancer cell line, OVCAR-3. Aptamers from each round were amplified by asymmetric PCR and subjected to high throughput NextGen sequencing. Eight ssDNA aptamers enriched through the selection process were identified by bioinformatics analysis and their selectivity and affinity for MUC16-positive cells was determined by flow cytometry. Two of these aptamers (Apt-1 and Apt-8) showed significant binding to the MUC16-positive OVCAR-3 with a Kd of 24 and 28 nM, respectively. In contrast, Apt-1 and Apt-8 only weakly recognized the MUC16-knockdown OVCAR-3 cells. M-Fold analysis indicated that Apt-1 and Apt-8 had defined secondary structures resulting from ordered base pairing of the ssDNA. The inclusion of NextGen sequencing techniques has therefore allowed rapid identification of theranostic aptamers from an exhaustive library of ssDNA sequences. This study provides a streamlined method for development of theranostic aptamers that can be used to recognize and target MUC16 expressing ovarian cancer cells. Citation Format: Rebecca J. Whelan, Arvinder Kapur, Mildred Felder, Jeff Nie, Manish S. Patankar. Selection of DNA aptamers for an ovarian cancer cell line using high-throughput sequencing. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4337. doi:10.1158/1538-7445.AM2013-4337