Abstract P6-01-05: Novel cytotoxic RNA aptamers that distinguish between metastasis-prone and indolent breast and prostate cancers
Authors: Bishopric NH , Speransky S , Serafini P , De la Fuente AC , Bicciato S , El-Ashry D , Lippman ME 
Published: March 2017

Abstract
Background: Prostate and breast cancers are, respectively, the most common malignancies diagnosed in men and women worldwide. These cancers develop in different organs but have significant biological similarities: both are typically hormone-dependent, and both require early detection and treatment, as metastatic disease is incurable. At the same time, early stage tumors are often over-treated. Better markers for tumor aggressiveness would help to optimize treatment strategies in both breast and prostate cancer.
Objective: Develop high affinity nucleic acid oligomers (aptamers) that can distinguish between indolent tumors that will remain organ-confined and those with heightened potential to metastasize.
Methods: We performed subtractive RNA Cell-SELEX to select for surface ligands specific to aggressive tumors, using as a positive selector the highly metastasis-competent LN3 subclone of prostate cancer cell line LNCaP, and as negative selectors parental LNCaP and a non-metastasizing subclone, Pro5. . The RNA aptamer pool was PCR amplified from a 40-mer random nucleotide cDNA library with appropriate flanking sequences, and transcribed in vitro. After 11 SELEX cycles, aptamer pools from cycles 0, 4, 9, and 11 were subjected to high-throughput sequencing. Eight aptamers, representing 4 sequence families, were chosen for further study. Representative relevant and irrelevant aptamers were labeled with Cy3 and used to stain LNCaP-LN3 and LNCaP-Pro5 in culture and as xenografts in NOD-SCID-gamma mice. Additional cell and tumor lines from both breast and prostate cancer were used for validation.
Results: Two aptamers bound avidly to the surface of the aggressive LNCaP-LN3 subclone, both in culture and in fixed xenograft tumors, but not to the indolent Pro5 subclone. Aptamer binding led to rapid and specific cytotoxicity in vitro but had no effect on other cell lines to which the aptamer did not bind. The same aptamers showed similar high specificity for multiple other metastasis-competent cancer cells, including the prostate adenocarcinoma PC-3 and PC-3ML subclones, breast cancer cell lines MDA-MB436 and MDA-MB231, and the primary dissociated breast tumor DT28 , while exhibiting no detectable binding to the non-metastasizing MCF-7 breast cancer cell line and DT22 primary dissociated breast tumor cells, and the non-tumorigenic prostate epithelial cell line RPWE-1.
Conclusion: We identified RNA aptamers that specifically bind to metastasis-prone prostate cancer and breast cancer cell surface targets, and exert cell-specific toxicity dependent upon aptamer binding. While the target(s) remain to be identified, we propose that these aptamers may discriminate between progressive and indolent breast and prostate cancers, and may have substantial promise as anticancer agents either alone or suitably liganded to toxic moieties.
Citation Format: Bishopric NH, Speransky S, Serafini P, De la Fuente AC, Bicciato S, El-Ashry D, Lippman ME. Novel cytotoxic RNA aptamers that distinguish between metastasis-prone and indolent breast and prostate cancers [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-01-05.