A Designer Artificial Transcription Factor Stably Reprograms Cancer Cells by Targeted DNA Methylation

Abstract

The ability to stably alter gene expression states via epigenetic reprogramming hold significant implications for controlling breast cancer and other cancers. Herein, we describe a novel approach using artificial transcription factors (ATFs) to epigenetically target and stably down‐regulate genes that are aberrantly expressed in breast cancer. Our objective was to develop ATFs that contain zinc finger proteins coupled with DNMT3a to target and epigenetically repress Maspin (tumor suppressor) and SOX2 (oncogene). Upon ATF transduction in SUM159 cells that express Maspin at a moderate level, we significantly down‐regulate Maspin expression levels and repression was directly associated with ATF‐mediated DNA methylation adjacent to the ATF binding site. ATF‐transduced cells formed colonies in soft agar and selected clonal populations expanded from these colonies displayed persistent, heritable silencing of Maspin over many cell generations due to promoter methylation. Upon ATF transduction in MCF7 cells that overexpress SOX2, we observed a significant down‐regulation of SOX2 followed by cell arrest and death. These observations combine to strongly suggest that this technology will enable directed DNA methylation that can be utilized to modify the epigenetic status of any target gene in any cancer cell type. A.G.R. supported by ACS Postdoctoral Fellowship 116066‐PF‐08‐166‐01‐GMC.