The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells

Abstract

Disease states, such as breast cancer, arise from the disruption of chromatin, the central DNA-protein structures that package human genetic material. Mounting evidence from genome-wide studies across cancers show that Polycomb-mediated repression of sets of genes, called Polycomb modules, is strongly linked to a poor prognosis. We developed a synthetic transcriptional activator to release silenced genes from the repressed state. The Polycomb-based Transcription Factor (PcTF) is a synthetic effector that accumulates at methyl-histone marks and regulates hundreds of gene targets, including tumor suppressors. We recently reported the activity of PcTF in bone, blood, and brain sarcoma-derived model cell lines. Here, we expand our investigation of PcTF to three breast cancer-derived cell lines. We expressed PcTF in drug-responsive (MCF-7, BT-474) and nonresponsive triple negative (BT-549) breast cancer cell lines. RNA-seq showed that hundreds of genes were up-or down-regulated by PcTF as early as 24 hours after transfection. BT-549, the triple-negative cancer cell line, showed the highest number of PcTF-activated genes. We demonstrate the anti-cancer potential of PcTF by identifying 15 tumor suppressor genes that are upregulated across the three cell types. The data also provide new mechanistic insights into the relationship between chromatin organization and PcTF-mediated regulation of genes. Our results have exciting implications for cancer treatment with engineered biologics.

Delivery of cell-penetrating chromatin sensor-actuators to human osteosarcoma cells

“…We have previously designed chromatin sensor-actuator proteins that bind histone post-translational modifications and co-activate groups of repressed genes. We demonstrated that a H3K27me3-specific sensor-actuator called PcTF activates epigenetically repressed tumor suppressor genes in several cancer cell lines [18,19] . However, experiments with epigenome editors and sensor-actuators have relied heavily on the delivery and overexpression of fusion-encoding transgenes.…”