Synthetic epigenetic reprogramming of mesenchymal to epithelial states using the CRISPR/dCas9 platform in triple negative breast cancer [RNA-seq]

Epithelial-mesenchymal transition (EMT) is a reversible transcriptional program subverted by cancer cells to drive cancer progression. Transcription factor ZEB1 is a master regulator of EMT, driving disease recurrence in poor outcome triple negative breast cancer (TNBC). Here, we silence ZEB1 in TNBC models by CRISPR-mediated epigenetic editing, resulting in nearly complete repression of ZEB1 in vivo, accompanied by long-lasting tumor inhibition. Integrated transcriptomic and epigenetic profiling identified a ZEB1-dependent gene-signature associated with transcriptional up-regulation, promoter DNA demethylation and enhanced chromatin accessibility in core cell adhesion loci, demonstrating epigenetic reprogramming towards a more epithelial state. Epigenetic shifts induced by ZEB1-silencing are enriched in a subset of human breast tumors, illuminating a clinically-relevant hybrid-like state. Thus, the synthetic epi-silencing of ZEB1 induces stable “lock-in” epigenetic reprogramming of mesenchymal tumors associated with a distinct epigenetic landscape. We outline approaches to stably reprogram EMT for targeting poor outcome breast cancers driven by oncogenic transcription factors. Overall design: RNA-sequencing (RNA-seq) data for SUM159 cells and MDA-MB-231 cells with the following conditions: wildtype cells, and cells with pLV-KRAB either with no targeting gRNAs (No targeting gRNA), a combination of 4 gRNAs targeting the promoter of ZEB1 (All 4 gRNAs), or a single gRNA targeting the promoter of ZEB1 (gRNA #4).