Durable and efficient gene silencing in vivo by hit-and-run epigenome editing [RNA-seq]
Permanent epigenetic silencing with programmable editors equipped with transcriptional repressors holds great promise for the treatment of human diseases. However, to unlock its full therapeutic potential, a formal proof of durable epigenetic silencing upon transient editors' delivery in vivo is needed. To this end, we targeted here Pcsk9, a hepatocyte-expressed gene involved in cholesterol homeostasis. In vitro screening of different editors' designs indicated zinc finger proteins as the best-performing DNA binding platform to efficiently silence murine Pcsk9, with minimal genome-wide transcriptional and epigenetic perturbations. A single administration of lipid nanoparticles loaded with the editors' mRNAs halved circulating levels of Pcsk9 for nearly 1 year  in mice. Notably, Pcsk9 silencing and accompanying epigenetic repressive marks persisted following forced also upon liver regeneration, further corroborating heritability of the newly installed epigenetic state. This study lays the foundation for the development of in vivo therapeutics  modalities based on epigenetic silencing. Overall design: Comparative analysis of transcriptome from Hepa 1-6 cells treated with ZFP-based or dCas9-based epi-editors, targeting Pcsk9 promoter. Three controls was added: i) untargeted ETRs, i.e. ZFP-based ETRs targeting the GFP; ii) Cas9 and a sgRNA targeting Pcsk9 exon 1; iii) cells transfected with the mRNA of a GFP