Targeted Epigenetic Modulation Outperforms Nuclease- and Deaminase-Based Editing for Durable Pcsk9 Silencing in a Clinically Relevant Delivery System

Abstract

Inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9) lowers low-density lipoprotein cholesterol, a major risk factor for cardiovascular disease. Although several gene therapy strategies targeting Pcsk9 have been developed, direct comparisons across modalities are limited. To address this, we systematically evaluated cytosine base editing, nuclease-based CRISPR-Cas9, and epigenetic gene editing for Pcsk9 suppression. We first engineered a cytosine base editor to introduce a premature stop codon, then optimized and characterized an epigenetic editor, and finally delivered all modalities as mRNA formulated in Arcturus lipid nanoparticles (LUNAR(R)) into wild-type mice, benchmarking them against conventional CRISPR-Cas9 and GalNAc-siRNA. Remarkably, epigenetic editing achieved the most efficient and sustained repression of PCSK9, maintaining low protein levels throughout the entire 30-day study period. By comparison, cytosine base editing reduced PCSK9 with minimal double-stranded DNA breaks and off-target effects, but editing precision requires further improvement, while GalNAc-siRNA produced only transient suppression, limiting its suitability for a one-time therapeutic approach. Collectively, these findings highlight the superior durability and efficacy of epigenetic gene editing and provide proof-of-concept for its combination with LUNAR(R) delivery as a promising strategy for long-lasting hepatic-targeted therapy.