EMBL Seminars

Abstract
Epigenome editing (EE), i.e. the targeted modulation of gene expression without altering the underlying DNA sequence, offers a promising therapeutic strategy for silencing disease-associated genes. For most clinical applications, an optimal EE platform should deliver robust, specific, and durable gene repression following only transient expression of the epi-editor. To demonstrate the feasibility of this approach, we engineered, optimized, and screened a series of evolved epi-editors. Specifically, we systematically refined: (i) the DNA-binding domain targeting the murine Pcsk9 locus; (ii) the composition and configuration of epigenetically active effector domains; and (iii) a liver-targeted non-viral delivery system. After extensive optimization, a single transient administration of the evolved epi-editor in mice yielded long-lasting (>300 days) and potent repression of circulating Pcsk9 levels (up to −70%). Genome-wide specificity profiling showed extensive methylation at the Pcsk9 promoter with minimal effects on other loci, demonstrating that epi-editors can be engineered for high specificity. Collectively, these findings provide the first in vivo proof-of-concept for “hit-and-run” epigenetic editing. Building on this foundation, we are now working to further evolve epi-editors and expand the applicability of EE to previously inaccessible tissues and disease contexts.

Abstract

Epigenetic components regulate many biological phenomena during development and normal physiology. When dysregulated, epigenetic components can also accompany or drive diseases. One main class of epigenetic components are Polycomb group proteins. Originally, Polycomb proteins were shown to silence gene expression. We found that this function involves the regulation of 3D chromosome folding and we found that Polycomb components can induce the formation of long-distance interactions or chromatin loops that may play instructive roles in gene regulation as well as serve as scaffolding elements that contribute to enhancer-promoter specificity. Perturbation of Polycomb components is involved in human cancer and leads to tumorigenesis in flies. Surprisingly, even upon a transient depletion followed by restoration of the full Polycomb compendium, epithelial cells lose their normal differentiated fate, continue proliferating and establish aggressive tumors, demonstrating that cancer can have a fully epigenetic origin. Similarly, transient perturbation of histone acetylation in mouse ES cells and gastruloids shows that they can record chromatin changes and that this results in cellular memory of the perturbation states. The implication of these data will be discussed.