The recent revolution in novel nucleic acid-targeting systems has generated incredible opportunities for treating disease by targeted manipulation of DNA and RNA. While the emphasis thus far has largely been on genome editing to treat rare, inherited disorders, this represents only one mechanism by which these DNA-targeting tools can be applied to improve human health. In fact, a significantly broader set of pathologies can be addressed by modulating gene regulation and epigenetic states, in contrast to altering underlying DNA sequences. Moreover, this approach has a number of advantages with respect to efficiency, safety, and reversibility. While several studies have demonstrated proof-of-principle that in vivo somatic cell epigenome editing can be used to program cell phentoypes and modulate therapeutic targets, there are a number of challenges that must be overcome to prepare this technology for treatment of human disease. First, an ideal DNA-targeting system that is facile and broadly applicable has yet to be developed. While CRISPR-Cas9 systems have dramatically transformed genome engineering, their application for human epigenome editing is limited by specificity, incompatibility with size-restricted viral vectors, and pre-existing immunity in the human population. Therefore, we will mine bacterial genomes for novel small CRISPR-Cas9/Cas12 systems that meet these criteria for in vivo epigenome editing. We will examine genome-wide specificity of epigenomic modifications with unbiased assays and assess both induced immunity in mouse models and pre-existing immunity in human samples. Second, it remains unclear in the field of epigenome editing which epigenetic modifications are necessary and sufficient to achieve desired outcomes in gene expression and genome structure. We will complete a comprehensive analysis of the relationship between epigenetic states and epigenome editing activity to develop a set of rules for achieving corresponding changes in gene expression. Finally, we will validate these epigenome editing tools in vivo in a set of pilot experiments in mouse models of neuromuscular disease encompassing a representative set of epigenomic states. In close collaboration with the Somatic Cell Genome Editing Consortium, this work will prepare epigenome editing technology for human clinical translation in which it may have a transformative effect on a broad array of both rare and common disease.

A recent revolution in DNA-targeting technologies has created new opportunities for treating human disease. While most effort has focused on using genome editing to alter DNA sequences to treat rare, inherited diseases, there is a tremendous opportunity to use these same tools to change the regulation of genes, rather than changing DNA sequence. This has the potential to extend the impact of these technologies to a greater diversity and number of diseases, and this proposal will address several key challenges to realizing this promise.