CRISPR-Based Epigenome Editing for Precision Medicine: Molecular Mechanisms, Therapeutic Applications, Delivery Challenges, and Future Clinical Translation

Abstract

Abstract Cancer, neurologic diseases, cardiovascular disease, metabolic disorders, immune disorders, and some inherited diseases are examples of epigenetic diseases. Traditional epigenetic drugs are non-specific and may be toxic at higher concentrations, may be unstable in transcription, and may have off-target effects in normal tissues. An epigenome editor consists of an epigenome modifier (e.g., DNA methylation or demethylation and histone-modification domain or transcription regulation domain) fused to a catalytically inactive Cas protein, typically nuclease-dead Cas9 (dCas9), which is a more precise method. With these systems, certain genes can be turned on or off and controlled by a programmable single-guide RNA, which does not cause permanent double-strand breaks in DNA. Locus-specific and, in some instances, heritable gene expression regulation has been shown by various experimental platforms such as dCas9-DNMT3A, dCas9-TET1, dCas9-p300, dCas9-LSD1, dCas9-KRAB, and CRISPRoff/CRISPRon. Potential applications for the preclinical use of these include reactivation of tumor suppressor genes, silencing of oncogenic pathways, regulation of FMR1 expression in fragile X syndrome, interference with fibrotic and inflammatory pathways, and the generation of stable immune-cell phenotypes. The drawbacks of these epigenetic-editor constructs include delivering them to tissues, resistance to the Cas proteins, possible off-target chromatin changes, inconsistent duration of effect, and the lack of regulatory parameters. This review focuses on the molecular basis, therapeutic applications, delivery systems, safety, and translational needs of epigenome editing with CRISPR. When combined with the power of AI, single-cell multi-omics, small Cas proteins, cell-inducible editors, and biomarker-guided patient selection, epigenome editing may emerge as a programmable element of precision medicine—potentially reversible. Keywords: CRISPR/dCas9, epigenome editing, DNA methylation, histone modification, precision medicine, gene regulation