Targeted epigenetic repression of oncogenic transcription factors via CRISPR/dCas9 locus-specific silencing

Abstract

Despite the revolutionary impact of genome engineering tools in medicine, the safe and effective intracellular delivery of CRISPR remains a major obstacle for clinical applications. Here, we implement precision molecular medicine and delivery strategies based on CRISPR/dCas9 systems adapted for epigenetic repression (dCas9-KRAB) to silence oncogenic drivers with high genomic selectivity. As proof-of-principle, we target the EWSR1-FLI1 translocation, which encodes a chimeric and hard-to-drug oncogenic transcription factor driving approximately 85% of the cases of Ewing Sarcoma (EWS)-an aggressive malignancy affecting children and adolescents. We describe the development of a non-viral and programmable polymeric system for the delivery of dCas9-KRAB as ribonucleoprotein (RNP) payloads for selective EWSR1-FLI1 repression. We demonstrate highly efficient intracellular delivery of RNPs loaded in polyamide-amine (PAMAM) polymers functionalized by guanidino groups, resulting in robust silencing of EWSR1-FLI1 both in established cell line xenografts and in patient-derived xenografts (PDXs) of EWS. Moreover, silencing of EWSR1-FLI1 is accompanied by potent anti-tumor effects. To our knowledge, we describe the first non-viral platform for in vivo delivery of dCas9-KRAB/RNPs, which can be adapted for the repression of any oncogene. We further outline dCas9/RNP formulations for future therapeutic applications to treat poor-prognosis cancers driven by hard-to-drug oncogenes.