A genome-wide CRISPR screen unveils the endosomal maturation protein WDR91 as a promoter of productive ASO activity in melanoma

Antisense oligonucleotides (ASOs) belong to promising therapeutics for the treatment of neurological, muscular, and metabolic disorders. Several ASOs have been approved so far and more than 100 clinical trials are currently underway covering a dozen therapeutic areas. Yet, the mechanisms of internalization and cell trafficking of these molecules remain poorly understood. Moreover, with only a small fraction of ASOs reaching the correct cellular compartment after systemic delivery, the majority of targeted diseases require recurrent injections of ASOs. A deeper understanding of these mechanisms would guide the improvement of their potency and, thus, reduce the amount of delivered ASOs and their potential side effects. Here, using a CRISPR screen, we investigated intracellular proteins involved in ASOs efficiency using a whole genome approach and identified several potential regulators that could significantly impact ASOs potency in melanoma cells. We validated WD repeat domain 91, a regulator of endosomal maturation, as a modulator whose depletion significantly inhibits ASO productive activity. This study provides a list of ASO modulators using a biologically relevant assay to estimate the role of these proteins. In conclusion, these data could lead to a better understanding of the mechanisms favoring productive uptake or improved endosomal escape of ASOs.