Base editing and nanoparticle transfection of airway cell types essential for treatment of cystic fibrosis

Abstract

Cystic Fibrosis (CF) is a life-limiting genetic disorder caused by deleterious variants in the CFTR gene that results in altered mucous impairing the airway epithelia. Durable correction of these variants in airway cells remain a therapeutic challenge for [~]10% of individuals unresponsive to CFTR modulators. A common disease-causing CFTR splice site variant was corrected in primary CF airway cells using base editor RNAs. Single-cell RNA sequencing revealed a remarkable increase in detectable CFTR transcript in most CF airway epithelial cell types with notable enrichment of CFTR-expressing ionocytes and secretory goblet cells. Progenitor basal cell subtypes were edited but they decreased as a fraction of total cells and CFTR expressing cells compared to unedited cells. CRISPR base editors delivered by polymeric nanoparticles (PNPs) facilitated functional rescue of CFTR to clinically meaningful levels in immortalized and primary airway cells. PNPs delivered reporter encoding RNA to progenitor airway cells in fully differentiated airway cultures. Vitronectin was a major component of the PNP corona that formed in vivo, but pre-incubation with vitronectin did not enhance delivery. Together, these findings validate a scalable, non-viral platform with significant translational promise for treating CF and other respiratory diseases involving respiratory epithelial cell dysfunction.