Adenine base editing with engineered virus-like particles rescues the CFTR mutation G542X in patient-derived intestinal organoids

Lucia Nicosia; Iwona Pranke; Roberta V Latorre; Joss B Murray; Lisa Lonetti; Kader Cavusoglu-Doran; Elise Dreano; James P Costello; Michael Carroll; Paola Melotti; Claudio Sorio; Isabelle Sermet-Gaudelus; Martina F Scallan; Patrick T Harrison

doi:10.1016/j.isci.2025.111979

Adenine base editing with engineered virus-like particles rescues the CFTR mutation G542X in patient-derived intestinal organoids

iScience. 2025 Feb 21;28(3):111979. doi: 10.1016/j.isci.2025.111979. eCollection 2025 Mar 21.

Authors

Lucia Nicosia^{1

2}, Iwona Pranke^{3

4}, Roberta V Latorre⁵, Joss B Murray¹, Lisa Lonetti¹, Kader Cavusoglu-Doran¹, Elise Dreano^{3

4}, James P Costello², Michael Carroll², Paola Melotti⁶, Claudio Sorio⁵, Isabelle Sermet-Gaudelus^{3

4

7

8}, Martina F Scallan², Patrick T Harrison^{1

9}

Affiliations

¹ Department of Physiology, University College Cork, Cork, Ireland.
² School of Microbiology, University College Cork, Cork, Ireland.
³ INSERM, CNRS, Institut Necker Enfants Malades, Paris, France.
⁴ Université Paris-Cité, Paris, France.
⁵ Department of Medicine, University of Verona, Verona, Italy.
⁶ Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy.
⁷ Cystic Fibrosis National Pediatric Reference Center, Pneumo-Allergologie Pédiatrique, Hôpital Necker Enfants Malades, , Assistance Publique Hôpitaux de Paris (AP-HP), Paris, France.
⁸ European Reference Network, ERN-Lung CF, Frankfurt am Mein, Germany.
⁹ Division of Pulmonary Medicine, Cincinnati Children's Hospital, Cincinnati, OH, USA.

Abstract

Cystic fibrosis (CF) is a life-shortening autosomal recessive disease, caused by loss-of-function mutations that affect the CF transmembrane conductance regulator (CFTR) anion channel. G542X is the second-most common CF-causing variant, and it does not respond to current CFTR modulator drugs. Our study explores the use of adenine base editing to edit G542X to a non-CF-causing variant, G542R, and recover CFTR function. Using base editor engineered virus-like particles (BE-eVLPs) in patient-derived intestinal organoids, we achieved ∼2% G542X-to-G542R editing efficiency and restored CFTR-mediated chloride transport to ∼6.4% of wild-type levels, independent of modulator treatment, and with no bystander edits. This proof-of-principle study demonstrates the potential of base editing to rescue G542X and provides a foundation for future in - vivo applications.

Keywords: Cellular therapy; Clinical genetics; Genetic engineering; Health sciences.