In Vivo Correction of Human Phenylketonuria Variants via Prime Editing and Base Editing: A Gateway to Equitable Treatment of Inborn Errors of Metabolism

Inborn errors of metabolism (IEMs) are rare, devastating disorders caused by pathogenic variants in genes encoding key metabolic enzymes, with the liver playing a critical role in over 140 IEMs. Liver transplantation is a treatment option but is limited by donor shortages and lifelong risks. To address this unmet need, we aim to develop a master protocol for personalized base-editing and prime-editing therapies for severe, rare hepatic IEMs.

We focused initially on phenylketonuria (PKU), an IEM resulting from variants in the phenylalanine hydroxylase (PAH) gene. Building on prior work with in vivo base-editing and prime-editing solutions for the common PAH variants R408W and P281L, we extended our research to other frequent PKU variants. Using a novel platform where collinear genomic segments with patient-specific variants were introduced into HuH-7 hepatocytes, we rapidly screened and identified base-editing solutions for the PAH c.1066–11G>A, R261Q, and R243Q variants. These solutions showed comparable or better efficacy in vitro and were validated in vivo in humanized mouse models, with off-target risks minimized.

Simultaneously, we applied this workflow to pathogenic variants from other liver-centered diseases such as galactosemia, citrullinemia type 1, argininosuccinic acidemia, methylmalonic acidemia, and pseudoxanthoma elasticum. Editing solutions were identified and validated in humanized mouse models. To accelerate testing, we are using multi-humanized mice with human variants inserted into the Rosa26 locus. Our goal is to establish a platform regulatory framework, where IND-enabling studies for a "leader" hepatic IEM therapy expedite “follower” IND amendments, facilitating personalized corrective editing therapies for patients within months.

Learning Objectives:

• Identify the role of base editing and prime editing in correcting genetic variants associated with phenylketonuria (PKU).
• Differentiate the efficacy of base-editing solutions for various PKU variants, including R408W, P281L, c.1066–11G>A, R261Q, and R243Q.
• Evaluate the application of editing technologies in treating additional liver-centered inborn errors of metabolism.