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A porcine model of phenylketonuria generated by CRISPR/Cas9 genome editing
Erik A. Koppes, Bethany K. Redel, Marie A. Johnson, Kristen J. Skvorak, Lina Ghaloul-Gonzalez, Megan E. Yates, Dale W. Lewis, Susanne M. Gollin, Yijen L. Wu, Shawn E. Christ, Martine Yerle, Angela Leshinski, Lee D. Spate, Joshua A. Benne, Stephanie L. Murphy, Melissa S. Samuel, Eric M. Walters, Sarah A. Hansen, Kevin D. Wells, Uta Lichter-Konecki, Robert A. Wagner, Joseph T. Newsome, Steven F. Dobrowolski, Jerry Vockley, Randall S. Prather, Robert D. Nicholls
Erik A. Koppes, Bethany K. Redel, Marie A. Johnson, Kristen J. Skvorak, Lina Ghaloul-Gonzalez, Megan E. Yates, Dale W. Lewis, Susanne M. Gollin, Yijen L. Wu, Shawn E. Christ, Martine Yerle, Angela Leshinski, Lee D. Spate, Joshua A. Benne, Stephanie L. Murphy, Melissa S. Samuel, Eric M. Walters, Sarah A. Hansen, Kevin D. Wells, Uta Lichter-Konecki, Robert A. Wagner, Joseph T. Newsome, Steven F. Dobrowolski, Jerry Vockley, Randall S. Prather, Robert D. Nicholls
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Research Article Genetics Metabolism

A porcine model of phenylketonuria generated by CRISPR/Cas9 genome editing

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Abstract

Phenylalanine hydroxylase–deficient (PAH-deficient) phenylketonuria (PKU) results in systemic hyperphenylalaninemia, leading to neurotoxicity with severe developmental disabilities. Dietary phenylalanine (Phe) restriction prevents the most deleterious effects of hyperphenylalaninemia, but adherence to diet is poor in adult and adolescent patients, resulting in characteristic neurobehavioral phenotypes. Thus, an urgent need exists for new treatments. Additionally, rodent models of PKU do not adequately reflect neurocognitive phenotypes, and thus there is a need for improved animal models. To this end, we have developed PAH-null pigs. After selection of optimal CRISPR/Cas9 genome-editing reagents by using an in vitro cell model, zygote injection of 2 sgRNAs and Cas9 mRNA demonstrated deletions in preimplantation embryos, with embryo transfer to a surrogate leading to 2 founder animals. One pig was heterozygous for a PAH exon 6 deletion allele, while the other was compound heterozygous for deletions of exon 6 and of exons 6–7. The affected pig exhibited hyperphenylalaninemia (2000–5000 μM) that was treatable by dietary Phe restriction, consistent with classical PKU, along with juvenile growth retardation, hypopigmentation, ventriculomegaly, and decreased brain gray matter volume. In conclusion, we have established a large-animal preclinical model of PKU to investigate pathophysiology and to assess new therapeutic interventions.

Authors

Erik A. Koppes, Bethany K. Redel, Marie A. Johnson, Kristen J. Skvorak, Lina Ghaloul-Gonzalez, Megan E. Yates, Dale W. Lewis, Susanne M. Gollin, Yijen L. Wu, Shawn E. Christ, Martine Yerle, Angela Leshinski, Lee D. Spate, Joshua A. Benne, Stephanie L. Murphy, Melissa S. Samuel, Eric M. Walters, Sarah A. Hansen, Kevin D. Wells, Uta Lichter-Konecki, Robert A. Wagner, Joseph T. Newsome, Steven F. Dobrowolski, Jerry Vockley, Randall S. Prather, Robert D. Nicholls

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Figure 5

DNA repair mechanisms for deletion and scarred gene-edited PAH alleles.

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DNA repair mechanisms for deletion and scarred gene-edited PAH alleles.
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(A and B) The intact (WT-size) allele for 116-2 (heterozygote) demonstrates gene editing (“scarring”) at each sgRNA target site. Inaccurate NHEJ mechanisms lead to (A) the insertion of 4 T nucleotides (red) on DNA repair of a DSB at the sgRNA5-1 position, while (B) DNA repair of a DSB at the sgRNA6-2 position leads to both deletion of 6 nt (AGAAAA) including the first nucleotide of the PAM sequence and insertion of 5 nt of novel sequence (red; TTACC), respectively. (C) The deletion allele for 116-2 (heterozygote) arose by DNA repair of DSBs at each sgRNA position with loss of the intervening PAH exon 6 segment. Two extra nucleotides were deleted as part of the mechanism either due to noncanonical positioning of each DSB by CRISPR/Cas9, or, perhaps most likely, the inaccurate NHEJ mechanism of DNA repair. (D) A complex NHEJ mechanism accounts for the exon 6 recombinant deletion allele 1 in 116-1 (affected PKU pig). CRISPR/Cas9-induced DSBs at the canonical positions 3 nt 5′ of the PAM sequences for the sgRNA5-1 and sgRNA6-2 sgRNAs lead to a series of potential events that can be described by 2 alternative DNA repair mechanisms (see main text). Descriptively, the recombinant chromosome is characterized by a 1166 bp deletion starting at the sgRNA5-1 canonical position and with insertion at the deletion breakpoint of a novel 12 nt sequence apparently derived from an adjacent sequence to generate a 13 nt duplication (this and an adjacent 8 nt tandem repeat in the distal parental sequence are underlined). The distal deletion breakpoint is localized between the 13 nt duplication at a position 56 nt upstream of the canonical position for a DSB at sgRNA6-2, with a 3 nt deletion (AAG) at the latter DSB. A single SNP (C→T) arising in the mutant allele is also detected. (E) A complex MMEJ mechanism accounts for the larger exon 6–7 deletion allele 2 in 116-1 (PKU). DNA repair of the paired DSBs at sgRNA5-1 and sgRNA6-2 led to a recombinant breakpoint at a 4 nt (TCTC, purple) sequence of patchy homology located 70 nt 5′ and 2755 nt 3′ of the sgRNA target sites, respectively, resulting in a 4063 nt deletion.

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