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Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy

Nature Biotechnology volume 36, pages 536–539 (2018)Cite this article

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Abstract

Adenine base editors (ABEs) composed of an engineered adenine deaminase and the Streptococcus pyogenes Cas9 nickase enable adenine-to-guanine (A-to-G) single-nucleotide substitutions in a guide RNA (gRNA)-dependent manner. Here we demonstrate application of this technology in mouse embryos and adult mice. We also show that long gRNAs enable adenine editing at positions one or two bases upstream of the window that is accessible with standard single guide RNAs (sgRNAs). We introduced the Himalayan point mutation in the Tyr gene by microinjecting ABE mRNA and an extended gRNA into mouse embryos, obtaining Tyr mutant mice with an albino phenotype. Furthermore, we delivered the split ABE gene, using trans-splicing adeno-associated viral vectors, to muscle cells in a mouse model of Duchenne muscular dystrophy to correct a nonsense mutation in the Dmd gene, demonstrating the therapeutic potential of base editing in adult animals.

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Figure 1: Extended sgRNAs broaden the base editing window in HEK293T cells.
Figure 2: Frequencies of ABE-induced substitutions in the Tyr gene in mouse embryos and newborn pups.
Figure 3: Therapeutic base editing with ABE in a mouse model of Duchenne muscular dystrophy.

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Acknowledgements

This work was supported by the Institute for Basic Science (IBS-R021-D1 to J.-S.K).

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Author notes

  1. Seuk-Min Ryu, Taeyoung Koo, Kyoungmi Kim and Kayeong Lim: These authors contributed equally to this work.

Authors and Affiliations

  1. Center for Genome Engineering, Institute for Basic Science, Seoul, Republic of Korea

    Seuk-Min Ryu, Taeyoung Koo, Kyoungmi Kim, Kayeong Lim, Gayoung Baek, Sang-Tae Kim, Heon Seok Kim, Da-eun Kim, Hyunji Lee, Eugene Chung & Jin-Soo Kim

  2. Department of Chemistry, Seoul National University, Seoul, Republic of Korea

    Seuk-Min Ryu, Kayeong Lim, Heon Seok Kim, Da-eun Kim, Eugene Chung & Jin-Soo Kim

  3. Department of Biomedical Sciences and Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea

    Kyoungmi Kim

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Contributions

S.-M.R., T.K., K.K., K.L., and J.-S.K. designed the research. S.-M.R., T.K., K.K., K.L., G.B., S.-T.K., H.S.K., D.K., H.L., and E.C. performed the experiments. J.-S.K. supervised the research. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Jin-Soo Kim.

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Competing interests

J.-S.K. and T.K. have filed a patent application based on this work. J.-S.K. is a co-founder of and holds stock in ToolGen, Inc.

Integrated supplementary information

Supplementary Figure 1 Activities of ABEs using extended sgRNAs in HEK293T cells.

Base editing efficiencies of ABEs with extended sgRNAs at Site 18 (a), Site 19 (b), the HBB-E2 site (c), and the HBB-E3 site (d). (Left Y axis) Grey or black bars indicate the percentage of alleles that have a base-substitution mutation at the target adenine within two windows [positions 1-30 or 18-30 (upstream from PAM)], respectively. (Right Y axis) Blue dots indicate the relative base editing ratio, which was calculated by dividing the substitution allele frequency within the window of positions 18-30 by that within the window of positions 1-30. The PAM is shown in blue. Data are presented as mean ± s.e.m. (n = 3 biologically independent samples).

Supplementary Figure 2 Adenine editing efficiencies in mouse embryos.

(a) The target sequence at the Tyrosinase (Tyr) locus. The PAM sequence is shown in blue. The sgRNA target sequence is underlined. The targeted adenine in the wild-type sequence and the expected change in the sequence are shown in green and red, respectively. (b) Point mutation efficiencies associated with sgRNAs of different lengths (gX19, GX20, and GX21). Data are presented as mean ± s.e.m. (n = 8, 16 and 12 blastocysts, respectively). (c) Frequencies of blastocysts that carry the H420R mutation (Himalayan allele). (d) Alignments of mutant sequences from blastocysts after microinjection of ABE mRNA and Tyr-targeting sgRNAs of different lengths. The PAM and substitutions are shown in blue and red, respectively. The numbers in the column on the right indicate the frequency of each allele. WT, wild-type. H420R mutant allele frequencies are shown in red.

Supplementary Figure 3 Tyr mutations in newborn pups.

Alignments of mutant sequences from newborn pups. The altered nucleotides and the PAM site are shown in red and blue, respectively. The targeted position is shown in green.

Supplementary Figure 4 Germline transmission of Tyr mutant alleles.

Germline transmission of mutant alleles to F1 pups (101, 201-206, and 301-303) from F0 Tyr mutant mice (Tyr #1, Tyr #2 and Tyr #3) was confirmed using targeted deep sequencing. The PAM site and altered nucleotides are shown in blue and red, respectively. The column on the right indicates frequencies of mutant alleles.

Supplementary Figure 5 No off-target mutations at candidate sites in Tyr mutant mice.

Potential off-target sites with up to 3 mismatches, relative to the wild-type sequence, were identified using Cas-OFFinder. Substitution frequencies at these potential off-target sites were measured using targeted deep sequencing. PAM sequences and mismatched nucleotides are shown in blue and red, respectively. Data are presented as mean ± s.e.m. (n = 9 animals).

Supplementary Figure 6 Whole genome sequencing to assess off-target effects in the Tyr mutant mouse.

Genomes from the Tyr mutant mouse (Tyr #4) and a wild-type (WT) control mouse were sequenced using Illumina HiSeq X10. We identified unique single nucleotide variants (SNVs) in Tyr #4 by trimming out those in the WT control using the program 'Strelka' with the default 'eland' option. None of these SNVs other than the variations at the on-target site were found at potential off-target sites, identified using Cas-OFFinder, with up to 7 mismatches (207,848 sites) or with up to 5 mismatches and a DNA or RNA bulge (1,030,669 sites).

Supplementary Figure 7 Schematic diagram of trans-splicing AAV vector encoding ABE.

The first vector carries a U6 promoter driven sgRNA, Spc512 promoter, ecTadA fused to 5′- end of nCas9-NT cDNA, splice donor signal at the 3′ -end of nCas9-NT cDNA. The second vector contains nCas9-CT flanked by splice acceptor at the 5′ -end of nCas9-CT, followed by NLS, HA tag, and the bGH poly A signal. (a) The two split AAV-ABE vectors are coinfected into the target cells. (b) The two viral vectors are rejoined at the ITRs by recombination and led to heterodimer formation. (c) Target specific sgRNA and Pre-mRNA of ABE are made. (d) The intron along with the ITR by splicing is removed and ABE protein is made. SD, splicing donor; SA, splicing acceptor; NLS, nuclear localization signal; ITR, inverted terminal repeat.

Supplementary Figure 8 Base editing specificity of ABE in Dmd knockout mice.

Base editing frequencies at potential off-target sites identified by Cas-OFFinder were measured using targeted deep sequencing of genomic DNA isolated from muscles 8 weeks after injection of tsAAV: ABE. Mismatched nucleotides and the PAM sequence are shown in red and blue, respectively. OT; off-target site. Data are presented as mean ± s.e.m. (n = 3 animals).

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Ryu, SM., Koo, T., Kim, K. et al. Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy. Nat Biotechnol 36, 536–539 (2018). https://doi.org/10.1038/nbt.4148

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