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Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice

Pengpeng Liu, Shun-Qing Liang, Chunwei Zheng and 9 more

Nature Communications · 2021 · CC BY

doi:10.1101/2020.12.15.422970

Abstract

Prime editors (PEs) mediate genome modification without utilizing double-stranded DNA breaks or exogenous donor DNA as a template. PEs facilitate nucleotide substitutions or local insertions or deletions within the genome based on the template sequence encoded within the prime editing guide RNA (pegRNA). However, the efficacy of prime editing in adult mice has not been established. Here we report an NLS-optimized SpCas9-based prime editor that improves genome editing efficiency in both fluorescent reporter cells and at endogenous loci in cultured cell lines. Using this genome modification system, we could also seed tumor formation through somatic cell editing in the adult mouse. Finally, we successfully utilize dual adeno-associated virus (AAVs) for the delivery of a split-intein prime editor and demonstrate that this system enables the correction of a pathogenic mutation in the mouse liver. Our findings further establish the broad potential of this genome editing technology for the directed installation of sequence modifications in vivo, with important implications for disease modeling and correction.

References 50

  1. 1.

    Porteus MH. A new class of medicines through DNA Editing. N. Engl. J. Med. 2019;380:947-959.

    Not in our library10.1056/nejmra1800729

  2. 2.

    Panier S, Boulton SJ. Double-strand break repair: 53BP1 comes into focus. Nat. Rev. Mol. Cell Biol. 2014;15:7-18.

    Not in our library10.1038/nrm3719

  3. 3.

    Suzuki K, et al. In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature. 2016;540:144-149.

    Not in our library10.1038/nature20565

  4. 4.

    Pickar-Oliver A, Gersbach CA. The next generation of CRISPR-Cas technologies and applications. Nat. Rev. Mol. Cell Biol. 2019;20:490-507.

    Not in our library10.1038/s41580-019-0131-5

  5. 5.

    Rees HA, Liu DR. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat. Rev. Genet. 2018;19:770-788.

    Not in our library10.1038/s41576-018-0059-1

  6. 6.

    Anzalone AV, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576:149-157.

    Not in our library10.1038/s41586-019-1711-4

  7. 7.

    Lin Q, et al. Prime genome editing in rice and wheat. Nat. Biotechnol. 2020;38:582-585.

    Not in our library10.1038/s41587-020-0455-x

  8. 8.
  9. 9.
  10. 10.
  11. 11.

    Aida, T. et al. Prime editing primarily induces undesired outcomes in mice. bioRxiv 2020.2008.2006.239723 (2020).

    Not in our library

  12. 12.

    Wu Y, et al. Highly efficient therapeutic gene editing of human hematopoietic stem cells. Nat. Med. 2019;25:776-783.

    Not in our library10.1038/s41591-019-0401-y

  13. 13.

    Koblan, L. W. et al. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat. Biotechnol.36, 843–846 (2018).

    Not in our library10.1038/nbt.4172

  14. 14.

    Zafra, M. P. et al. Optimized base editors enable efficient editing in cells, organoids and mice. Nat. Biotechnol.36, 888–893 (2018).

    Not in our library10.1038/nbt.4194

  15. 15.

    Song C-Q, et al. Adenine base editing in an adult mouse model of tyrosinaemia. Nat. Biomed. Eng. 2020;4:125-130.

    Not in our library10.1038/s41551-019-0357-8

  16. 16.

    Walton, R. T., Christie, K. A., Whittaker, M. N. & Kleinstiver, B. P. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science368, 290–296 (2020).

    Not in our library10.1126/science.aba8853

  17. 17.

    Ray M, Tang R, Jiang Z, Rotello VM. Quantitative tracking of protein trafficking to the nucleus using cytosolic protein delivery by nanoparticle-stabilized nanocapsules. Bioconjugate Chem. 2015;26:1004-1007.

    Not in our library10.1021/acs.bioconjchem.5b00141

  18. 18.

    Makkerh JP, Dingwall C, Laskey RA. Comparative mutagenesis of nuclear localization signals reveals the importance of neutral and acidic amino acids. Curr. Biol. 1996;6:1025-1027.

    Not in our library10.1016/s0960-9822(02)00648-6

  19. 19.

    Ran FA, et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature. 2015;520:186-191.

    Not in our library10.1038/nature14299

  20. 20.

    Kleinstiver BP, et al. Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nat. Biotechnol. 2015;33:1293-1298.

    Not in our library10.1038/nbt.3404

  21. 21.

    Certo MT, et al. Tracking genome engineering outcome at individual DNA breakpoints. Nat. Methods. 2011;8:671-676.

    Not in our library10.1038/nmeth.1648

  22. 22.

    Mir A, et al. Heavily and fully modified RNAs guide efficient SpyCas9-mediated genome editing. Nat. Commun. 2018;9:2641.

    Not in our library10.1038/s41467-018-05073-z

  23. 23.

    Iyer, S. et al. Efficient homology-directed repair with circular ssDNA donors. bioRxiv 864199 (2019).

    Not in our library10.1089/crispr.2022.0058

  24. 24.

    Dean M, et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science. 1996;273:1856-1862.

    Not in our library10.1126/science.273.5283.1856

  25. 25.

    Liu R, et al. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell. 1996;86:367-377.

    Not in our library10.1016/s0092-8674(00)80110-5

  26. 26.

    Samson M, et al. Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature. 1996;382:722-725.

    Not in our library10.1038/382722a0

  27. 27.

    Bolukbasi MF, et al. Orthogonal Cas9-Cas9 chimeras provide a versatile platform for genome editing. Nat. Commun. 2018;9:4856.

    Not in our library10.1038/s41467-018-07310-x

  28. 28.

    Loring HS, Flotte TR. Current status of gene therapy for alpha-1 antitrypsin deficiency. Expert Opin. Biol. Ther. 2015;15:329-336.

    Not in our library10.1517/14712598.2015.978854

  29. 29.

    Carlson JA, et al. Accumulation of PiZ alpha 1-antitrypsin causes liver damage in transgenic mice. J. Clin. Invest. 1989;83:1183-1190.

    Not in our library10.1172/jci113999

  30. 30.

    Gaudelli NM, et al. Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature. 2017;551:464-471.

    Not in our library10.1038/nature24644

  31. 31.

    Liu F, Song Y, Liu D. Hydrodynamics-based transfection in animals by systemic administration of plasmid DNA. Gene Ther. 1999;6:1258-1266.

    Not in our library10.1038/sj.gt.3300947

  32. 32.

    Zucman-Rossi J, Villanueva A, Nault JC, Llovet JM. Genetic landscape and biomarkers of hepatocellular carcinoma. Gastroenterology. 2015;149:1226-1239.

    Not in our library10.1053/j.gastro.2015.05.061

  33. 33.

    Liu P, et al. A functional mammalian target of rapamycin complex 1 signaling is indispensable for c-Myc-driven hepatocarcinogenesis. Hepatology. 2017;66:167-181.

    Not in our library10.1002/hep.29183

  34. 34.

    Marquardt JU, Andersen JB, Thorgeirsson SS. Functional and genetic deconstruction of the cellular origin in liver cancer. Nat. Rev. Cancer. 2015;15:653-667.

    Not in our library10.1038/nrc4017

  35. 35.

    Wang, D. A.-O., Tai, P. A.-O. & Gao, G. A.-O. Adeno-associated virus vector as a platform for gene therapy delivery. 18, 358–378 (2019).

    Not in our library10.1038/s41573-019-0012-9

  36. 36.

    Levy JM, et al. Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses. Nat. Biomed. Eng. 2020;4:97-110.

    Not in our library10.1038/s41551-019-0501-5

  37. 37.

    Zettler J, Schütz V, Mootz HD. The naturally split Npu DnaE intein exhibits an extraordinarily high rate in the protein trans-splicing reaction. FEBS Lett. 2009;583:909-914.

    Not in our library10.1016/j.febslet.2009.02.003

  38. 38.

    Wright AV, et al. Rational design of a split-Cas9 enzyme complex. Proc. Natl Acad. Sci. USA. 2015;112:2984-2989.

    Not in our library10.1073/pnas.1501698112

  39. 39.
  40. 40.

    Yao X, et al. CRISPR/Cas9-mediated precise targeted integration in vivo using a double cut donor with short homology arms. EBioMedicine. 2017;20:19-26.

    Not in our library10.1016/j.ebiom.2017.05.015

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