Prime editing: therapeutic advances and mechanistic insights

Scholefield J, Harrison PT. Prime editing - an update on the field. Gene Ther. 2021;28:396–401.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576:149–57.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Anzalone AV, Gao XD, Podracky CJ, Nelson AT, Koblan LW, Raguram A, et al. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat Biotechnol. 2022;40:731–40.

Article  CAS  PubMed  Google Scholar 

Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533:420–4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Geurts MH, de Poel E, Pleguezuelos-Manzano C, Oka R, Carrillo L, Andersson-Rolf A, et al. Evaluating CRISPR-based prime editing for cancer modeling and CFTR repair in organoids. Life Sci Alliance. 2021;4:e202000940.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Landrum MJ, Kattman BL. ClinVar at five years: Delivering on the promise. Hum Mutat. 2018;39:1623–30.

Article  PubMed  PubMed Central  Google Scholar 

Testa LC, Musunuru K. Base editing and prime editing: potential therapeutic options for rare and common diseases. BioDrugs. 2023;37:453–62.

Article  CAS  PubMed  Google Scholar 

Godbout K, Tremblay JP. Prime Editing for human gene therapy: where are we now? Cells. 2023;12:536.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen PJ, Hussmann JA, Yan J, Knipping F, Ravisankar P, Chen PF, et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell. 2021;184:5635–52.e29.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Davis JR, Banskota S, Levy JM, Newby GA, Wang X, Anzalone AV, et al. Efficient prime editing in mouse brain, liver and heart with dual AAVs. Nat Biotechnol. 2024;42:253–64.

Article  CAS  PubMed  Google Scholar 

Doman JL, Pandey S, Neugebauer ME, An M, Davis JR, Randolph PB, et al. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell. 2023;186:3983–4002.e26.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Peterka M, Akrap N, Li S, Wimberger S, Hsieh PP, Degtev D, et al. Harnessing DSB repair to promote efficient homology-dependent and -independent prime editing. Nat Commun. 2022;13:1240.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wimberger S, Akrap N, Firth M, Brengdahl J, Engberg S, Schwinn MK, et al. Simultaneous inhibition of DNA-PK and Polϴ improves integration efficiency and precision of genome editing. Nat Commun. 2023;14:4761.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Antoniou P, Dacquay L, Selfjord N, Madeyski-Bengtson K, Loyd A-L, Gordon E, et al. Improved nuclease-based prime editing by DNA repair modulation and pegRNA engineering. bioRxiv. 2024. https://doi.org/10.1101/2024.02.01.578377.

Li X, Zhang G, Huang S, Liu Y, Tang J, Zhong M, et al. Development of a versatile nuclease prime editor with upgraded precision. Nat Commun. 2023;14:305.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Canny MD, Moatti N, Wan LCK, Fradet-Turcotte A, Krasner D, Mateos-Gomez PA, et al. Inhibition of 53BP1 favors homology-dependent DNA repair and increases CRISPR-Cas9 genome-editing efficiency. Nat Biotechnol. 2018;36:95–102.

Article  CAS  PubMed  Google Scholar 

Grunewald J, Miller BR, Szalay RN, Cabeceiras PK, Woodilla CJ, Holtz EJB, et al. Engineered CRISPR prime editors with compact, untethered reverse transcriptases. Nat Biotechnol. 2023;41:337–43.

Article  CAS  PubMed  Google Scholar 

Liu B, Dong X, Cheng H, Zheng C, Chen Z, Rodriguez TC, et al. A split prime editor with untethered reverse transcriptase and circular RNA template. Nat Biotechnol. 2022;40:1388–93.

Article  CAS  PubMed  Google Scholar 

Mu S, Chen H, Li Q, Gou S, Liu X, Wang J, et al. Enhancing prime editor flexibility with coiled-coil heterodimers. Genome Biol. 2024;25:108.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liang R, He Z, Zhao KT, Zhu H, Hu J, Liu G, et al. Prime editing using CRISPR-Cas12a and circular RNAs in human cells. Nat Biotechnol. 2024. https://doi.org/10.1038/s41587-023-02095-x.

Lan T, Chen H, Tang C, Wei Y, Liu Y, Zhou J, et al. Mini-PE, a prime editor with compact Cas9 and truncated reverse transcriptase. Mol Ther Nucleic Acids. 2023;33:890–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim HK, Yu G, Park J, Min S, Lee S, Yoon S, et al. Predicting the efficiency of prime editing guide RNAs in human cells. Nat Biotechnol. 2021;39:198–206.

Article  CAS  PubMed  Google Scholar 

Hsu JY, Lam KC, Shih J, Pinello L, Joung JK. MOSAIC enables in situ saturation mutagenesis of genes and CRISPR prime editing guide RNA optimization in human cells. bioRxiv. 2024. https://doi.org/10.1101/2024.04.25.591078.

Tak YE, Hsu JY, Shih J, Schultz HT, Nguyen IT, Lam KC, et al. CRISPR PERSIST-On enables heritable and fine-tunable human gene activation. bioRxiv. 2024. https://doi.org/10.1101/2024.04.26.590475.

Koeppel J, Weller J, Peets EM, Pallaseni A, Kuzmin I, Raudvere U, et al. Prediction of prime editing insertion efficiencies using sequence features and DNA repair determinants. Nat Biotechnol. 2023;41:1446–56.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Karasu ME, Toufektchan E, Maciejowski J, Corn JE. TREX1 restricts CRISPR-Cas9 genome editing in human cells. bioRxiv. 2022. https://doi.org/10.1101/2022.12.12.520063.

Mathis N, Allam A, Kissling L, Marquart KF, Schmidheini L, Solari C, et al. Predicting prime editing efficiency and product purity by deep learning. Nat Biotechnol. 2023;41:1151–9.

Article  CAS  PubMed  Google Scholar 

Mathis N, Allam A, Talas A, Kissling L, Benvenuto E, Schmidheini L, et al. Machine learning prediction of prime editing efficiency across diverse chromatin contexts. Nat Biotechnol. 2024. https://doi.org/10.1038/s41587-024-02268-2.

Liu F, Huang S, Hu J, Chen X, Song Z, Dong J, et al. Design of prime-editing guide RNAs with deep transfer learning. Nat Mach Intell. 2023;5:1261–74.

Article  Google Scholar 

Yu G, Kim HK, Park J, Kwak H, Cheong Y, Kim D, et al. Prediction of efficiencies for diverse prime editing systems in multiple cell types. Cell. 2023;186:2256–2272.e23.

Article  CAS  PubMed  Google Scholar 

Sousa AA, Hemez C, Lei L, Traore S, Kulhankova K, Newby GA, et al. Systematic optimization of prime editing for the efficient functional correction of CFTR F508del in human airway epithelial cells. Nat Biomed Eng. 2024. https://doi.org/10.1038/s41551-024-01233-3.

Nelson JW, Randolph PB, Shen SP, Everette KA, Chen PJ, Anzalone AV, et al. Engineered pegRNAs improve prime editing efficiency. Nat Biotechnol. 2022;40:402–10.

Article  CAS  PubMed  Google Scholar 

Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, et al. ViennaRNA Package 2.0. Algorithms Mol Biol. 2011;6:26.

Article  PubMed  PubMed Central  Google Scholar 

Zhang G, Liu Y, Huang S, Qu S, Cheng D, Yao Y, et al. Enhancement of prime editing via xrRNA motif-joined pegRNA. Nat Commun. 2022;13:1856.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yan J, Oyler-Castrillo P, Ravisankar P, Ward CC, Levesque S, Jing Y, et al. Improving prime editing with an endogenous small RNA-binding protein. Nature. 2024;628:639–47.

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