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      Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope

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          Abstract

          CRISPR-Cas9-associated base editing is a promising tool to correct pathogenic single nucleotide mutations in research or therapeutic settings. Efficient base editing requires cellular exposure to levels of base editors that can be difficult to attain in hard-to-transfect cells or in vivo. Here we engineer a chemically modified mRNA-encoded adenine base editor that mediates robust editing at various cellular genomic sites together with moderately modified guide RNA, and show its therapeutic potential in correcting pathogenic single nucleotide mutations in cell and animal models of diseases. The optimized chemical modifications of adenine base editor mRNA and guide RNA expand the applicability of CRISPR-associated gene editing tools in vitro and in vivo.

          Abstract

          Cas9 base editors are promising tools for correcting pathogenic single nucleotide mutations. Here the authors chemically modify mRNA encoding the editor and the gRNA to enhance editing and broaden its application.

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          Most cited references14

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          Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells.

          CRISPR-Cas-mediated genome editing relies on guide RNAs that direct site-specific DNA cleavage facilitated by the Cas endonuclease. Here we report that chemical alterations to synthesized single guide RNAs (sgRNAs) enhance genome editing efficiency in human primary T cells and CD34(+) hematopoietic stem and progenitor cells. Co-delivering chemically modified sgRNAs with Cas9 mRNA or protein is an efficient RNA- or ribonucleoprotein (RNP)-based delivery method for the CRISPR-Cas system, without the toxicity associated with DNA delivery. This approach is a simple and effective way to streamline the development of genome editing with the potential to accelerate a wide array of biotechnological and therapeutic applications of the CRISPR-Cas technology.
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            Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing

            Efficient genome editing with Cas9–sgRNA in vivo has required the use of viral delivery systems, which have limitations for clinical applications. Translational efforts to develop other RNA therapeutics have shown that judicious chemical modification of RNAs can improve therapeutic efficacy by reducing susceptibility to nuclease degradation. Guided by the structure of the Cas9–sgRNA complex, we identify regions of sgRNA that can be modified while maintaining or enhancing genome-editing activity, and we develop an optimal set of chemical modifications for in vivo applications. Using lipid nanoparticle formulations of these enhanced sgRNAs (e-sgRNA) and mRNA encoding Cas9, we show that a single intravenous injection into mice induces >80% editing of Pcsk9 in the liver. Serum Pcsk9 is reduced to undetectable levels, and cholesterol levels are significantly lowered about 35% to 40% in animals. This strategy may enable non-viral, Cas9-based genome editing in the liver in clinical settings.
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              Optimized base editors enable efficient editing in cells, organoids and mice

              CRISPR base editing enables the creation of targeted single-base conversions without generating double stranded breaks. However, the efficiency of current base editors is very low in many cell types. We re-engineered the sequences of BE3, BE4Gam, and xBE3 by codon optimization and incorporation of additional nuclear localization sequences. Our collection of optimized constitutive and inducible base-editing vector systems dramatically improves the efficiency by which single nucleotide variants can be created. The re-engineered base editors enable target modification in a wide range of mouse and human cell lines, and intestinal organoids. We also show that the optimized base editors mediate efficient in vivo somatic editing in the liver of adult mice.
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                Author and article information

                Contributors
                Wen.Xue@umassmed.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                24 April 2020
                24 April 2020
                2020
                : 11
                : 1979
                Affiliations
                [1 ]ISNI 0000 0001 0742 0364, GRID grid.168645.8, RNA Therapeutics Institute, , University of Massachusetts Medical School, ; Worcester, MA 01605 USA
                [2 ]GRID grid.421853.9, TriLink BioTechnologies, ; San Diego, CA USA
                [3 ]ISNI 0000 0001 0710 9146, GRID grid.427709.f, Cystic Fibrosis Foundation, CFFT Lab, ; Lexington, MA 02421 USA
                [4 ]ISNI 0000 0001 0742 0364, GRID grid.168645.8, Program in Bioinformatics and Integrative Biology, , University of Massachusetts Medical School, ; Worcester, MA USA
                [5 ]ISNI 0000000123704535, GRID grid.24516.34, School of Life Sciences and Technology, , Tongji University, ; 200092 Shanghai, China
                [6 ]ISNI 0000 0001 2341 2786, GRID grid.116068.8, David H. Koch Institute for Integrative Cancer Research, , Massachusetts Institute of Technology, ; Cambridge, MA USA
                [7 ]ISNI 0000 0001 2341 2786, GRID grid.116068.8, Department of Chemical Engineering, , Massachusetts Institute of Technology, ; Cambridge, MA USA
                [8 ]GRID grid.66859.34, Merkin Institute of Transformative Technologies in Healthcare, , Broad Institute of Harvard and MIT, ; Cambridge, MA USA
                [9 ]ISNI 000000041936754X, GRID grid.38142.3c, Howard Hughes Medical Institute, , Harvard University, ; Cambridge, MA 02138 USA
                [10 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Chemistry and Chemical Biology, , Harvard University, ; Cambridge, MA 02138 USA
                [11 ]ISNI 0000 0001 2341 2786, GRID grid.116068.8, Institute for Medical Engineering and Science, , Massachusetts Institute of Technology, ; Cambridge, MA USA
                [12 ]ISNI 0000 0001 2341 2786, GRID grid.116068.8, Harvard-MIT Division of Health Sciences & Technology, , Massachusetts Institute of Technology, ; Cambridge, MA USA
                [13 ]ISNI 0000 0001 0742 0364, GRID grid.168645.8, Department of Molecular, Cell and Cancer Biology, , University of Massachusetts Medical School, ; Worcester, MA USA
                [14 ]ISNI 0000 0001 0742 0364, GRID grid.168645.8, Department of Molecular Medicine, , University of Massachusetts Medical School, ; Worcester, MA USA
                [15 ]ISNI 0000 0001 0742 0364, GRID grid.168645.8, Li Weibo Institute for Rare Diseases Research, , University of Massachusetts Medical School, ; 368 Plantation Street, Worcester, MA 01605 USA
                Author information
                http://orcid.org/0000-0002-2027-1313
                http://orcid.org/0000-0003-1991-5246
                http://orcid.org/0000-0002-8167-1548
                http://orcid.org/0000-0003-0280-9789
                http://orcid.org/0000-0001-5629-4798
                http://orcid.org/0000-0002-9797-8042
                Article
                15892
                10.1038/s41467-020-15892-8
                7181807
                32332735
                1c739012-73da-4ff0-a276-321551ccd14b
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 2 December 2019
                : 2 April 2020
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000048, American Cancer Society (American Cancer Society, Inc.);
                Award ID: 129056-RSG-16-093
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000897, Cystic Fibrosis Foundation (CF Foundation);
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                targeted gene repair,crispr-cas9 genome editing
                Uncategorized
                targeted gene repair, crispr-cas9 genome editing

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