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      Therapeutic base editing and prime editing of COL7A1 mutations in recessive dystrophic epidermolysis bullosa

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          Abstract

          Recessive dystrophic epidermolysis bullosa (RDEB) is a severe skin fragility disorder caused by loss-of-function mutations in the COL7A1 gene, which encodes type VII collagen (C7), a protein that functions in skin adherence. From 36 Korean RDEB patients, we identified a total of 69 pathogenic mutations (40 variants without recurrence), including point mutations (72.5%) and insertion/deletion mutations (27.5%). For fibroblasts from two patients (Pat1 and Pat2), we applied adenine base editors (ABEs) to correct the pathogenic mutation of COL7A1 or to bypass a premature stop codon in Pat1-derived primary fibroblasts. To expand the targeting scope, we also utilized prime editors (PEs) to correct the COL7A1 mutations in Pat1- and Pat2-derived fibroblasts. Ultimately, we found that transfer of edited patient-derived skin equivalents (i.e., RDEB keratinocytes and PE-corrected RDEB fibroblasts from the RDEB patient) into the skin of immunodeficient mice led to C7 deposition and anchoring fibril formation within the dermal-epidermal junction, suggesting that base editing and prime editing could be feasible strategies for ex vivo gene editing to treat RDEB.

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          Abstract

          Hong et al. demonstrate adenine base editing and prime editing to correct the COL7A1 gene in recessive dystrophic epidermolysis bullosa (RDEB) patient-derived fibroblasts and keratinocytes. They ultimately transferred edited patient-derived skin equivalents into the skin of immunodeficient mice, leading to C7 deposition and anchoring fibril formation within the dermal-epidermal junction.

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          Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

          Current genome-editing technologies introduce double-stranded (ds) DNA breaks at a target locus as the first step to gene correction. 1,2 Although most genetic diseases arise from point mutations, current approaches to point mutation correction are inefficient and typically induce an abundance of random insertions and deletions (indels) at the target locus from the cellular response to dsDNA breaks. 1,2 Here we report the development of base editing, a new approach to genome editing that enables the direct, irreversible conversion of one target DNA base into another in a programmable manner, without requiring dsDNA backbone cleavage or a donor template. We engineered fusions of CRISPR/Cas9 and a cytidine deaminase enzyme that retain the ability to be programmed with a guide RNA, do not induce dsDNA breaks, and mediate the direct conversion of cytidine to uridine, thereby effecting a C→T (or G→A) substitution. The resulting “base editors” convert cytidines within a window of approximately five nucleotides (nt), and can efficiently correct a variety of point mutations relevant to human disease. In four transformed human and murine cell lines, second- and third-generation base editors that fuse uracil glycosylase inhibitor (UGI), and that use a Cas9 nickase targeting the non-edited strand, manipulate the cellular DNA repair response to favor desired base-editing outcomes, resulting in permanent correction of ∼15-75% of total cellular DNA with minimal (typically ≤ 1%) indel formation. Base editing expands the scope and efficiency of genome editing of point mutations.
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            Search-and-replace genome editing without double-strand breaks or donor DNA

            Summary Most genetic variants that contribute to disease 1 are challenging to correct efficiently and without excess byproducts 2–5 . Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. We performed >175 edits in human cells including targeted insertions, deletions, and all 12 types of point mutations without requiring double-strand breaks or donor DNA templates. We applied prime editing in human cells to correct efficiently and with few byproducts the primary genetic causes of sickle cell disease (requiring a transversion in HBB) and Tay-Sachs disease (requiring a deletion in HEXA), to install a protective transversion in PRNP, and to precisely insert various tags and epitopes into target loci. Four human cell lines and primary post-mitotic mouse cortical neurons support prime editing with varying efficiencies. Prime editing shows higher or similar efficiency and fewer byproducts than homology-directed repair, complementary strengths and weaknesses compared to base editing, and much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle can correct up to 89% of known genetic variants associated with human diseases.
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              Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

              Summary The spontaneous deamination of cytosine is a major source of C•G to T•A transitions, which account for half of known human pathogenic point mutations. The ability to efficiently convert target A•T base pairs to G•C therefore could advance the study and treatment of genetic diseases. While the deamination of adenine yields inosine, which is treated as guanine by polymerases, no enzymes are known to deaminate adenine in DNA. Here we report adenine base editors (ABEs) that mediate conversion of A•T to G•C in genomic DNA. We evolved a tRNA adenosine deaminase to operate on DNA when fused to a catalytically impaired CRISPR-Cas9. Extensive directed evolution and protein engineering resulted in seventh-generation ABEs (e.g., ABE7.10), that convert target A•T to G•C base pairs efficiently (~50% in human cells) with very high product purity (typically ≥ 99.9%) and very low rates of indels (typically ≤ 0.1%). ABEs introduce point mutations more efficiently and cleanly than a current Cas9 nuclease-based method, induce less off-target genome modification than Cas9, and can install disease-correcting or disease-suppressing mutations in human cells. Together with our previous base editors, ABEs advance genome editing by enabling the direct, programmable introduction of all four transition mutations without double-stranded DNA cleavage.
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                Author and article information

                Contributors
                Journal
                Mol Ther
                Mol Ther
                Molecular Therapy
                American Society of Gene & Cell Therapy
                1525-0016
                1525-0024
                03 August 2022
                10 June 2022
                : 30
                : 8
                : 2664-2679
                Affiliations
                [1 ]Genomic Medicine Institute, Medical Research Center, Seoul National University College of Medicine, Seoul 03080, South Korea
                [2 ]Department of Dermatology, Gangnam Severance Hospital, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul 06273, South Korea
                [3 ]Department of Chemistry, Hanyang University, Seoul 04763, South Korea
                [4 ]Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
                [5 ]Department of Dermatology, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin 16995, South Korea
                [6 ]Department of Biomedical Sciences, Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, South Korea
                Author notes
                []Corresponding author: Sangsu Bae, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea. sbae7@ 123456snu.ac.kr
                [∗∗ ]Corresponding author: Sang Eun Lee, Department of Dermatology and Cutaneous Biology Research Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, South Korea. jennifer823@ 123456yuhs.ac
                [7]

                These authors contributed equally

                Article
                S1525-0016(22)00365-3
                10.1016/j.ymthe.2022.06.005
                9372317
                35690907
                0d95565b-a6fe-4f61-acd3-78bb95530c53
                © 2022 The Author(s)

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 12 December 2021
                : 6 June 2022
                Categories
                Original Article

                Molecular medicine
                recessive dystrophic epidermolysis bullosa,crispr,genome editing,base editing,prime editing,type vii collagen,col7a1

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