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      Is Open Access

      The NIH Somatic Cell Genome Editing program

      review-article
      1 , 2 , 3 , 4 , , 5 , , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 8 , 18 , 14 , 19 , 20 , 21 , 22 , 23 , 8 , 24 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 14 , 35 , 36 , 37 , 38 , 39 , 40 , 30 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 4 , 48 , 49 , 50 , 51 , 1 , 3 , 4 , 52 , 53 , 54 , 5 , 55 , 34 , 56 , 57 , 42 , 58 , 12 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 14 , 66 , 67 , 68 , 69 , 1 , 3 , 4 , 70 , 71 , 72 , 32 , 73 , 74 , 1 , 4 , 75 , 76 , 77 , 78 , 79 , 80 , 8 , 66 , 5 , 67 , 81 , 82 , 5 , 83 , 84 , The SCGE Consortium
      Nature
      Nature Publishing Group UK
      Targeted gene repair, Genetics research

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          Abstract

          The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-effective methods to edit the genomes of disease-relevant somatic cells in patients, even in tissues that are difficult to reach. Here we discuss the consortium’s plans to develop and benchmark approaches to induce and measure genome modifications, and to define downstream functional consequences of genome editing within human cells. Central to this effort is a rigorous and innovative approach that requires validation of the technology through third-party testing in small and large animals. New genome editors, delivery technologies and methods for tracking edited cells in vivo, as well as newly developed animal models and human biological systems, will be assembled—along with validated datasets—into an SCGE Toolkit, which will be disseminated widely to the biomedical research community. We visualize this toolkit—and the knowledge generated by its applications—as a means to accelerate the clinical development of new therapies for a wide range of conditions.

          Abstract

          This Perspective discusses how the Somatic Cell Genome Editing Consortium aims to accelerate the implementation of safe and effective genome-editing therapies in the clinic.

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          Most cited references154

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          A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.

          Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.
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            Multiplex genome engineering using CRISPR/Cas systems.

            Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.
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              RNA-guided human genome engineering via Cas9.

              Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II bacterial CRISPR system to function with custom guide RNA (gRNA) in human cells. For the endogenous AAVS1 locus, we obtained targeting rates of 10 to 25% in 293T cells, 13 to 8% in K562 cells, and 2 to 4% in induced pluripotent stem cells. We show that this process relies on CRISPR components; is sequence-specific; and, upon simultaneous introduction of multiple gRNAs, can effect multiplex editing of target loci. We also compute a genome-wide resource of ~190 K unique gRNAs targeting ~40.5% of human exons. Our results establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.
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                Author and article information

                Contributors
                ksaha@wisc.edu
                erik.sontheimer@umassmed.edu
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                7 April 2021
                7 April 2021
                2021
                : 592
                : 7853
                : 195-204
                Affiliations
                [1 ]GRID grid.14003.36, ISNI 0000 0001 2167 3675, Department of Biomedical Engineering, , University of Wisconsin-Madison, ; Madison, WI USA
                [2 ]GRID grid.14003.36, ISNI 0000 0001 2167 3675, Department of Medical History & Bioethics, , University of Wisconsin-Madison, ; Madison, WI USA
                [3 ]GRID grid.14003.36, ISNI 0000 0001 2167 3675, Wisconsin Institute for Discovery, , University of Wisconsin-Madison, ; Madison, WI USA
                [4 ]GRID grid.14003.36, ISNI 0000 0001 2167 3675, McPherson Eye Research Institute, , University of Wisconsin-Madison, ; Madison, WI USA
                [5 ]GRID grid.168645.8, ISNI 0000 0001 0742 0364, RNA Therapeutics Institute, , University of Massachusetts Medical School, ; Worcester, MA USA
                [6 ]GRID grid.94365.3d, ISNI 0000 0001 2297 5165, Office of Rare Diseases Research, National Center for Advancing Translational Sciences (NCATS), , National Institutes of Health, ; Bethesda, MD USA
                [7 ]GRID grid.30760.32, ISNI 0000 0001 2111 8460, Department of Physiology, , Medical College of Wisconsin, ; Milwaukee, WI USA
                [8 ]GRID grid.26009.3d, ISNI 0000 0004 1936 7961, Department of Biomedical Engineering, , Duke University, ; Durham, NC USA
                [9 ]GRID grid.66859.34, Merkin Institute of Transformative Technologies, , Broad Institute of MIT and Harvard, ; Cambridge, MA USA
                [10 ]GRID grid.38142.3c, ISNI 000000041936754X, Department of Chemistry and Chemical Biology, , Harvard University, ; Cambridge, MA USA
                [11 ]GRID grid.413575.1, ISNI 0000 0001 2167 1581, Howard Hughes Medical Institute, ; Cambridge, MA USA
                [12 ]GRID grid.249880.f, ISNI 0000 0004 0374 0039, The Jackson Laboratory, ; Bar Harbor, ME USA
                [13 ]GRID grid.240871.8, ISNI 0000 0001 0224 711X, Department of Hematology, , St Jude Children’s Research Hospital, ; Memphis, TN USA
                [14 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Innovative Genomics Institute, , University of California, Berkeley, ; Berkeley, CA USA
                [15 ]GRID grid.116068.8, ISNI 0000 0001 2341 2786, Department of Chemical Engineering, , Massachusetts Institute of Technology, ; Cambridge, MA USA
                [16 ]GRID grid.116068.8, ISNI 0000 0001 2341 2786, Institute for Medical Engineering and Science, , Massachusetts Institute of Technology, ; Cambridge, MA USA
                [17 ]GRID grid.116068.8, ISNI 0000 0001 2341 2786, David H. Koch Institute for Integrative Cancer Research at the Massachusetts Institute of Technology, ; Cambridge, MA USA
                [18 ]GRID grid.26009.3d, ISNI 0000 0004 1936 7961, Department of Surgery, , Duke University School of Medicine, ; Durham, NC USA
                [19 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Department of Earth and Planetary Sciences, , University of California, Berkeley, ; Berkeley, CA USA
                [20 ]GRID grid.261331.4, ISNI 0000 0001 2285 7943, Department of Neurological Surgery, , Ohio State University, ; Columbus, OH USA
                [21 ]GRID grid.21940.3e, ISNI 0000 0004 1936 8278, Department of Bioengineering, , Rice University, ; Houston, TX USA
                [22 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, , Johns Hopkins University School of Medicine, ; Baltimore, MD USA
                [23 ]GRID grid.21107.35, ISNI 0000 0001 2171 9311, Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, , Johns Hopkins University School of Medicine, ; Baltimore, MD USA
                [24 ]GRID grid.427259.f, Recombinetics, Inc, ; Eagan, MN USA
                [25 ]GRID grid.239395.7, ISNI 0000 0000 9011 8547, Department of Surgery, , Beth Israel Deaconess Medical Center, ; Boston, MA USA
                [26 ]GRID grid.38142.3c, ISNI 000000041936754X, Department of Otolaryngology-Head and Neck Surgery, , Harvard Medical School, ; Boston, MA USA
                [27 ]GRID grid.38142.3c, ISNI 000000041936754X, Program in Neuroscience, , Harvard Medical School, ; Boston, MA USA
                [28 ]GRID grid.39479.30, ISNI 0000 0000 8800 3003, Eaton-Peabody Laboratory, , Massachusetts Eye and Ear Infirmary, ; Boston, MA USA
                [29 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Department of Molecular and Cellular Biology, , University of California, Davis, ; Davis, CA USA
                [30 ]GRID grid.66875.3a, ISNI 0000 0004 0459 167X, Department of Biochemistry and Molecular Biology, , Mayo Clinic Rochester, ; Rochester, MN USA
                [31 ]GRID grid.4367.6, ISNI 0000 0001 2355 7002, Department of Radiation Oncology, , Washington University in St Louis, ; St Louis, MO USA
                [32 ]GRID grid.213917.f, ISNI 0000 0001 2097 4943, Wallace H. Coulter Department of Biomedical Engineering, , Georgia Institute of Technology, ; Atlanta, GA USA
                [33 ]GRID grid.66859.34, Stanley Center for Psychiatric Research, Broad Institute, ; Cambridge, MA USA
                [34 ]GRID grid.39382.33, ISNI 0000 0001 2160 926X, Department of Molecular Physiology and Biophysics, , Baylor College of Medicine, ; Houston, TX USA
                [35 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Department of Chemistry, , University of California, Berkeley, ; Berkeley, CA USA
                [36 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Department of Molecular and Cell Biology, , University of California, Berkeley, ; Berkeley, CA USA
                [37 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, California Institute for Quantitative Biosciences (QB3), , University of California, Berkeley, ; Berkeley, CA USA
                [38 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Howard Hughes Medical Institute, , University of California, Berkeley, ; Berkeley, CA USA
                [39 ]GRID grid.184769.5, ISNI 0000 0001 2231 4551, Molecular Biophysics and Integrated Bioimaging Division, , Lawrence Berkeley National Laboratory, ; Berkeley, CA USA
                [40 ]GRID grid.249878.8, ISNI 0000 0004 0572 7110, Gladstone Institute of Data Science and Biotechnology, , Gladstone Institutes, ; San Francisco, CA USA
                [41 ]GRID grid.14003.36, ISNI 0000 0001 2167 3675, Department of Medical Physics, , University of Wisconsin-Madison, ; Madison, WI USA
                [42 ]GRID grid.14003.36, ISNI 0000 0001 2167 3675, Wisconsin National Primate Research Center, , University of Wisconsin-Madison, ; Madison, WI USA
                [43 ]GRID grid.116068.8, ISNI 0000 0001 2341 2786, McGovern Institute for Brain Research, , Massachusetts Institute of Technology, ; Cambridge, MA USA
                [44 ]GRID grid.34477.33, ISNI 0000000122986657, Division of Nephrology, , University of Washington, ; Seattle, WA USA
                [45 ]GRID grid.34477.33, ISNI 0000000122986657, Kidney Research Institute, , University of Washington, ; Seattle, WA USA
                [46 ]GRID grid.34477.33, ISNI 0000000122986657, Institute for Stem Cell and Regenerative Medicine, , University of Washington, ; Seattle, WA USA
                [47 ]GRID grid.34477.33, ISNI 0000000122986657, Department of Medicine, , University of Washington, ; Seattle, WA USA
                [48 ]GRID grid.14003.36, ISNI 0000 0001 2167 3675, Department of Ophthalmology and Visual Sciences, , University of Wisconsin-Madison, ; Madison, WI USA
                [49 ]GRID grid.168645.8, ISNI 0000 0001 0742 0364, Horae Gene Therapy Center, , University of Massachusetts Medical School, ; Worcester, MA USA
                [50 ]GRID grid.239395.7, ISNI 0000 0000 9011 8547, Department of Medicine, , Beth Israel Deaconess Medical Center, ; Boston, MA USA
                [51 ]GRID grid.47100.32, ISNI 0000000419368710, Department of Therapeutic Radiology, , Yale University, ; New Haven, CT USA
                [52 ]GRID grid.39382.33, ISNI 0000 0001 2160 926X, Department of Molecular and Human Genetics, , Baylor College of Medicine, ; Houston, TX USA
                [53 ]GRID grid.410436.4, ISNI 0000 0004 0619 6542, Division of Reproductive and Developmental Sciences, , Oregon National Primate Research Center, Oregon Health and Science University, ; Beaverton, OR USA
                [54 ]GRID grid.208078.5, ISNI 0000000419370394, Pat and Jim Calhoun Cardiology Center, , University of Connecticut School of Medicine, ; Farmington, CT USA
                [55 ]GRID grid.21925.3d, ISNI 0000 0004 1936 9000, Pittsburgh Liver Research Center, Department of Pathology, , University of Pittsburgh School of Medicine, ; Pittsburgh, PA USA
                [56 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Department of Biochemistry and Molecular Medicine, , University of California, Davis, ; Davis, CA USA
                [57 ]GRID grid.21729.3f, ISNI 0000000419368729, Department of Biomedical Engineering, , Columbia University, ; New York, NY USA
                [58 ]GRID grid.38142.3c, ISNI 000000041936754X, Wyss Institute, , Harvard University, ; Cambridge, MA USA
                [59 ]GRID grid.147455.6, ISNI 0000 0001 2097 0344, Department of Chemistry, , Carnegie-Mellon University, ; Pittsburgh, PA USA
                [60 ]GRID grid.94225.38, ISNI 000000012158463X, Biomarker and Genomic Sciences Group, , National Institute of Standards and Technology, ; Gaithersburg, MD USA
                [61 ]GRID grid.214572.7, ISNI 0000 0004 1936 8294, Department of Pediatrics, , University of Iowa, ; Iowa City, IA USA
                [62 ]GRID grid.249878.8, ISNI 0000 0004 0572 7110, Gladstone Institute of Cardiovascular Disease, , Gladstone Institutes, ; San Francisco, CA USA
                [63 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Department of Bioengineering and Therapeutic Sciences, , University of California, San Francisco, ; San Francisco, CA USA
                [64 ]GRID grid.453125.4, Office of Research Infrastructure Programs, , Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director, National Institutes of Health, ; Bethesda, MD USA
                [65 ]GRID grid.38142.3c, ISNI 000000041936754X, Department of Medicine, Massachusetts General Hospital, , Harvard Medical School, ; Boston, MA USA
                [66 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Department of Bioengineering, , University of California, Berkeley, ; Berkeley, CA USA
                [67 ]GRID grid.134936.a, ISNI 0000 0001 2162 3504, Division of Animal Sciences, , University of Missouri, ; Columbia, MO USA
                [68 ]GRID grid.39381.30, ISNI 0000 0004 1936 8884, Robarts Research Institute and Department of Medical Biophysics, , The University of Western Ontario, London, ; Ontario, Canada
                [69 ]GRID grid.266100.3, ISNI 0000 0001 2107 4242, Department of Pathology, , University of California, San Diego, ; La Jolla, CA USA
                [70 ]GRID grid.14003.36, ISNI 0000 0001 2167 3675, Department of Biostatistics and Medical Informatics, , University of Wisconsin-Madison, ; Madison, WI USA
                [71 ]GRID grid.62560.37, ISNI 0000 0004 0378 8294, Department of Medicine, , Brigham and Women’s Hospital, ; Boston, MA USA
                [72 ]GRID grid.47100.32, ISNI 0000000419368710, Department of Biomedical Engineering, , Yale University, ; New Haven, CT USA
                [73 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Department of Biochemistry and Molecular Medicine, , University of California, Davis, ; Davis, CA USA
                [74 ]GRID grid.30760.32, ISNI 0000 0001 2111 8460, Department of Biomedical Engineering, , Marquette University and Medical College of Wisconsin, ; Milwaukee, WI USA
                [75 ]GRID grid.14003.36, ISNI 0000 0001 2167 3675, Morgridge Institute for Research, ; Madison, WI USA
                [76 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Department of Pediatrics, , University of California, Davis, ; Davis, CA USA
                [77 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Department of Cell Biology and Human Anatomy, , University of California, Davis, ; Davis, CA USA
                [78 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, School of Medicine, , University of California, Davis, ; Davis, CA USA
                [79 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, California National Primate Research Center, , University of California, Davis, ; Davis, CA USA
                [80 ]GRID grid.67105.35, ISNI 0000 0001 2164 3847, Department of Nutrition, , Case Western Reserve University, ; Cleveland, OH USA
                [81 ]GRID grid.168645.8, ISNI 0000 0001 0742 0364, Department of Molecular, Cell and Cancer Biology, , University of Massachusetts Medical School, Worcester, ; Worcester, MA USA
                [82 ]GRID grid.429997.8, ISNI 0000 0004 1936 7531, Department of Biomedical Engineering, , Tufts University, ; Medford, MA USA
                [83 ]GRID grid.267310.1, ISNI 0000 0000 9704 5790, Department of Pulmonary Immunology, , University of Texas Health Sciences Center at Tyler, ; Tyler, TX USA
                [84 ]GRID grid.47100.32, ISNI 0000000419368710, Department of Neurosurgery, , Yale University, ; New Haven, CT USA
                Author information
                http://orcid.org/0000-0003-2837-0858
                http://orcid.org/0000-0002-0881-0310
                http://orcid.org/0000-0003-1478-4013
                http://orcid.org/0000-0002-9943-7557
                http://orcid.org/0000-0001-9161-3993
                http://orcid.org/0000-0002-0644-5540
                http://orcid.org/0000-0001-5629-4798
                http://orcid.org/0000-0001-5563-4877
                http://orcid.org/0000-0001-8203-8771
                http://orcid.org/0000-0001-6095-2108
                http://orcid.org/0000-0001-6184-4571
                http://orcid.org/0000-0002-1452-4193
                http://orcid.org/0000-0002-9637-0967
                http://orcid.org/0000-0003-0726-4212
                http://orcid.org/0000-0002-9351-6641
                http://orcid.org/0000-0002-8021-277X
                http://orcid.org/0000-0002-8152-613X
                http://orcid.org/0000-0003-0097-9012
                http://orcid.org/0000-0003-4525-5560
                http://orcid.org/0000-0001-8475-8828
                http://orcid.org/0000-0001-6928-8071
                http://orcid.org/0000-0002-8133-4955
                http://orcid.org/0000-0002-0280-2774
                http://orcid.org/0000-0002-4067-577X
                http://orcid.org/0000-0002-8905-4931
                http://orcid.org/0000-0002-6012-4035
                http://orcid.org/0000-0001-8696-2726
                http://orcid.org/0000-0002-2163-549X
                http://orcid.org/0000-0001-7352-0339
                http://orcid.org/0000-0001-8962-3105
                http://orcid.org/0000-0002-6320-7637
                http://orcid.org/0000-0002-7042-201X
                http://orcid.org/0000-0002-1201-5360
                Article
                3191
                10.1038/s41586-021-03191-1
                8026397
                33828315
                76416048-9451-4d79-8609-96c1090f9de8
                © The Author(s) 2021

                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
                : 13 August 2020
                : 5 January 2021
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                © The Author(s), under exclusive licence to Springer Nature Limited 2021

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                targeted gene repair,genetics research
                Uncategorized
                targeted gene repair, genetics research

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