1
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Cowan QT, Gu S, Gu W, Ranzau BL, Simonson TS, Komor AC. Development of multiplexed orthogonal base editor (MOBE) systems. Nat Biotechnol 2024:10.1038/s41587-024-02240-0. [PMID: 38773305 DOI: 10.1038/s41587-024-02240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 04/10/2024] [Indexed: 05/23/2024]
Abstract
Base editors (BEs) enable efficient, programmable installation of point mutations while avoiding the use of double-strand breaks. Simultaneous application of two or more different BEs, such as an adenine BE (which converts A·T base pairs to G·C) and a cytosine BE (which converts C·G base pairs to T·A), is not feasible because guide RNA crosstalk results in non-orthogonal editing, with all BEs modifying all target loci. Here we engineer both adenine BEs and cytosine BEs that can be orthogonally multiplexed by using RNA aptamer-coat protein systems to recruit the DNA-modifying enzymes directly to the guide RNAs. We generate four multiplexed orthogonal BE systems that enable rates of precise co-occurring edits of up to 7.1% in the same DNA strand without enrichment or selection strategies. The addition of a fluorescent enrichment strategy increases co-occurring edit rates up to 24.8% in human cells. These systems are compatible with expanded protospacer adjacent motif and high-fidelity Cas9 variants, function well in multiple cell types, have equivalent or reduced off-target propensities compared with their parental systems and can model disease-relevant point mutation combinations.
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Affiliation(s)
- Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Sifeng Gu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Tatum S Simonson
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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2
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Lawrence ES, Gu W, Bohlender RJ, Anza-Ramirez C, Cole AM, Yu JJ, Hu H, Heinrich EC, O’Brien KA, Vasquez CA, Cowan QT, Bruck PT, Mercader K, Alotaibi M, Long T, Hall JE, Moya EA, Bauk MA, Reeves JJ, Kong MC, Salem RM, Vizcardo-Galindo G, Macarlupu JL, Figueroa-Mujíca R, Bermudez D, Corante N, Gaio E, Fox KP, Salomaa V, Havulinna AS, Murray AJ, Malhotra A, Powel FL, Jain M, Komor AC, Cavalleri GL, Huff CD, Villafuerte FC, Simonson TS. Functional EPAS1/ HIF2A missense variant is associated with hematocrit in Andean highlanders. Sci Adv 2024; 10:eadj5661. [PMID: 38335297 PMCID: PMC10857371 DOI: 10.1126/sciadv.adj5661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
Hypoxia-inducible factor pathway genes are linked to adaptation in both human and nonhuman highland species. EPAS1, a notable target of hypoxia adaptation, is associated with relatively lower hemoglobin concentration in Tibetans. We provide evidence for an association between an adaptive EPAS1 variant (rs570553380) and the same phenotype of relatively low hematocrit in Andean highlanders. This Andean-specific missense variant is present at a modest frequency in Andeans and absent in other human populations and vertebrate species except the coelacanth. CRISPR-base-edited human cells with this variant exhibit shifts in hypoxia-regulated gene expression, while metabolomic analyses reveal both genotype and phenotype associations and validation in a lowland population. Although this genocopy of relatively lower hematocrit in Andean highlanders parallels well-replicated findings in Tibetans, it likely involves distinct pathway responses based on a protein-coding versus noncoding variants, respectively. These findings illuminate how unique variants at EPAS1 contribute to the same phenotype in Tibetans and a subset of Andean highlanders despite distinct evolutionary trajectories.
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Affiliation(s)
- Elijah S. Lawrence
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ryan J. Bohlender
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cecilia Anza-Ramirez
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Amy M. Cole
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - James J. Yu
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erica C. Heinrich
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Katie A. O’Brien
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Carlos A. Vasquez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Quinn T. Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Patrick T. Bruck
- Department of Anthropology and Global Health, University of California, San Diego, La Jolla, CA, USA
| | - Kysha Mercader
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Tao Long
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - James E. Hall
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Esteban A. Moya
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marco A. Bauk
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer J. Reeves
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mitchell C. Kong
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Rany M. Salem
- Herbert Wertheim School of Public Health and Longevity Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gustavo Vizcardo-Galindo
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jose-Luis Macarlupu
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Rómulo Figueroa-Mujíca
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Daniela Bermudez
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Noemi Corante
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Eduardo Gaio
- Laboratório de Fisiologia Respiratória, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Keolu P. Fox
- Department of Anthropology and Global Health, University of California, San Diego, La Jolla, CA, USA
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aki S. Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM-HiLIFE), Helsinki, Finland
| | - Andrew J. Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frank L. Powel
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mohit Jain
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Gianpiero L. Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francisco C. Villafuerte
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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3
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Medina-Munoz HC, Kofman E, Jagannatha P, Boyle EA, Yu T, Jones KL, Mueller JR, Lykins GD, Doudna AT, Park SS, Blue SM, Ranzau BL, Kohli RM, Komor AC, Yeo GW. Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies. Nat Commun 2024; 15:875. [PMID: 38287010 PMCID: PMC10825223 DOI: 10.1038/s41467-024-45009-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/03/2024] [Indexed: 01/31/2024] Open
Abstract
RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.
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Affiliation(s)
- Hugo C Medina-Munoz
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eric Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Pratibha Jagannatha
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Evan A Boyle
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tao Yu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Krysten L Jones
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jasmine R Mueller
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Grace D Lykins
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrew T Doudna
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Samuel S Park
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
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4
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Medina-Munoz HC, Kofman E, Jagannatha P, Boyle EA, Yu T, Jones KL, Mueller JR, Lykins GD, Doudna AT, Park SS, Blue SM, Ranzau BL, Kohli RM, Komor AC, Yeo GW. Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies. bioRxiv 2023:2023.09.25.558915. [PMID: 37808757 PMCID: PMC10557582 DOI: 10.1101/2023.09.25.558915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.
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Affiliation(s)
- Hugo C. Medina-Munoz
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eric Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Pratibha Jagannatha
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Evan A. Boyle
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tao Yu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Krysten L. Jones
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jasmine R. Mueller
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Grace D. Lykins
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrew T. Doudna
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Samuel S. Park
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Steven M. Blue
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brodie L. Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Rahul M. Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
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5
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Ranzau BL, Rallapalli KL, Evanoff M, Paesani F, Komor AC. The Wild-Type tRNA Adenosine Deaminase Enzyme TadA Is Capable of Sequence-Specific DNA Base Editing. Chembiochem 2023; 24:e202200788. [PMID: 36947856 PMCID: PMC10514239 DOI: 10.1002/cbic.202200788] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/11/2023] [Accepted: 03/22/2023] [Indexed: 03/24/2023]
Abstract
Base editors are genome editing tools that enable site-specific base conversions through the chemical modification of nucleobases in DNA. Adenine base editors (ABEs) convert A ⋅ T to G ⋅ C base pairs in DNA by using an adenosine deaminase enzyme to modify target adenosines to inosine intermediates. Due to the lack of a naturally occurring adenosine deaminase that can modify DNA, ABEs were evolved from a tRNA-deaminating enzyme, TadA. Previous experiments with an ABE comprising a wild-type (wt) TadA showed no detectable activity on DNA, and directed evolution was therefore required to enable this enzyme to accept DNA as a substrate. Here we show that wtTadA can perform base editing in DNA in both bacterial and mammalian cells, with a strict sequence motif requirement of TAC. We leveraged this discovery to optimize a reporter assay to detect base editing levels as low as 0.01 %. Finally, we used this assay along with molecular dynamics simulations of full ABE:DNA complexes to better understand how the sequence recognition of mutant TadA variants change as they accumulate mutations to better edit DNA substrates.
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Affiliation(s)
- Brodie L. Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Kartik L. Rallapalli
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Mallory Evanoff
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California 92093, USA
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
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6
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Vasquez CA, Evanoff M, Ranzau BL, Gu S, Deters E, Komor AC. Curing "GFP-itis" in Bacteria with Base Editors: Development of a Genome Editing Science Program Implemented with High School Biology Students. CRISPR J 2023. [PMID: 37083425 DOI: 10.1089/crispr.2023.0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
The flexibility and precision of CRISPR-Cas9 and related technologies have made these genome editing tools increasingly popular in agriculture, medicine, and basic science research for the past decade. Genome editing will continue to be relevant and utilized across diverse scientific fields in the future. Given this, students should be introduced to genome editing technologies and encouraged to consider their ethical implications early on in precollege biology curricula. Furthermore, instruction on this topic presents an opportunity to create partnerships between researchers and educators at the K-12 levels that can strengthen student engagement in science, technology, engineering, and mathematics. To this end, we present a 3-day student-centered learning program to introduce high school students to genome editing technologies through a hands-on base editing experiment in Escherichia coli, accompanied by a relevant background lecture and facilitated ethics discussion. This unique partnership aims to educate students and provides a framework for research institutions to implement genome editing outreach programs at local high schools. We have included all requisite materials, including lecture slides, worksheets, experimental protocols, and suggestions on active learning strategies for others to reproduce our program with their local communities.
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Affiliation(s)
- Carlos A Vasquez
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Mallory Evanoff
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Sifeng Gu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Emma Deters
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
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Abstract
DNA-editing enzymes perform chemical reactions on DNA nucleobases. These reactions can change the genetic identity of the modified base or modulate gene expression. Interest in DNA-editing enzymes has burgeoned in recent years due to the advent of clustered regularly interspaced short palindromic repeat-associated (CRISPR-Cas) systems, which can be used to direct their DNA-editing activity to specific genomic loci of interest. In this review, we showcase DNA-editing enzymes that have been repurposed or redesigned and developed into programmable base editors. These include deaminases, glycosylases, methyltransferases, and demethylases. We highlight the astounding degree to which these enzymes have been redesigned, evolved, and refined and present these collective engineering efforts as a paragon for future efforts to repurpose and engineer other families of enzymes. Collectively, base editors derived from these DNA-editing enzymes facilitate programmable point mutation introduction and gene expression modulation by targeted chemical modification of nucleobases. Expected final online publication date for the Annual Review of Biochemistry, Volume 92 is June 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Kartik L Rallapalli
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA;
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA;
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8
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Abstract
With the advent of recombinant DNA technology in the 1970s, the idea of using gene therapies to treat human genetic diseases captured the interest and imagination of scientists around the world. Years later, enabled largely by the development of CRISPR-based genome editing tools, the field has exploded, with academic labs, startup biotechnology companies, and large pharmaceutical corporations working in concert to develop life-changing therapeutics. In this Essay, we highlight base editing technologies and their development from bench to bedside. Base editing, first reported in 2016, is capable of installing C•G to T•A and A•T to G•C point mutations, while largely circumventing some of the pitfalls of traditional CRISPR/Cas9 gene editing. Despite their youth, these technologies have been widely used by both academic labs and therapeutics-based companies. Here, we provide an overview of the mechanics of base editing and its use in clinical trials.
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Affiliation(s)
- Elizabeth M. Porto
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America
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9
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Vasquez CA, Evanoff M, Ranzau BL, Gu S, Deters E, Komor AC. Curing "GFP-itis" in Bacteria with Base Editors: Development of a Genome Editing Science Program Implemented with High School Biology Students. bioRxiv 2023:2023.02.06.527367. [PMID: 36798336 PMCID: PMC9934571 DOI: 10.1101/2023.02.06.527367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The flexibility and precision of CRISPR-Cas9 and related technologies have made these genome editing tools increasingly popular in agriculture, medicine, and basic science research over the past decade. Genome editing will continue to be relevant and utilized across diverse scientific fields in the future. Given this, students should be introduced to genome editing technologies and encouraged to consider their ethical implications early on in pre-college biology curricula. Furthermore, instruction on this topic presents an opportunity to create partnerships between researchers and educators at the K-12 levels that can strengthen student engagement in science, technology, engineering, and mathematics (STEM). To this end, we present a three-day student-centered learning program to introduce high school students to genome editing technologies through a hands-on base editing experiment in E. coli , accompanied by a relevant background lecture and facilitated ethics discussion. This unique partnership aims to educate students and provides a framework for research institutions to implement genome editing outreach programs at local high schools.
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Affiliation(s)
- Carlos A. Vasquez
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA,These authors contributed equally
| | - Mallory Evanoff
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA,These authors contributed equally
| | - Brodie L. Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Sifeng Gu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Emma Deters
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA,Correspondence:
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10
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Burnett CA, Wong AT, Vasquez CA, McHugh CA, Yeo GW, Komor AC. Examination of the Cell Cycle Dependence of Cytosine and Adenine Base Editors. Front Genome Ed 2022; 4:923718. [PMID: 35910415 PMCID: PMC9333457 DOI: 10.3389/fgeed.2022.923718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/21/2022] [Indexed: 11/27/2022] Open
Abstract
Base editors (BEs) are genome editing agents that install point mutations with high efficiency and specificity. Due to their reliance on uracil and inosine DNA damage intermediates (rather than double-strand DNA breaks, or DSBs), it has been hypothesized that BEs rely on more ubiquitous DNA repair pathways than DSB-reliant genome editing methods, which require processes that are only active during certain phases of the cell cycle. We report here the first systematic study of the cell cycle-dependence of base editing using cell synchronization experiments. We find that nickase-derived BEs (which introduce DNA backbone nicks opposite the uracil or inosine base) function independently of the cell cycle, while non-nicking BEs are highly dependent on S-phase (DNA synthesis phase). We found that synchronization in G1 (growth phase) during the process of cytosine base editing causes significant increases in C•G to A•T “byproduct” introduction rates, which can be leveraged to discover new strategies for precise C•G to A•T base editing. We observe that endogenous expression levels of DNA damage repair pathways are sufficient to process base editing intermediates into desired editing outcomes, and the process of base editing does not significantly perturb transcription levels. Overall, our study provides mechanistic data demonstrating the robustness of nickase-derived BEs for performing genome editing across the cell cycle.
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Affiliation(s)
- Cameron A. Burnett
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Ashley T. Wong
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Carlos A. Vasquez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Colleen A. McHugh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Gene W. Yeo
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
- *Correspondence: Alexis C. Komor,
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11
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Bishop AL, López Del Amo V, Okamoto EM, Bodai Z, Komor AC, Gantz VM. Double-tap gene drive uses iterative genome targeting to help overcome resistance alleles. Nat Commun 2022; 13:2595. [PMID: 35534475 PMCID: PMC9085836 DOI: 10.1038/s41467-022-29868-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/28/2022] [Indexed: 01/07/2023] Open
Abstract
Homing CRISPR gene drives could aid in curbing the spread of vector-borne diseases and controlling crop pest and invasive species populations due to an inheritance rate that surpasses Mendelian laws. However, this technology suffers from resistance alleles formed when the drive-induced DNA break is repaired by error-prone pathways, which creates mutations that disrupt the gRNA recognition sequence and prevent further gene-drive propagation. Here, we attempt to counteract this by encoding additional gRNAs that target the most commonly generated resistance alleles into the gene drive, allowing a second opportunity at gene-drive conversion. Our presented "double-tap" strategy improved drive efficiency by recycling resistance alleles. The double-tap drive also efficiently spreads in caged populations, outperforming the control drive. Overall, this double-tap strategy can be readily implemented in any CRISPR-based gene drive to improve performance, and similar approaches could benefit other systems suffering from low HDR frequencies, such as mammalian cells or mouse germline transformations.
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Affiliation(s)
- Alena L Bishop
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Víctor López Del Amo
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Emily M Okamoto
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Zsolt Bodai
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Valentino M Gantz
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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12
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Bodai Z, Bishop AL, Gantz VM, Komor AC. Targeting double-strand break indel byproducts with secondary guide RNAs improves Cas9 HDR-mediated genome editing efficiencies. Nat Commun 2022; 13:2351. [PMID: 35534455 PMCID: PMC9085776 DOI: 10.1038/s41467-022-29989-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/07/2022] [Indexed: 12/26/2022] Open
Abstract
Programmable double-strand DNA breaks (DSBs) can be harnessed for precision genome editing through manipulation of the homology-directed repair (HDR) pathway. However, end-joining repair pathways often outcompete HDR and introduce insertions and deletions of bases (indels) at the DSB site, decreasing precision outcomes. It has been shown that indel sequences for a given DSB site are reproducible and can even be predicted. Here, we report a general strategy (the "double tap" method) to improve HDR-mediated precision genome editing efficiencies that takes advantage of the reproducible nature of indel sequences. The method simply involves the use of multiple gRNAs: a primary gRNA that targets the wild-type genomic sequence, and one or more secondary gRNAs that target the most common indel sequence(s), which in effect provides a "second chance" at HDR-mediated editing. This proof-of-principle study presents the double tap method as a simple yet effective option for enhancing precision editing in mammalian cells.
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Affiliation(s)
- Zsolt Bodai
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alena L Bishop
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Valentino M Gantz
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
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13
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Weng N, Miller M, Pham AK, Komor AC, Broide DH. Single-base editing of rs12603332 on chromosome 17q21 with a cytosine base editor regulates ORMDL3 and ATF6α expression. Allergy 2022; 77:1139-1149. [PMID: 34525218 DOI: 10.1111/all.15092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Genetic association studies have demonstrated that the SNP rs12603332 located on chromosome 17q21 is highly associated with the risk of the development of asthma. METHODS To determine whether SNP rs1260332 is functional in regulating levels of ORMDL3 expression, we used a Cytosine Base Editor (CBE) plasmid DNA or a CBE mRNA to edit the rs12603332 C risk allele to the T non-risk allele in a human lymphocyte cell line (i.e., Jurkat cells) and in primary human CD4 T cells that carry the C risk alleles. RESULTS Jurkat cells with the rs12603332 C risk allele expressed significantly higher levels of ORMDL3 mRNA, as well as the ORMDL3 regulated gene ATF6α as assessed by qPCR compared to Jurkat clones with the T non-risk allele. In primary human CD4 T cells, we edited 90 ± 3% of the rs12603332-C risk allele to the T non-risk allele and observed a reduction in ORMDL3 and ATF6α expression. Bioinformatic analysis predicted that the non-risk allele rs12603332-T could be the central element of the E-box binding motif (CANNTG) recognized by the E47 transcription factor. An EMSA assay confirmed the bioinformatics prediction demonstrating that a rs12603332-T containing probe bound to the transcription factor E47 in vitro. CONCLUSIONS SNP rs12603332 is functional in regulating the expression of ORMDL3 as well as ORMDL3 regulated gene ATF6α expression. In addition, we demonstrate the use of CBE technology in functionally interrogating asthma-associated SNPs using studies of primary human CD4 cells.
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Affiliation(s)
- Ning Weng
- Department of Medicine University of California San Diego La Jolla California USA
| | - Marina Miller
- Department of Medicine University of California San Diego La Jolla California USA
| | - Alexa K. Pham
- Department of Medicine University of California San Diego La Jolla California USA
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry University of California San Diego La Jolla California USA
| | - David H. Broide
- Department of Medicine University of California San Diego La Jolla California USA
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14
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Rallapalli KL, Ranzau BL, Ganapathy KR, Paesani F, Komor AC. Combined Theoretical, Bioinformatic, and Biochemical Analyses of RNA Editing by Adenine Base Editors. CRISPR J 2022; 5:294-310. [PMID: 35353638 DOI: 10.1089/crispr.2021.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adenine base editors (ABEs) have been subjected to multiple rounds of mutagenesis with the goal of optimizing their function as efficient and precise genome editing agents. Despite an ever-expanding data set of ABE mutants and their corresponding DNA or RNA-editing activity, the molecular mechanisms defining these changes remain to be elucidated. In this study, we provide a systematic interpretation of the nature of these mutations using an entropy-based classification model that relies on evolutionary data from extant protein sequences. Using this model in conjunction with experimental analyses, we identify two previously reported mutations that form an epistatic pair in the RNA-editing functional landscape of ABEs. Molecular dynamics simulations reveal the atomistic details of how these two mutations affect substrate-binding and catalytic activity, via both individual and cooperative effects, hence providing insights into the mechanisms through which these two mutations are epistatically coupled.
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Affiliation(s)
- Kartik L Rallapalli
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
| | - Kaushik R Ganapathy
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA.,Materials Science and Engineering, University of California San Diego, La Jolla, California, USA; and University of California San Diego, La Jolla, California, USA.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
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15
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Rees HA, Minella AC, Burnett CA, Komor AC, Gaudelli NM. CRISPR-derived genome editing therapies: Progress from bench to bedside. Mol Ther 2021; 29:3125-3139. [PMID: 34619370 PMCID: PMC8572140 DOI: 10.1016/j.ymthe.2021.09.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/22/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022] Open
Abstract
The development of CRISPR-derived genome editing technologies has enabled the precise manipulation of DNA sequences within the human genome. In this review, we discuss the initial development and cellular mechanism of action of CRISPR nucleases and DNA base editors. We then describe factors that must be taken into consideration when developing these tools into therapeutic agents, including the potential for unintended and off-target edits when using these genome editing tools, and methods to characterize these types of edits. We finish by considering specific challenges associated with bringing a CRISPR-based therapy to the clinic, including manufacturing, regulatory oversight, and considerations for clinical trials that involve genome editing agents.
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16
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Abstract
Base editors are an innovative addition to the genome editing toolbox that introduced a new genome editing strategy to the field. Instead of using double-stranded DNA breaks, base editors use nucleobase modification chemistry to efficiently and precisely incorporate single nucleotide variants (SNVs) into the genome of living cells. Two classes of DNA base editors currently exist: deoxycytidine deamination-derived editors (CBEs, which facilitate C•G to T•A mutations) and deoxyadenosine deamination-derived base editors (ABEs, which facilitate A•T to G•C mutations). More recently, the development of mitochondrial base editors allowed the introduction of C•G to T•A mutations into mitochondrial DNA as well. Base editors show great potential as therapeutic agents and research tools, and extensive studies have been carried out to improve upon the original base editor constructs to aid researchers in a variety of disciplines. Despite their widespread use, there are few publications that focus on elucidating the biological pathways involved during the processing of base editor intermediates. Because base editors introduce unique types of DNA damage products (a U•G mismatch with a DNA backbone nick for CBEs, and an I•T mismatch with a DNA backbone nick for ABEs) to facilitate genome editing, a deep understanding of the DNA damage repair pathways that facilitate or impede base editing represents an important aspect for the further expansion and improvement of the technologies. Here, we first review canonical deoxyuridine, deoxyinosine, and single-stranded break repair. Then, we discuss how interactions among these different repair processes can lead to different base editing outcomes. Through this review, we hope to promote thoughtful discussions on the DNA repair mechanisms of base editing, as well as help researchers in the improvement of the current base editors and the development of new base editors.
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Affiliation(s)
- Sifeng Gu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Zsolt Bodai
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
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17
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Affiliation(s)
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
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18
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Abstract
Base editing - the introduction of single-nucleotide variants (SNVs) into DNA or RNA in living cells - is one of the most recent advances in the field of genome editing. As around half of known pathogenic genetic variants are due to SNVs, base editing holds great potential for the treatment of numerous genetic diseases, through either temporary RNA or permanent DNA base alterations. Recent advances in the specificity, efficiency, precision and delivery of DNA and RNA base editors are revealing exciting therapeutic opportunities for these technologies. We expect the correction of single point mutations will be a major focus of future precision medicine.
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Affiliation(s)
- Elizabeth M Porto
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
| | - Ian M Slaymaker
- Synthetic Biology Department, Beam Therapeutics, Cambridge, MA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences and Bioinformatics and Systems Biology Graduate Programs, University of California, San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
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19
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Vasquez CA, Cowan QT, Komor AC. Base Editing in Human Cells to Produce Single-Nucleotide-Variant Clonal Cell Lines. ACTA ACUST UNITED AC 2020; 133:e129. [PMID: 33151638 DOI: 10.1002/cpmb.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Base-editing technologies enable the introduction of point mutations at targeted genomic sites in mammalian cells, with higher efficiency and precision than traditional genome-editing methods that use DNA double-strand breaks, such as zinc finger nucleases (ZFNs), transcription-activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (CRISPR-Cas9) system. This allows the generation of single-nucleotide-variant isogenic cell lines (i.e., cell lines whose genomic sequences differ from each other only at a single, edited nucleotide) in a more time- and resource-effective manner. These single-nucleotide-variant clonal cell lines represent a powerful tool with which to assess the functional role of genetic variants in a native cellular context. Base editing can therefore facilitate genotype-to-phenotype studies in a controlled laboratory setting, with applications in both basic research and clinical applications. Here, we provide optimized protocols (including experimental design, methods, and analyses) to design base-editing constructs, transfect adherent cells, quantify base-editing efficiencies in bulk, and generate single-nucleotide-variant clonal cell lines. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Design and production of plasmids for base-editing experiments Basic Protocol 2: Transfection of adherent cells and harvesting of genomic DNA Basic Protocol 3: Genotyping of harvested cells using Sanger sequencing Alternate Protocol 1: Next-generation sequencing to quantify base editing Basic Protocol 4: Single-cell isolation of base-edited cells using FACS Alternate Protocol 2: Single-cell isolation of base-edited cells using dilution plating Basic Protocol 5: Clonal expansion to generate isogenic cell lines and genotyping of clones.
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Affiliation(s)
- Carlos A Vasquez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
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20
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Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC. Global chemical effects of the microbiome include new bile-acid conjugations. Nature 2020; 579:123-129. [PMID: 32103176 PMCID: PMC7252668 DOI: 10.1038/s41586-020-2047-9] [Citation(s) in RCA: 266] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/03/2020] [Indexed: 12/26/2022]
Abstract
A mosaic of cross-phylum chemical interactions occurs between all metazoans and their microbiomes. A number of molecular families that are known to be produced by the microbiome have a marked effect on the balance between health and disease1-9. Considering the diversity of the human microbiome (which numbers over 40,000 operational taxonomic units10), the effect of the microbiome on the chemistry of an entire animal remains underexplored. Here we use mass spectrometry informatics and data visualization approaches11-13 to provide an assessment of the effects of the microbiome on the chemistry of an entire mammal by comparing metabolomics data from germ-free and specific-pathogen-free mice. We found that the microbiota affects the chemistry of all organs. This included the amino acid conjugations of host bile acids that were used to produce phenylalanocholic acid, tyrosocholic acid and leucocholic acid, which have not previously been characterized despite extensive research on bile-acid chemistry14. These bile-acid conjugates were also found in humans, and were enriched in patients with inflammatory bowel disease or cystic fibrosis. These compounds agonized the farnesoid X receptor in vitro, and mice gavaged with the compounds showed reduced expression of bile-acid synthesis genes in vivo. Further studies are required to confirm whether these compounds have a physiological role in the host, and whether they contribute to gut diseases that are associated with microbiome dysbiosis.
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Affiliation(s)
- Robert A Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Alison Vrbanac
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Ting Fu
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Kathryn A Patras
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Mitchell P Christy
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Zsolt Bodai
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Anupriya Tripathi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Lawton K Chung
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Ryan D Welch
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA
| | - Melissa Quinn
- Department of Kinesiology, Michigan State University, East Lansing, MI, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,UCSD Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
| | - Alexander Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Ricardo da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | | | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sena Bae
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Himel Mallick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jason Lloyd-Price
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Robert Bussell
- Department of Radiology, University of California San Diego, San Diego, CA, USA
| | - Taren Thron
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrew T Nelson
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Eric Leszczynski
- Department of Kinesiology, Michigan State University, East Lansing, MI, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Emily Gentry
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Timothy D Arthur
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA, USA
| | - Orit Poulsen
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - John T Chang
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - William J Sandborn
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Meerana Lim
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.,Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
| | - Julie C Lumeng
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Ruchi Jain
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Marie Egan
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Kyung E Rhee
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - David Ferguson
- Department of Kinesiology, Michigan State University, East Lansing, MI, USA
| | - Manuela Raffatellu
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriel G Haddad
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Dionicio Siegel
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA, USA.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, San Diego, CA, USA
| | - Victor Nizet
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,UCSD Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,UCSD Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.,Department of Engineering, University of California San Diego, San Diego, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA. .,Department of Pediatrics, University of California San Diego, San Diego, CA, USA. .,UCSD Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA.
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21
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Rallapalli KL, Komor AC, Paesani F. Computer simulations explain mutation-induced effects on the DNA editing by adenine base editors. Sci Adv 2020; 6:eaaz2309. [PMID: 32181363 PMCID: PMC7056309 DOI: 10.1126/sciadv.aaz2309] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Abstract
Adenine base editors, which were developed by engineering a transfer RNA adenosine deaminase enzyme (TadA) into a DNA editing enzyme (TadA*), enable precise modification of A:T to G⋮C base pairs. Here, we use molecular dynamics simulations to uncover the structural and functional roles played by the initial mutations in the onset of the DNA editing activity by TadA*. Atomistic insights reveal that early mutations lead to intricate conformational changes in the structure of TadA*. In particular, the first mutation, Asp108Asn, induces an enhancement in the binding affinity of TadA to DNA. In silico and in vivo reversion analyses verify the importance of this single mutation in imparting functional promiscuity to TadA* and demonstrate that TadA* performs DNA base editing as a monomer rather than a dimer.
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Affiliation(s)
- Kartik L. Rallapalli
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Materials Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
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22
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Fox K, Rallapalli KL, Komor AC. Rewriting Human History and Empowering Indigenous Communities with Genome Editing Tools. Genes (Basel) 2020; 11:E88. [PMID: 31940934 PMCID: PMC7016644 DOI: 10.3390/genes11010088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 12/12/2022] Open
Abstract
Appropriate empirical-based evidence and detailed theoretical considerations should be used for evolutionary explanations of phenotypic variation observed in the field of human population genetics (especially Indigenous populations). Investigators within the population genetics community frequently overlook the importance of these criteria when associating observed phenotypic variation with evolutionary explanations. A functional investigation of population-specific variation using cutting-edge genome editing tools has the potential to empower the population genetics community by holding "just-so" evolutionary explanations accountable. Here, we detail currently available precision genome editing tools and methods, with a particular emphasis on base editing, that can be applied to functionally investigate population-specific point mutations. We use the recent identification of thrifty mutations in the CREBRF gene as an example of the current dire need for an alliance between the fields of population genetics and genome editing.
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Affiliation(s)
- Keolu Fox
- Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Global Health, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kartik Lakshmi Rallapalli
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA;
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA;
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23
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Abstract
Base editors are a new family of programmable genome editing tools that fuse ssDNA (single stranded DNA) modifying enzymes to catalytically inactive CRISPR-associated (Cas) endonucleases to induce highly efficient single base changes. With dozens of base editors now reported, it is apparent that these tools are highly modular; many combinations of ssDNA modifying enzymes and Cas proteins have resulted in a variety of base editors, each with its own unique properties and potential uses. In this perspective, we describe currently available base editors, highlighting their modular nature and describing the various options available for each component. Furthermore, we briefly discuss applications in synthetic biology and genome engineering where base editors have presented unique advantages over alternative techniques.
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Affiliation(s)
- Mallory Evanoff
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093
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24
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25
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Abstract
Base editors are tools that chemically modify the nucleobases of DNA and RNA in a programmable manner, allowing for genome, epigenome, and transcriptome editing in live cells. These tools can be used to introduce specific base transitions in DNA or RNA, manipulate methylation patterns in the epigenome, and create genetically encoded libraries in target genes. These various functions can be used to modulate every aspect of the central dogma. The efficiency and precision of base editors makes them useful in both basic research and the development of new therapies. Here we describe currently available base editors and the ways that they can be used to better understand and manipulate different aspects of the central dogma.
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Affiliation(s)
- Brodie L Ranzau
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Alexis C Komor
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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26
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Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR. Publisher Correction: Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 2018; 559:E8. [PMID: 29720650 DOI: 10.1038/s41586-018-0070-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this Article, owing to an error during the production process, in Fig. 1a, the dark blue and light blue wedges were incorrectly labelled as 'G•C → T•A' and 'G•C → A•T', instead of 'C•G → T•A' and 'C•G → A•T', respectively. Fig. 1 has been corrected online.
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Affiliation(s)
- Nicole M Gaudelli
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexis C Komor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Holly A Rees
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Beam Therapeutics, Cambridge, MA, USA
| | - Ahmed H Badran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David I Bryson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Beam Therapeutics, Cambridge, MA, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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27
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28
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Abstract
Genome editing methods have commonly relied on the initial introduction of double-stranded DNA breaks (DSBs), resulting in stochastic insertions, deletions, and translocations at the target genomic locus. To achieve gene correction, these methods typically require the introduction of exogenous DNA repair templates and low-efficiency homologous recombination processes. In this review, we describe alternative, mechanistically motivated strategies to perform chemistry on the genome of unmodified cells without introducing DSBs. One such strategy, base editing, uses chemical and biological insights to directly and permanently convert one target base pair to another. Despite its recent introduction, base editing has already enabled a number of new capabilities and applications in the genome editing community. We summarize these advances here and discuss the new possibilities that this method has unveiled, concluding with a brief analysis of future prospects for genome and transcriptome editing without double-stranded DNA cleavage.
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Affiliation(s)
- Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093
| | | | - David R. Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, 021413
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138
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29
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Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 2017. [PMID: 29160308 DOI: 10.1038/nature24644.] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The spontaneous deamination of cytosine is a major source of transitions from C•G to T•A base pairs, which account for half of known pathogenic point mutations in humans. The ability to efficiently convert targeted A•T base pairs to G•C could therefore advance the study and treatment of genetic diseases. The deamination of adenine yields inosine, which is treated as guanine by polymerases, but no enzymes are known to deaminate adenine in DNA. Here we describe adenine base editors (ABEs) that mediate the conversion of A•T to G•C in genomic DNA. We evolved a transfer RNA adenosine deaminase to operate on DNA when fused to a catalytically impaired CRISPR-Cas9 mutant. Extensive directed evolution and protein engineering resulted in seventh-generation ABEs that convert targeted A•T base pairs efficiently to G•C (approximately 50% efficiency in human cells) with high product purity (typically at least 99.9%) and low rates of indels (typically no more than 0.1%). ABEs introduce point mutations more efficiently and cleanly, and with less off-target genome modification, than a current Cas9 nuclease-based method, and can install disease-correcting or disease-suppressing mutations in human cells. Together with previous base editors, ABEs enable the direct, programmable introduction of all four transition mutations without double-stranded DNA cleavage.
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Affiliation(s)
- Nicole M Gaudelli
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Alexis C Komor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Holly A Rees
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ahmed H Badran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David I Bryson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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30
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Abstract
The spontaneous deamination of cytosine is a major source of transitions from C•G to T•A base pairs, which account for half of known pathogenic point mutations in humans. The ability to efficiently convert targeted A•T base pairs to G•C could therefore advance the study and treatment of genetic diseases. The deamination of adenine yields inosine, which is treated as guanine by polymerases, but no enzymes are known to deaminate adenine in DNA. Here we describe adenine base editors (ABEs) that mediate the conversion of A•T to G•C in genomic DNA. We evolved a transfer RNA adenosine deaminase to operate on DNA when fused to a catalytically impaired CRISPR-Cas9 mutant. Extensive directed evolution and protein engineering resulted in seventh-generation ABEs that convert targeted A•T base pairs efficiently to G•C (approximately 50% efficiency in human cells) with high product purity (typically at least 99.9%) and low rates of indels (typically no more than 0.1%). ABEs introduce point mutations more efficiently and cleanly, and with less off-target genome modification, than a current Cas9 nuclease-based method, and can install disease-correcting or disease-suppressing mutations in human cells. Together with previous base editors, ABEs enable the direct, programmable introduction of all four transition mutations without double-stranded DNA cleavage.
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Affiliation(s)
- Nicole M Gaudelli
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Alexis C Komor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Holly A Rees
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ahmed H Badran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David I Bryson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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31
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Komor AC, Zhao KT, Packer MS, Gaudelli NM, Waterbury AL, Koblan LW, Kim YB, Badran AH, Liu DR. Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity. Sci Adv 2017; 3:eaao4774. [PMID: 28875174 PMCID: PMC5576876 DOI: 10.1126/sciadv.aao4774] [Citation(s) in RCA: 470] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/04/2017] [Indexed: 05/17/2023]
Abstract
We recently developed base editing, the programmable conversion of target C:G base pairs to T:A without inducing double-stranded DNA breaks (DSBs) or requiring homology-directed repair using engineered fusions of Cas9 variants and cytidine deaminases. Over the past year, the third-generation base editor (BE3) and related technologies have been successfully used by many researchers in a wide range of organisms. The product distribution of base editing-the frequency with which the target C:G is converted to mixtures of undesired by-products, along with the desired T:A product-varies in a target site-dependent manner. We characterize determinants of base editing outcomes in human cells and establish that the formation of undesired products is dependent on uracil N-glycosylase (UNG) and is more likely to occur at target sites containing only a single C within the base editing activity window. We engineered CDA1-BE3 and AID-BE3, which use cytidine deaminase homologs that increase base editing efficiency for some sequences. On the basis of these observations, we engineered fourth-generation base editors (BE4 and SaBE4) that increase the efficiency of C:G to T:A base editing by approximately 50%, while halving the frequency of undesired by-products compared to BE3. Fusing BE3, BE4, SaBE3, or SaBE4 to Gam, a bacteriophage Mu protein that binds DSBs greatly reduces indel formation during base editing, in most cases to below 1.5%, and further improves product purity. BE4, SaBE4, BE4-Gam, and SaBE4-Gam represent the state of the art in C:G-to-T:A base editing, and we recommend their use in future efforts.
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Affiliation(s)
- Alexis C. Komor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin T. Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S. Packer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicole M. Gaudelli
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amanda L. Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Luke W. Koblan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Y. Bill Kim
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmed H. Badran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R. Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Corresponding author.
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32
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Rees HA, Komor AC, Yeh WH, Caetano-Lopes J, Warman M, Edge ASB, Liu DR. Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery. Nat Commun 2017; 8:15790. [PMID: 28585549 PMCID: PMC5467206 DOI: 10.1038/ncomms15790] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/27/2017] [Indexed: 12/26/2022] Open
Abstract
We recently developed base editing, a genome-editing approach that enables the programmable conversion of one base pair into another without double-stranded DNA cleavage, excess stochastic insertions and deletions, or dependence on homology-directed repair. The application of base editing is limited by off-target activity and reliance on intracellular DNA delivery. Here we describe two advances that address these limitations. First, we greatly reduce off-target base editing by installing mutations into our third-generation base editor (BE3) to generate a high-fidelity base editor (HF-BE3). Next, we purify and deliver BE3 and HF-BE3 as ribonucleoprotein (RNP) complexes into mammalian cells, establishing DNA-free base editing. RNP delivery of BE3 confers higher specificity even than plasmid transfection of HF-BE3, while maintaining comparable on-target editing levels. Finally, we apply these advances to deliver BE3 RNPs into both zebrafish embryos and the inner ear of live mice to achieve specific, DNA-free base editing in vivo. Third-generation base editors consist of a catalytically disabled Cas9 fused to a cytidine deaminase and a base excision repair inhibitor, enabling efficient, precise editing of individual base pairs in DNA. Here the authors describe engineering and protein delivery of base editors to improve their DNA specificity and enable specific base editing in live animals.
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Affiliation(s)
- Holly A Rees
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Alexis C Komor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Wei-Hsi Yeh
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.,Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, USA.,Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joana Caetano-Lopes
- Orthopaedic Research Laboratories, Boston Children's Hospital, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Matthew Warman
- Orthopaedic Research Laboratories, Boston Children's Hospital, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Albert S B Edge
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, USA.,Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Otology and Laryngology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
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34
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Komor AC, Badran AH, Liu DR. CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes. Cell 2017; 168:20-36. [PMID: 27866654 PMCID: PMC5235943 DOI: 10.1016/j.cell.2016.10.044] [Citation(s) in RCA: 581] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/20/2016] [Accepted: 10/22/2016] [Indexed: 12/18/2022]
Abstract
The CRISPR-Cas9 RNA-guided DNA endonuclease has contributed to an explosion of advances in the life sciences that have grown from the ability to edit genomes within living cells. In this Review, we summarize CRISPR-based technologies that enable mammalian genome editing and their various applications. We describe recent developments that extend the generality, DNA specificity, product selectivity, and fundamental capabilities of natural CRISPR systems, and we highlight some of the remarkable advancements in basic research, biotechnology, and therapeutics science that these developments have facilitated.
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Affiliation(s)
- Alexis C Komor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Ahmed H Badran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
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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. [PMID: 27096365 DOI: 10.1038/nature17946.] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Current genome-editing technologies introduce double-stranded (ds) DNA breaks at a target locus as the first step to gene correction. 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 resulting from the cellular response to dsDNA breaks. 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, 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, and that use a Cas9 nickase targeting the non-edited strand, manipulate the cellular DNA repair response to favour 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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Affiliation(s)
- Alexis C Komor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Yongjoo B Kim
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
| | - John A Zuris
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
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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. [PMID: 27096365 PMCID: PMC4873371 DOI: 10.1038/nature17946] [Citation(s) in RCA: 2952] [Impact Index Per Article: 369.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/30/2016] [Indexed: 12/11/2022]
Abstract
Current genome-editing technologies introduce double-stranded (ds) DNA breaks at a target locus as the first step to gene correction. 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 resulting from the cellular response to dsDNA breaks. 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, 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, and that use a Cas9 nickase targeting the non-edited strand, manipulate the cellular DNA repair response to favour 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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Affiliation(s)
- Alexis C. Komor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138
| | - Yongjoo B. Kim
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138
| | - Michael S. Packer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138
| | - John A. Zuris
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138
| | - David R. Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138
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Komor AC, Barton JK. An unusual ligand coordination gives rise to a new family of rhodium metalloinsertors with improved selectivity and potency. J Am Chem Soc 2014; 136:14160-72. [PMID: 25254630 PMCID: PMC4195389 DOI: 10.1021/ja5072064] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Rhodium
metalloinsertors are octahedral complexes that bind DNA
mismatches with high affinity and specificity and exhibit unique cell-selective
cytotoxicity, targeting mismatch repair (MMR)-deficient cells over
MMR-proficient cells. Here we describe a new generation of metalloinsertors
with enhanced biological potency and selectivity, in which the complexes
show Rh–O coordination. In particular, it has been found that
both Δ- and Λ-[Rh(chrysi)(phen)(DPE)]2+ (where
chrysi =5,6 chrysenequinone diimmine, phen =1,10-phenanthroline, and
DPE = 1,1-di(pyridine-2-yl)ethan-1-ol) bind to DNA containing a single
CC mismatch with similar affinities and without racemization. This
is in direct contrast with previous metalloinsertors and suggests
a possible different binding disposition for these complexes in the
mismatch site. We ascribe this difference to the higher pKa of the coordinated immine of the chrysi ligand in these
complexes, so that the complexes must insert into the DNA helix with
the inserting ligand in a buckled orientation; spectroscopic studies
in the presence and absence of DNA along with the crystal structure
of the complex without DNA support this assignment. Remarkably, all
members of this new family of compounds have significantly increased
potency in a range of cellular assays; indeed, all are more potent
than cisplatin and N-methyl-N′-nitro-nitrosoguanidine
(MNNG, a common DNA-alkylating chemotherapeutic agent). Moreover,
the activities of the new metalloinsertors are coupled with high levels
of selective cytotoxicity for MMR-deficient versus proficient colorectal
cancer cells.
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Affiliation(s)
- Alexis C Komor
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena California 91125, United States
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Abstract
Classical chemotherapeutics, such as cisplatin and its analogues, have been highly successful in the clinic, yet improvements can certainly be made, given the significant side effects associated with the killing of healthy cells. Recent advances in the field of chemotherapy include the development of targeted anticancer agents, compounds that are directed towards a specific biomarker of cancer, with the hopes that such targeted therapies might have reduced side effects given their greater selectivity. Here we discuss several transition metal complexes that are tailored towards various biomolecules associated with cancer. Most notably, the success of rhodium metalloinsertors, which specifically bind to nucleic acid base mismatches in DNA, highlight the enormous potential of this exciting new strategy.
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Affiliation(s)
- Alyson G Weidmann
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Alexis C Komor
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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Bailis JM, Gordon ML, Gurgel JL, Komor AC, Barton JK, Kirsch IR. An inducible, isogenic cancer cell line system for targeting the state of mismatch repair deficiency. PLoS One 2013; 8:e78726. [PMID: 24205301 PMCID: PMC3812133 DOI: 10.1371/journal.pone.0078726] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 09/17/2013] [Indexed: 11/18/2022] Open
Abstract
The DNA mismatch repair system (MMR) maintains genome stability through recognition and repair of single-base mismatches and small insertion-deletion loops. Inactivation of the MMR pathway causes microsatellite instability and the accumulation of genomic mutations that can cause or contribute to cancer. In fact, 10-20% of certain solid and hematologic cancers are MMR-deficient. MMR-deficient cancers do not respond to some standard of care chemotherapeutics because of presumed increased tolerance of DNA damage, highlighting the need for novel therapeutic drugs. Toward this goal, we generated isogenic cancer cell lines for direct comparison of MMR-proficient and MMR-deficient cells. We engineered NCI-H23 lung adenocarcinoma cells to contain a doxycycline-inducible shRNA designed to suppress the expression of the mismatch repair gene MLH1, and compared single cell subclones that were uninduced (MLH1-proficient) versus induced for the MLH1 shRNA (MLH1-deficient). Here we present the characterization of these MMR-inducible cell lines and validate a novel class of rhodium metalloinsertor compounds that differentially inhibit the proliferation of MMR-deficient cancer cells.
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Affiliation(s)
- Julie M. Bailis
- Oncology Research, Amgen Inc., South San Francisco, California, United States of America
- * E-mail:
| | - Marcia L. Gordon
- Oncology Research, Amgen Inc., Seattle, Washington, United States of America
| | - Jesse L. Gurgel
- Oncology Research, Amgen Inc., Seattle, Washington, United States of America
| | - Alexis C. Komor
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Ilan R. Kirsch
- Oncology Research, Amgen Inc., Seattle, Washington, United States of America
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Abstract
DNA mismatch repair (MMR) is crucial to ensuring the fidelity of the genome. The inability to correct single base mismatches leads to elevated mutation rates and carcinogenesis. Using metalloinsertors-bulky metal complexes that bind with high specificity to mismatched sites in the DNA duplex-our laboratory has adopted a new chemotherapeutic strategy through the selective targeting of MMR-deficient cells, that is, those that have a propensity for cancerous transformation. Rhodium metalloinsertors display inhibitory effects selectively in cells that are deficient in the MMR machinery, consistent with this strategy. However, a highly sensitive structure-function relationship is emerging with the development of new complexes that highlights the importance of subcellular localization. We have found that small structural modifications, for example a hydroxyl versus a methyl functional group, can yield profound differences in biological function. Despite similar binding affinities and selectivities for DNA mismatches, only one metalloinsertor shows selective inhibition of cellular proliferation in MMR-deficient versus -proficient cells. Studies of whole-cell, nuclear and mitochondrial uptake reveal that this selectivity depends upon targeting DNA mismatches in the cell nucleus.
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Abstract
The discovery of cisplatin as a therapeutic agent stimulated a new era in the application of transition metal complexes for therapeutic design. Here we describe recent results on a variety of transition metal complexes targeted to DNA to illustrate many of the issues involved in new therapeutic design. We describe first structural studies of complexes bound covalently and non-covalently to DNA to identify potential lesions within the cell. We then review the biological fates of these complexes, illustrating the key elements in obtaining potent activity, the importance of uptake and subcellular localization of the complexes, as well as the techniques used to delineate these characteristics. Genomic DNA provides a challenging but valuable target for new transition metal-based therapeutics.
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Affiliation(s)
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA. Fax: 626-577-4976; Tel: 626-395-6075;
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Komor AC, Schneider CJ, Weidmann AG, Barton JK. Correction to Cell-Selective Biological Activity of Rhodium Metalloinsertors Correlates with Subcellular Localization. J Am Chem Soc 2013. [DOI: 10.1021/ja400471q] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Komor AC, Schneider CJ, Weidmann AG, Barton JK. Cell-selective biological activity of rhodium metalloinsertors correlates with subcellular localization. J Am Chem Soc 2012; 134:19223-33. [PMID: 23137296 PMCID: PMC3740518 DOI: 10.1021/ja3090687] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Deficiencies in the mismatch repair (MMR) pathway are associated with several types of cancers, as well as resistance to commonly used chemotherapeutics. Rhodium metalloinsertors have been found to bind DNA mismatches with high affinity and specificity in vitro, and also exhibit cell-selective cytotoxicity, targeting MMR-deficient cells over MMR-proficient cells. Ten distinct metalloinsertors with varying lipophilicities have been synthesized and their mismatch binding affinities and biological activities determined. Although DNA photocleavage experiments demonstrate that their binding affinities are quite similar, their cell-selective antiproliferative and cytotoxic activities vary significantly. Inductively coupled plasma mass spectrometry (ICP-MS) experiments have uncovered a relationship between the subcellular distribution of these metalloinsertors and their biological activities. Specifically, we find that all of our metalloinsertors localize in the nucleus at sufficient concentrations for binding to DNA mismatches. However, the metalloinsertors with high rhodium localization in the mitochondria show toxicity that is not selective for MMR-deficient cells, whereas metalloinsertors with less mitochondrial rhodium show activity that is highly selective for MMR-deficient versus proficient cells. This work supports the notion that specific targeting of the metalloinsertors to nuclear DNA gives rise to their cell-selective cytotoxic and antiproliferative activities. The selectivity in cellular targeting depends upon binding to mismatches in genomic DNA.
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Affiliation(s)
- Alexis C. Komor
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Curtis J. Schneider
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Alyson G. Weidmann
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
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Abstract
Mismatches in DNA occur naturally during replication and as a result of endogenous DNA damaging agents, but the mismatch repair (MMR) pathway acts to correct mismatches before subsequent rounds of replication. Rhodium metalloinsertors bind to DNA mismatches with high affinity and specificity and represent a promising strategy to target mismatches in cells. Here we examine the biological fate of rhodium metalloinsertors bearing dipyridylamine ancillary ligands in cells deficient in MMR versus those that are MMR-proficient. These complexes are shown to exhibit accelerated cellular uptake which permits the observation of various cellular responses, including disruption of the cell cycle, monitored by flow cytometry assays, and induction of necrosis, monitored by dye exclusion and caspase inhibition assays, that occur preferentially in the MMR-deficient cell line. These cellular responses provide insight into the mechanisms underlying the selective activity of this novel class of targeted anticancer agents.
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Affiliation(s)
- Russell J Ernst
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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Soo HS, Komor AC, Iavarone AT, Chang CJ. A Hydrogen-Bond Facilitated Cycle for Oxygen Reduction by an Acid- and Base-Compatible Iron Platform. Inorg Chem 2009; 48:10024-35. [DOI: 10.1021/ic9006668] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Han Sen Soo
- Department of Chemistry
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | | | | | - Christopher J. Chang
- Department of Chemistry
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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