1
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Li B, Zhu X, Zhao D, Li Y, Yang Y, Li J, Bi C, Zhang X. igRNA Prediction and Selection AI Models (igRNA-PS) for Bystander-less ABE Base Editing. J Mol Biol 2024; 436:168714. [PMID: 39029887 DOI: 10.1016/j.jmb.2024.168714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/28/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
Abstract
CRISPR derived base editing techniques tend to edit multiple bases in the targeted region, which impedes precise reversion of disease-associated single nucleotide variations (SNVs). We designed an imperfect gRNA (igRNA) editing strategy to achieve bystander-less single-base editing. To predict the performance and provide ready-to-use igRNAs, we employed a high-throughput method to edit 5000 loci, each with approximate 19 systematically designed ABE igRNAs. Through deep learning of the relationship of editing efficiency, original gRNA sequence and igRNA sequence, AI models were constructed and tested, designated igRNA Prediction and Selection AI models (igRNA-PS). The models have three functions, First, they can identify the major editing site from the bystanders on a gRNA protospacer with a near 90% accuracy. second, a modified single-base editing efficiency (SBE), considering both single-base editing efficiency and product purity, can be predicted for any given igRNAs. Third, for an editing locus, a set of 64 igRNAs derived from a gRNA can be generated, evaluated through igRNA-PS to select for the best performer, and provided to the user. In this work, we overcome one of the most significant obstacles of base editors, and provide a convenient and efficient approach for single-base bystander-less ABE base editing.
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Affiliation(s)
- Bo Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300000, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300000, China
| | - Xiagu Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300000, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300000, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300222, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300000, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300000, China
| | - Yaqiu Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300000, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300000, China
| | - Yuanzhao Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300000, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300000, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300222, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300000, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300000, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300000, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300000, China.
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2
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Yang X, Zhu P, Gui J. Advancements of CRISPR-Mediated Base Editing in Crops and Potential Applications in Populus. Int J Mol Sci 2024; 25:8314. [PMID: 39125884 PMCID: PMC11313136 DOI: 10.3390/ijms25158314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 08/12/2024] Open
Abstract
Base editing represents a cutting-edge genome editing technique that utilizes the CRISPR system to guide base deaminases with high precision to specific genomic sites, facilitating the targeted alteration of individual nucleotides. Unlike traditional gene editing approaches, base editing does not require DNA double-strand breaks or donor templates. It functions independently of the cellular DNA repair machinery, offering significant advantages in terms of both efficiency and accuracy. In this review, we summarize the core design principles of various DNA base editors, their distinctive editing characteristics, and tactics to refine their efficacy. We also summarize their applications in crop genetic improvement and explore their potential contributions to forest genetic engineering.
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Affiliation(s)
| | | | - Jinshan Gui
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (X.Y.); (P.Z.)
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3
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Prasad K, Devaraju N, George A, Ravi NS, Paul J, Mahalingam G, Rajendiran V, Panigrahi L, Venkatesan V, Lakhotiya K, Periyasami Y, Pai AA, Nakamura Y, Kurita R, Balasubramanian P, Thangavel S, Velayudhan SR, Newby GA, Marepally S, Srivastava A, Mohankumar KM. Precise correction of a spectrum of β-thalassemia mutations in coding and non-coding regions by base editors. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102205. [PMID: 38817682 PMCID: PMC11137594 DOI: 10.1016/j.omtn.2024.102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 04/26/2024] [Indexed: 06/01/2024]
Abstract
β-thalassemia/HbE results from mutations in the β-globin locus that impede the production of functional adult hemoglobin. Base editors (BEs) could facilitate the correction of the point mutations with minimal or no indel creation, but its efficiency and bystander editing for the correction of β-thalassemia mutations in coding and non-coding regions remains unexplored. Here, we screened BE variants in HUDEP-2 cells for their ability to correct a spectrum of β-thalassemia mutations that were integrated into the genome as fragments of HBB. The identified targets were introduced into their endogenous genomic location using BEs and Cas9/homology-directed repair (HDR) to create cellular models with β-thalassemia/HbE. These β-thalassemia/HbE models were then used to assess the efficiency of correction in the native locus and functional β-globin restoration. Most bystander edits produced near target sites did not interfere with adult hemoglobin expression and are not predicted to be pathogenic. Further, the effectiveness of BE was validated for the correction of the pathogenic HbE variant in severe β0/βE-thalassaemia patient cells. Overall, our study establishes a novel platform to screen and select optimal BE tools for therapeutic genome editing by demonstrating the precise, efficient, and scarless correction of pathogenic point mutations spanning multiple regions of HBB including the promoter, intron, and exons.
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Affiliation(s)
- Kirti Prasad
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
| | - Nivedhitha Devaraju
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
| | - Anila George
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Nithin Sam Ravi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Joshua Paul
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
| | - Gokulnath Mahalingam
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Vignesh Rajendiran
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Lokesh Panigrahi
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
| | - Vigneshwaran Venkatesan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
| | - Kartik Lakhotiya
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington Street, Boston MA 02111, USA
| | - Yogapriya Periyasami
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Aswin Anand Pai
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
- Department of Haematology, Christian Medical College & Hospital, Vellore 632 004, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 3050074, Japan
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Poonkuzhali Balasubramanian
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
- Department of Haematology, Christian Medical College & Hospital, Vellore 632 004, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Shaji R. Velayudhan
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Department of Haematology, Christian Medical College & Hospital, Vellore 632 004, India
| | - Gregory A. Newby
- Departments of Genetic Medicine and Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Srujan Marepally
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
| | - Alok Srivastava
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Department of Haematology, Christian Medical College & Hospital, Vellore 632 004, India
| | - Kumarasamypet M. Mohankumar
- Centre for Stem Cell Research (a Unit of inStem, Bengaluru), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu 632002, India
- Manipal Academy of Higher Education, Karnataka 576104, India
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4
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Bamidele N, Zhang H, Dong X, Cheng H, Gaston N, Feinzig H, Cao H, Kelly K, Watts JK, Xie J, Gao G, Sontheimer EJ. Domain-inlaid Nme2Cas9 adenine base editors with improved activity and targeting scope. Nat Commun 2024; 15:1458. [PMID: 38368418 PMCID: PMC10874451 DOI: 10.1038/s41467-024-45763-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 02/04/2024] [Indexed: 02/19/2024] Open
Abstract
Nme2Cas9 has been established as a genome editing platform with compact size, high accuracy, and broad targeting range, including single-AAV-deliverable adenine base editors. Here, we engineer Nme2Cas9 to further increase the activity and targeting scope of compact Nme2Cas9 base editors. We first use domain insertion to position the deaminase domain nearer the displaced DNA strand in the target-bound complex. These domain-inlaid Nme2Cas9 variants exhibit shifted editing windows and increased activity in comparison to the N-terminally fused Nme2-ABE. We next expand the editing scope by swapping the Nme2Cas9 PAM-interacting domain with that of SmuCas9, which we had previously defined as recognizing a single-cytidine PAM. We then use these enhancements to introduce therapeutically relevant edits in a variety of cell types. Finally, we validate domain-inlaid Nme2-ABEs for single-AAV delivery in vivo.
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Affiliation(s)
- Nathan Bamidele
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Han Zhang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | | | - Haoyang Cheng
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Nicholas Gaston
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Hailey Feinzig
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Hanbing Cao
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Massachusetts, MA, 01605, USA.
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5
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Chen X, Zhao D, Hou X, Li J, Pu S, Fei J, Li S, Zhou Z, Bi C, Zhang X. Genomic allele-specific base editing with imperfect gRNA. J Genet Genomics 2023; 50:799-802. [PMID: 37269979 DOI: 10.1016/j.jgg.2023.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/05/2023]
Affiliation(s)
- Xuxu Chen
- School of Life Sciences, Guangxi Normal University, Guilin, Guangxi 541006, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xueting Hou
- School of Life Sciences, Guangxi Normal University, Guilin, Guangxi 541006, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China; Hubei College of Chinese Medicine, JingZhou, Hubei 434020, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Shiming Pu
- School of Life Sciences, Guangxi Normal University, Guilin, Guangxi 541006, China; Guangxi Universities Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, Guangxi 541006, China
| | - Jidong Fei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Zuping Zhou
- School of Life Sciences, Guangxi Normal University, Guilin, Guangxi 541006, China; Guangxi Universities Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, Guangxi 541006, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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6
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Mantena S, Pillai PP, Petros BA, Welch NL, Myhrvold C, Sabeti PC, Metsky HC. Model-directed generation of CRISPR-Cas13a guide RNAs designs artificial sequences that improve nucleic acid detection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.557569. [PMID: 37786711 PMCID: PMC10541601 DOI: 10.1101/2023.09.20.557569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Generating maximally-fit biological sequences has the potential to transform CRISPR guide RNA design as it has other areas of biomedicine. Here, we introduce model-directed exploration algorithms (MEAs) for designing maximally-fit, artificial CRISPR-Cas13a guides-with multiple mismatches to any natural sequence-that are tailored for desired properties around nucleic acid diagnostics. We find that MEA-designed guides offer more sensitive detection of diverse pathogens and discrimination of pathogen variants compared to guides derived directly from natural sequences, and illuminate interpretable design principles that broaden Cas13a targeting.
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Affiliation(s)
- Sreekar Mantena
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | | | - Brittany A. Petros
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/Massachusetts Institute of Technology, MD-PhD Program, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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7
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Shi Y, Zhao Y, Lu L, Gao Q, Yu D, Sun M. CRISPR/Cas9: implication for modeling and therapy of amyotrophic lateral sclerosis. Front Neurosci 2023; 17:1223777. [PMID: 37483353 PMCID: PMC10359984 DOI: 10.3389/fnins.2023.1223777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a deadly neurological disease with a complicated and variable pathophysiology yet to be fully understood. There is currently no effective treatment available to either slow or terminate it. However, recent advances in ALS genomics have linked genes to phenotypes, encouraging the creation of novel therapeutic approaches and giving researchers more tools to create efficient animal models. Genetically engineered rodent models replicating ALS disease pathology have a high predictive value for translational research. This review addresses the history of the evolution of gene editing tools, the most recent ALS disease models, and the application of CRISPR/Cas9 against ALS disease.
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Affiliation(s)
- Yajun Shi
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yan Zhao
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Likui Lu
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Qinqin Gao
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Dongyi Yu
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
| | - Miao Sun
- Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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8
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Lue NZ, Liau BB. Base editor screens for in situ mutational scanning at scale. Mol Cell 2023; 83:2167-2187. [PMID: 37390819 PMCID: PMC10330937 DOI: 10.1016/j.molcel.2023.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 07/02/2023]
Abstract
A fundamental challenge in biology is understanding the molecular details of protein function. How mutations alter protein activity, regulation, and response to drugs is of critical importance to human health. Recent years have seen the emergence of pooled base editor screens for in situ mutational scanning: the interrogation of protein sequence-function relationships by directly perturbing endogenous proteins in live cells. These studies have revealed the effects of disease-associated mutations, discovered novel drug resistance mechanisms, and generated biochemical insights into protein function. Here, we discuss how this "base editor scanning" approach has been applied to diverse biological questions, compare it with alternative techniques, and describe the emerging challenges that must be addressed to maximize its utility. Given its broad applicability toward profiling mutations across the proteome, base editor scanning promises to revolutionize the investigation of proteins in their native contexts.
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Affiliation(s)
- Nicholas Z Lue
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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9
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Bamidele N, Zhang H, Dong X, Gaston N, Cheng H, Kelly K, Watts JK, Xie J, Gao G, Sontheimer EJ. Engineering Nme2Cas9 Adenine Base Editors with Improved Activity and Targeting Scope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.14.536905. [PMID: 37131611 PMCID: PMC10153126 DOI: 10.1101/2023.04.14.536905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Nme2Cas9 has been established as a genome editing platform with compact size, high accuracy, and broad targeting range, including single-AAV-deliverable adenine base editors. Here, we have engineered Nme2Cas9 to further increase the activity and targeting scope of compact Nme2Cas9 base editors. We first used domain insertion to position the deaminase domain nearer the displaced DNA strand in the target-bound complex. These domain-inlaid Nme2Cas9 variants exhibited shifted editing windows and increased activity in comparison to the N-terminally fused Nme2-ABE. We next expanded the editing scope by swapping the Nme2Cas9 PAM-interacting domain with that of SmuCas9, which we had previously defined as recognizing a single-cytidine PAM. We used these enhancements to correct two common MECP2 mutations associated with Rett syndrome with little or no bystander editing. Finally, we validated domain-inlaid Nme2-ABEs for single-AAV delivery in vivo.
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Affiliation(s)
- Nathan Bamidele
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Han Zhang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | | | - Nicholas Gaston
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Haoyang Cheng
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Jonathan K. Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Viral Vector Core, University of Massachusetts Chan Medical, School, Worcester, MA, 01605, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
| | - Erik J. Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, Massachusetts, 01605, USA
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10
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Li B, Zhao D, Li Y, Yang Y, Zhu X, Li J, Bi C, Zhang X. Obtaining the best igRNAs for bystander-less correction of all ABE-reversible pathogenic SNVs using high-throughput screening. Mol Ther 2023; 31:1167-1176. [PMID: 36733252 PMCID: PMC10124137 DOI: 10.1016/j.ymthe.2023.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/07/2022] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Imperfect -gRNA (igRNA) provides a simple strategy for single-base editing of a base editor. However, a significant number of igRNAs need to be generated and tested for each target locus to achieve efficient single-base reversion of pathogenic single nucleotide variations (SNVs), which hinders the direct application of this technology. To provide ready-to-use igRNAs for single-base and bystander-less correction of all the adenine base editor (ABE)-reversible pathogenic SNVs, we employed a high-throughput method to edit all 5,253 known ABE-reversible pathogenic SNVs, each with multiple systematically designed igRNAs, and two libraries of 96,000 igRNAs were tested. A total of 1,988 SNV loci could be single-base reversed by igRNA with a >30% efficiency. Among these 1,988 loci, 378 SNV loci exhibited an efficiency of more than 90%. At the same time, the bystander editing efficiency of 76.62% of the SNV loci was reduced to 0%, while remaining below 1% for another 18.93% of the loci. These ready-to-use igRNAs provided the best solutions for a substantial portion of the 4,657 pathogenic/likely pathogenic SNVs. In this work, we overcame one of the most significant obstacles of base editors and provide a ready-to-use platform for the genetic treatment of diseases caused by ABE-reversible SNVs.
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Affiliation(s)
- Bo Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yaqiu Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yuanzhao Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300222, China
| | - Xiagu Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300222, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.
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11
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Abstract
The advent of clustered regularly interspaced short palindromic repeat (CRISPR) genome editing, coupled with advances in computing and imaging capabilities, has initiated a new era in which genetic diseases and individual disease susceptibilities are both predictable and actionable. Likewise, genes responsible for plant traits can be identified and altered quickly, transforming the pace of agricultural research and plant breeding. In this Review, we discuss the current state of CRISPR-mediated genetic manipulation in human cells, animals, and plants along with relevant successes and challenges and present a roadmap for the future of this technology.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.,Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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12
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Chen R, Cao Y, Liu Y, Zhao D, Li J, Cheng Z, Bi C, Zhang X. Enhancement of a prime editing system via optimal recruitment of the pioneer transcription factor P65. Nat Commun 2023; 14:257. [PMID: 36650182 PMCID: PMC9845348 DOI: 10.1038/s41467-023-35919-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Prime editing is a versatile gene editing tool that enables precise sequence changes of all types in the genome, but its application is rather limited by the editing efficiency. Here, we first apply the Suntag system to recruit the transcription factor P65 and enhance the desired editing outcomes in the prime editing system. Next, MS2 hairpins are used to recruit MS2-fused P65 and confirmed that the recruitment of the P65 protein could effectively improve the prime editing efficiency in both the PE3 and PE5 systems. Moreover, this suggests the increased editing efficiency is most likely associated with the induction of chromatin accessibility change by P65. In conclusion, we apply different systems to recruit P65 and enhance the prime editing efficiency of various PE systems. Furthermore, our work provides a variety of methods to work as protein scaffolds for screening target factors and thus supports further optimization of prime editing systems.
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Affiliation(s)
- Ronghao Chen
- College of Life Science, Nankai University, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yu Cao
- College of Life Science, Nankai University, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yajing Liu
- College of Life Science, Nankai University, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin, China
| | - Zhihui Cheng
- College of Life Science, Nankai University, Tianjin, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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13
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Becklin KL, Draper GM, Madden RA, Kluesner MG, Koga T, Huang M, Weiss WA, Spector LG, Largaespada DA, Moriarity BS, Webber BR. Developing Bottom-Up Induced Pluripotent Stem Cell Derived Solid Tumor Models Using Precision Genome Editing Technologies. CRISPR J 2022; 5:517-535. [PMID: 35972367 PMCID: PMC9529369 DOI: 10.1089/crispr.2022.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in genome and tissue engineering have spurred significant progress and opportunity for innovation in cancer modeling. Human induced pluripotent stem cells (iPSCs) are an established and powerful tool to study cellular processes in the context of disease-specific genetic backgrounds; however, their application to cancer has been limited by the resistance of many transformed cells to undergo successful reprogramming. Here, we review the status of human iPSC modeling of solid tumors in the context of genetic engineering, including how base and prime editing can be incorporated into "bottom-up" cancer modeling, a term we coined for iPSC-based cancer models using genetic engineering to induce transformation. This approach circumvents the need to reprogram cancer cells while allowing for dissection of the genetic mechanisms underlying transformation, progression, and metastasis with a high degree of precision and control. We also discuss the strengths and limitations of respective engineering approaches and outline experimental considerations for establishing future models.
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Affiliation(s)
- Kelsie L. Becklin
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Garrett M. Draper
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Rebecca A. Madden
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Mitchell G. Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Tomoyuki Koga
- Ludwig Cancer Research San Diego Branch, La Jolla, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Miller Huang
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - William A. Weiss
- Departments of Neurology, Pediatrics, Neurosurgery, Brain Tumor Research Center, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; and Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Departments of Pediatrics, Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Logan G. Spector
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - David A. Largaespada
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Branden S. Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Beau R. Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
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