1
|
Jin YY, Zhang P, Liu LL, Zhao X, Hu XQ, Liu SZ, Li ZK, Liu Q, Wang JQ, Hao DL, Zhang ZQ, Chen HZ, Liu DP. Enhancing homology-directed repair efficiency with HDR-boosting modular ssDNA donor. Nat Commun 2024; 15:6843. [PMID: 39122671 PMCID: PMC11315919 DOI: 10.1038/s41467-024-50788-x] [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: 10/02/2023] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Despite the potential of small molecules and recombinant proteins to enhance the efficiency of homology-directed repair (HDR), single-stranded DNA (ssDNA) donors, as currently designed and chemically modified, remain suboptimal for precise gene editing. Here, we screen the biased ssDNA binding sequences of DNA repair-related proteins and engineer RAD51-preferred sequences into HDR-boosting modules for ssDNA donors. Donors with these modules exhibit an augmented affinity for RAD51, thereby enhancing HDR efficiency across various genomic loci and cell types when cooperated with Cas9, nCas9, and Cas12a. By combining with an inhibitor of non-homologous end joining (NHEJ) or the HDRobust strategy, these modular ssDNA donors achieve up to 90.03% (median 74.81%) HDR efficiency. The HDR-boosting modules targeting an endogenous protein enable a chemical modification-free strategy to improve the efficacy of ssDNA donors for precise gene editing.
Collapse
Affiliation(s)
- Ying-Ying Jin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Peng Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Le-Le Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiang Zhao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiao-Qing Hu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Si-Zhe Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Ze-Kun Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Qian Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Jian-Qiao Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - De-Long Hao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Zhu-Qin Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Hou-Zao Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
- Medical Epigenetics Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China.
| | - De-Pei Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
- Medical Epigenetics Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China.
- Haihe Laboratory of Cell Ecosystem, Tianjin, 300301, China.
| |
Collapse
|
2
|
Peng D, Vangipuram M, Wong J, Leonetti MD. protoSpaceJAM: an open-source, customizable and web-accessible design platform for CRISPR/Cas insertional knock-in. Nucleic Acids Res 2024:gkae553. [PMID: 38922690 DOI: 10.1093/nar/gkae553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
CRISPR/Cas-mediated knock-in of DNA sequences enables precise genome engineering for research and therapeutic applications. However, designing effective guide RNAs (gRNAs) and homology-directed repair (HDR) donors remains a bottleneck. Here, we present protoSpaceJAM, an open-source algorithm to automate and optimize gRNA and HDR donor design for CRISPR/Cas insertional knock-in experiments, currently supporting SpCas9, SpCas9-VQR and enAsCas12a Cas enzymes. protoSpaceJAM utilizes biological rules to rank gRNAs based on specificity, distance to insertion site, and position relative to regulatory regions. protoSpaceJAM can introduce 'recoding' mutations (silent mutations and mutations in non-coding sequences) in HDR donors to prevent re-cutting and increase knock-in efficiency. Users can customize parameters and design double-stranded or single-stranded donors. We validated protoSpaceJAM's design rules by demonstrating increased knock-in efficiency with recoding mutations and optimal strand selection for single-stranded donors. An additional module enables the design of genotyping primers for deep sequencing of edited alleles. Overall, protoSpaceJAM streamlines and optimizes CRISPR knock-in experimental design in a flexible and modular manner to benefit diverse research and therapeutic applications. protoSpaceJAM is available open-source as an interactive web tool at protospacejam.czbiohub.org or as a standalone Python package at github.com/czbiohub-sf/protoSpaceJAM.
Collapse
Affiliation(s)
- Duo Peng
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Joan Wong
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | |
Collapse
|
3
|
Zhang Z, Zhang S, Wong HT, Li D, Feng B. Targeted Gene Insertion: The Cutting Edge of CRISPR Drug Development with Hemophilia as a Highlight. BioDrugs 2024; 38:369-385. [PMID: 38489061 PMCID: PMC11055778 DOI: 10.1007/s40259-024-00654-5] [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] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
The remarkable advance in gene editing technology presents unparalleled opportunities for transforming medicine and finding cures for hereditary diseases. Human trials of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease (Cas9)-based therapeutics have demonstrated promising results in disrupting or deleting target sequences to treat specific diseases. However, the potential of targeted gene insertion approaches, which offer distinct advantages over disruption/deletion methods, remains largely unexplored in human trials due to intricate technical obstacles and safety concerns. This paper reviews the recent advances in preclinical studies demonstrating in vivo targeted gene insertion for therapeutic benefits, targeting somatic solid tissues through systemic delivery. With a specific emphasis on hemophilia as a prominent disease model, we highlight advancements in insertion strategies, including considerations of DNA repair pathways, targeting site selection, and donor design. Furthermore, we discuss the complex challenges and recent breakthroughs that offer valuable insights for progressing towards clinical trials.
Collapse
Affiliation(s)
- Zhenjie Zhang
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
| | - Siqi Zhang
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China
| | - Hoi Ting Wong
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Bo Feng
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong SAR, China.
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| |
Collapse
|
4
|
Han W, Li Z, Guo Y, He K, Li W, Xu C, Ge L, He M, Yin X, Zhou J, Li C, Yao D, Bao J, Liang H. Efficient precise integration of large DNA sequences with 3'-overhang dsDNA donors using CRISPR/Cas9. Proc Natl Acad Sci U S A 2023; 120:e2221127120. [PMID: 37216515 PMCID: PMC10235934 DOI: 10.1073/pnas.2221127120] [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: 12/14/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
CRISPR/Cas9 genome-editing tools have tremendously boosted our capability of manipulating the eukaryotic genomes in biomedical research and innovative biotechnologies. However, the current approaches that allow precise integration of gene-sized large DNA fragments generally suffer from low efficiency and high cost. Herein, we developed a versatile and efficient approach, termed LOCK (Long dsDNA with 3'-Overhangs mediated CRISPR Knock-in), by utilizing specially designed 3'-overhang double-stranded DNA (odsDNA) donors harboring 50-nt homology arm. The length of the 3'-overhangs of odsDNA is specified by the five consecutive phosphorothioate modifications. Compared with existing methods, LOCK allows highly efficient targeted insertion of kilobase-sized DNA fragments into the mammalian genomes with low cost and low off-target effects, yielding >fivefold higher knock-in frequencies than conventional homologous recombination-based approaches. This newly designed LOCK approach based on homology-directed repair is a powerful tool suitable for gene-sized fragment integration that is urgently needed for genetic engineering, gene therapies, and synthetic biology.
Collapse
Affiliation(s)
- Wenjie Han
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Zhigang Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Yijun Guo
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Kaining He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Wenqing Li
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Caoling Xu
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Lishuang Ge
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Miao He
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Xue Yin
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Junxiang Zhou
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Chengxu Li
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Dongbao Yao
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| | - Jianqiang Bao
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- The First Affiliated Hospital of University of Science and Technology of China, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China230001Hefei, Anhui, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China230026Hefei, Anhui, China
- School of Chemistry and Materials Science, Department of Polymer Science and Engineering, Chinese Academy of Sciences Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China230026Hefei, Anhui, China
| |
Collapse
|
5
|
Bracamonte AG. Current Advances in Nanotechnology for the Next Generation of Sequencing (NGS). BIOSENSORS 2023; 13:260. [PMID: 36832027 PMCID: PMC9954403 DOI: 10.3390/bios13020260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
This communication aims at discussing strategies based on developments from nanotechnology focused on the next generation of sequencing (NGS). In this regard, it should be noted that even in the advanced current situation of many techniques and methods accompanied with developments of technology, there are still existing challenges and needs focused on real samples and low concentrations of genomic materials. The approaches discussed/described adopt spectroscopical techniques and new optical setups. PCR bases are introduced to understand the role of non-covalent interactions by discussing about Nobel prizes related to genomic material detection. The review also discusses colorimetric methods, polymeric transducers, fluorescence detection methods, enhanced plasmonic techniques such as metal-enhanced fluorescence (MEF), semiconductors, and developments in metamaterials. In addition, nano-optics, challenges linked to signal transductions, and how the limitations reported in each technique could be overcome are considered in real samples. Accordingly, this study shows developments where optical active nanoplatforms generate signal detection and transduction with enhanced performances and, in many cases, enhanced signaling from single double-stranded deoxyribonucleic acid (DNA) interactions. Future perspectives on miniaturized instrumentation, chips, and devices aimed at detecting genomic material are analyzed. However, the main concept in this report derives from gained insights into nanochemistry and nano-optics. Such concepts could be incorporated into other higher-sized substrates and experimental and optical setups.
Collapse
Affiliation(s)
- Angel Guillermo Bracamonte
- Instituto de Investigaciones en Físicoquímica de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5000 Córdoba, Argentina; or
- Departement de Chimie et Centre d’Optique, Photonique et Laser (COPL), Université Laval, Québec, QC G1V 0A6, Canada
| |
Collapse
|
6
|
Iyer S, Mir A, Vega-Badillo J, Roscoe BP, Ibraheim R, Zhu LJ, Lee J, Liu P, Luk K, Mintzer E, Guo D, Soares de Brito J, Emerson CP, Zamore PD, Sontheimer EJ, Wolfe SA. Efficient Homology-Directed Repair with Circular Single-Stranded DNA Donors. CRISPR J 2022; 5:685-701. [PMID: 36070530 PMCID: PMC9595650 DOI: 10.1089/crispr.2022.0058] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
While genome editing has been revolutionized by the advent of CRISPR-based nucleases, difficulties in achieving efficient, nuclease-mediated, homology-directed repair (HDR) still limit many applications. Commonly used DNA donors such as plasmids suffer from low HDR efficiencies in many cell types, as well as integration at unintended sites. In contrast, single-stranded DNA (ssDNA) donors can produce efficient HDR with minimal off-target integration. In this study, we describe the use of ssDNA phage to efficiently and inexpensively produce long circular ssDNA (cssDNA) donors. These cssDNA donors serve as efficient HDR templates when used with Cas9 or Cas12a, with integration frequencies superior to linear ssDNA (lssDNA) donors. To evaluate the relative efficiencies of imprecise and precise repair for a suite of different Cas9 or Cas12a nucleases, we have developed a modified traffic light reporter (TLR) system (TLR-multi-Cas variant 1 [MCV1]) that permits side-by-side comparisons of different nuclease systems. We used this system to assess editing and HDR efficiencies of different nuclease platforms with distinct DNA donor types. We then extended the analysis of DNA donor types to evaluate efficiencies of fluorescent tag knockins at endogenous sites in HEK293T and K562 cells. Our results show that cssDNA templates produce efficient and robust insertion of reporter tags. Targeting efficiency is high, allowing production of biallelic integrants using cssDNA donors. cssDNA donors also outcompete lssDNA donors in template-driven repair at the target site. These data demonstrate that circular donors provide an efficient, cost-effective method to achieve knockins in mammalian cell lines.
Collapse
Affiliation(s)
- Sukanya Iyer
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA
| | - Aamir Mir
- RNA Therapeutics Institute; Worcester, Massachusetts, USA
| | | | - Benjamin P. Roscoe
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA
| | - Raed Ibraheim
- RNA Therapeutics Institute; Worcester, Massachusetts, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA.,Program in Bioinformatics and Integrative Biology; Worcester, Massachusetts, USA
| | - Jooyoung Lee
- RNA Therapeutics Institute; Worcester, Massachusetts, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA
| | - Esther Mintzer
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA
| | - Dongsheng Guo
- Wellstone Program, Department of Neurology; Worcester, Massachusetts, USA
| | | | - Charles P. Emerson
- Wellstone Program, Department of Neurology; Worcester, Massachusetts, USA
| | - Phillip D. Zamore
- RNA Therapeutics Institute; Worcester, Massachusetts, USA.,Howard Hughes Medical Institute; Worcester, Massachusetts, USA
| | - Erik J. Sontheimer
- RNA Therapeutics Institute; Worcester, Massachusetts, USA.,Program in Molecular Medicine; and Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Disease Research; University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.,Address correspondence to: Erik J. Sontheimer, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605-2324, USA,
| | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Disease Research; University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.,Address correspondence to: Scot A. Wolfe, Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, L.R.B. 619, 364 Plantation Street, Worcester, MA 01605, USA,
| |
Collapse
|
7
|
Umbach A, Maule G, Kheir E, Cutarelli A, Foglia M, Guarrera L, Fava LL, Conti L, Garattini E, Terao M, Cereseto A. Generation of corrected hiPSC clones from a Cornelia de Lange Syndrome (CdLS) patient through CRISPR-Cas-based technology. Stem Cell Res Ther 2022; 13:440. [PMID: 36056433 PMCID: PMC9438151 DOI: 10.1186/s13287-022-03135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022] Open
Abstract
Background Cornelia de Lange syndrome (CdLS) is a rare multisystem genetic disorder which is caused by genetic defects involving the Nipped-B-like protein (NIPBL) gene in the majority of clinical cases (60–70%). Currently, there are no specific cures available for CdLS and clinical management is needed for life. Disease models are highly needed to find a cure. Among therapeutic possibilities are genome editing strategies based on CRISPR-Cas technology. Methods A comparative analysis was performed to test the most recent CRISPR-Cas technologies comprising base- and prime-editors which introduce modifications without DNA cleavages and compared with sequence substitution approaches through homology directed repair (HDR) induced by Cas9 nuclease activity. The HDR method that was found more efficient was applied to repair a CdLS-causing mutation in the NIPBL gene. Human-induced pluripotent stem cells (hiPSCs) derived from a CdLS patient carrying the c.5483G > A mutation in the NIPBL were modified through HDR to generate isogenic corrected clones. Results This study reports an efficient method to repair the NIPBL gene through HDR mediated by CRISPR-Cas and induced with a compound (NU7441) inhibiting non-homologous end joining (NHEJ) repair. This sequence repair method allowed the generation of isogenic wild-type hiPSCs clones with regular karyotype and preserved pluripotency. Conclusions CdLS cellular models were generated which will facilitate the investigation of the disease molecular determinants and the identification of therapeutic targets. In particular, the hiPSC-based cellular models offer the paramount advantage to study the tissue differentiation stages which are altered in the CdLS clinical development. Importantly, the hiPSCs that were generated are isogenic thus providing the most controlled experimental set up between wild-type and mutated conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-03135-0.
Collapse
Affiliation(s)
- Alessandro Umbach
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Giulia Maule
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Eyemen Kheir
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | | | - Marika Foglia
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Luca Guarrera
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Luca L Fava
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Luciano Conti
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Mineko Terao
- Laboratory of Molecular Biology, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156, Milan, Italy
| | - Anna Cereseto
- Department CIBIO, University of Trento, Via Sommarive 9, 38123, Povo, Italy.
| |
Collapse
|
8
|
Chen J, Li S, He Y, Li J, Xia L. An update on precision genome editing by homology-directed repair in plants. PLANT PHYSIOLOGY 2022; 188:1780-1794. [PMID: 35238390 PMCID: PMC8968426 DOI: 10.1093/plphys/kiac037] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/20/2022] [Indexed: 05/22/2023]
Abstract
Beneficial alleles derived from local landraces or related species, or even orthologs from other plant species, are often caused by differences of one or several single-nucleotide polymorphisms or indels in either the promoter region or the encoding region of a gene and often account for major differences in agriculturally important traits. Clustered regularly interspaced short palindromic repeats-associated endonuclease Cas9 system (CRISPR/Cas9)-mediated precision genome editing enables targeted allele replacement or insertion of flag or foreign genes at specific loci via homology-directed repair (HDR); however, HDR efficiency is low due to the intrinsic rare occurrence of HDR and insufficient DNA repair template in the proximity of a double-stranded break (DSB). Precise replacement of the targeted gene with elite alleles from landraces or relatives into a commercial variety through genome editing has been a holy grail in the crop genome editing field. In this update, we briefly summarize CRISPR/Cas-mediated HDR in plants. We describe diverse strategies to improve HDR efficiency by manipulating the DNA repair pathway, timing DSB induction, and donor delivery, and so on. Lastly, we outline open questions and challenges in HDR-mediated precision genome editing in both plant biological research and crop improvement.
Collapse
Affiliation(s)
| | | | - Yubing He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingying Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
| | | |
Collapse
|
9
|
Barbon L, Offord V, Radford EJ, Butler AP, Gerety SS, Adams DJ, Tan HK, Waters AJ. Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments. Bioinformatics 2022; 38:892-899. [PMID: 34791067 PMCID: PMC8796380 DOI: 10.1093/bioinformatics/btab776] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/13/2021] [Accepted: 11/10/2021] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION CRISPR/Cas9-based technology allows for the functional analysis of genetic variants at single nucleotide resolution whilst maintaining genomic context. This approach, known as saturation genome editing (SGE), a form of deep mutational scanning, systematically alters each position in a target region to explore its function. SGE experiments require the design and synthesis of oligonucleotide variant libraries which are introduced into the genome. This technology is applicable to diverse fields such as disease variant identification, drug development, structure-function studies, synthetic biology, evolutionary genetics and host-pathogen interactions. Here, we present the Variant Library Annotation Tool (VaLiAnT) which can be used to generate variant libraries from user-defined genomic coordinates and standard input files. The software can accommodate user-specified species, reference sequences and transcript annotations. RESULTS Coordinates for a genomic range are provided by the user to retrieve a corresponding oligonucleotide reference sequence. A user-specified range within this sequence is then subject to systematic, nucleotide and/or amino acid saturating mutator functions. VaLiAnT provides a novel way to retrieve, mutate and annotate genomic sequences for oligonucleotide library generation. Specific features for SGE library generation can be employed. In addition, VaLiAnT is configurable, allowing for cDNA and prime editing saturation library generation, with other diverse applications possible. AVAILABILITY AND IMPLEMENTATION VaLiAnT is a command line tool written in Python. Source code, testing data, example input and output files and executables are available (https://github.com/cancerit/VaLiAnT) in addition to a detailed user manual (https://github.com/cancerit/VaLiAnT/wiki). VaLiAnT is licensed under AGPLv3. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Luca Barbon
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Victoria Offord
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Elizabeth J Radford
- Human Genetics Programme, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Adam P Butler
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Sebastian S Gerety
- Human Genetics Programme, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - David J Adams
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Hong Kee Tan
- Human Genetics Programme, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Andrew J Waters
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| |
Collapse
|
10
|
Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell 2022; 82:348-388. [PMID: 35063100 PMCID: PMC8887926 DOI: 10.1016/j.molcel.2021.12.026] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Genome editing technologies operate by inducing site-specific DNA perturbations that are resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks generated by CRISPR-associated nucleases, base modifications induced by base editors, DNA flaps created by prime editors, and integration intermediates formed by site-specific recombinases and transposases associated with CRISPR systems. Here, we discuss the cellular processes that repair CRISPR-generated DNA lesions and describe strategies to obtain desirable genomic changes through modulation of DNA repair pathways. Advances in our understanding of the DNA repair circuitry, in conjunction with the rapid development of innovative genome editing technologies, promise to greatly enhance our ability to improve food production, combat environmental pollution, develop cell-based therapies, and cure genetic and infectious diseases.
Collapse
Affiliation(s)
- Tarun S. Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032
| | - Lou Baudrier
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada
| | - Pierre Billon
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada,Corresponding authors: ,
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032,Lead Contact,Corresponding authors: ,
| |
Collapse
|
11
|
Tulin F. Two stones, one bird: co-targeting facilitates precise gene editing of non-selectable genes in Chlamydomonas. PLANT PHYSIOLOGY 2022; 188:16-18. [PMID: 35051288 PMCID: PMC8774741 DOI: 10.1093/plphys/kiab515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Frej Tulin
- Plant Science Department, Botany, Technische Universität München, 85354 Freising, Germany
| |
Collapse
|
12
|
Ou T, He W, Quinlan BD, Guo Y, Tran MH, Karunadharma P, Park H, Davis-Gardner ME, Yin Y, Zhang X, Wang H, Zhong G, Farzan M. Reprogramming of the heavy-chain CDR3 regions of a human antibody repertoire. Mol Ther 2022; 30:184-197. [PMID: 34740791 PMCID: PMC8753427 DOI: 10.1016/j.ymthe.2021.10.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/09/2021] [Accepted: 10/27/2021] [Indexed: 01/07/2023] Open
Abstract
B cells have been engineered ex vivo to express an HIV-1 broadly neutralizing antibody (bNAb). B cell reprograming may be scientifically and therapeutically useful, but current approaches limit B cell repertoire diversity and disrupt the organization of the heavy-chain locus. A more diverse and physiologic B cell repertoire targeting a key HIV-1 epitope could facilitate evaluation of vaccines designed to elicit bNAbs, help identify more potent and bioavailable bNAb variants, or directly enhance viral control in vivo. Here we address the challenges of generating such a repertoire by replacing the heavy-chain CDR3 (HCDR3) regions of primary human B cells. To do so, we identified and utilized an uncharacterized Cas12a ortholog that recognizes PAM motifs present in human JH genes. We also optimized the design of 200 nucleotide homology-directed repair templates (HDRT) by minimizing the required 3'-5' deletion of the HDRT-complementary strand. Using these techniques, we edited primary human B cells to express a hemagglutinin epitope tag and the HCDR3 regions of the bNAbs PG9 and PG16. Those edited with bNAb HCDR3 efficiently bound trimeric HIV-1 antigens, implying they could affinity mature in vivo in response to the same antigens. This approach generates diverse B cell repertoires recognizing a key HIV-1 neutralizing epitope.
Collapse
Affiliation(s)
- Tianling Ou
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Wenhui He
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Brian D Quinlan
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Yan Guo
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Mai H Tran
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Hajeung Park
- X-ray Crystallography Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Yiming Yin
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xia Zhang
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Haimin Wang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Guocai Zhong
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China; School of Biology and Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Michael Farzan
- Department of Microbiology and Immunology, The Scripps Research Institute, Jupiter, FL 33458, USA.
| |
Collapse
|
13
|
Akella S, Ma X, Bacova R, Harmer ZP, Kolackova M, Wen X, Wright DA, Spalding MH, Weeks DP, Cerutti H. Co-targeting strategy for precise, scarless gene editing with CRISPR/Cas9 and donor ssODNs in Chlamydomonas. PLANT PHYSIOLOGY 2021; 187:2637-2655. [PMID: 34618092 PMCID: PMC8644747 DOI: 10.1093/plphys/kiab418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/30/2021] [Indexed: 05/20/2023]
Abstract
Programmable site-specific nucleases, such as the clustered regularly interspaced short palindromic repeat (CRISPR)/ CRISPR-associated protein 9 (Cas9) ribonucleoproteins (RNPs), have allowed creation of valuable knockout mutations and targeted gene modifications in Chlamydomonas (Chlamydomonas reinhardtii). However, in walled strains, present methods for editing genes lacking a selectable phenotype involve co-transfection of RNPs and exogenous double-stranded DNA (dsDNA) encoding a selectable marker gene. Repair of the dsDNA breaks induced by the RNPs is usually accompanied by genomic insertion of exogenous dsDNA fragments, hindering the recovery of precise, scarless mutations in target genes of interest. Here, we tested whether co-targeting two genes by electroporation of pairs of CRISPR/Cas9 RNPs and single-stranded oligodeoxynucleotides (ssODNs) would facilitate the recovery of precise edits in a gene of interest (lacking a selectable phenotype) by selection for precise editing of another gene (creating a selectable marker)-in a process completely lacking exogenous dsDNA. We used PPX1 (encoding protoporphyrinogen IX oxidase) as the generated selectable marker, conferring resistance to oxyfluorfen, and identified precise edits in the homolog of bacterial ftsY or the WD and TetratriCopeptide repeats protein 1 genes in ∼1% of the oxyfluorfen resistant colonies. Analysis of the target site sequences in edited mutants suggested that ssODNs were used as templates for DNA synthesis during homology directed repair, a process prone to replicative errors. The Chlamydomonas acetolactate synthase gene could also be efficiently edited to serve as an alternative selectable marker. This transgene-free strategy may allow creation of individual strains containing precise mutations in multiple target genes, to study complex cellular processes, pathways, or structures.
Collapse
Affiliation(s)
- Soujanya Akella
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - Xinrong Ma
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - Romana Bacova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Zachary P Harmer
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - Martina Kolackova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Xiaoxue Wen
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - David A Wright
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Martin H Spalding
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Donald P Weeks
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| |
Collapse
|
14
|
Ferenczi A, Chew YP, Kroll E, von Koppenfels C, Hudson A, Molnar A. Mechanistic and genetic basis of single-strand templated repair at Cas12a-induced DNA breaks in Chlamydomonas reinhardtii. Nat Commun 2021; 12:6751. [PMID: 34799578 PMCID: PMC8604939 DOI: 10.1038/s41467-021-27004-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
Single-stranded oligodeoxynucleotides (ssODNs) are widely used as DNA repair templates in CRISPR/Cas precision genome editing. However, the underlying mechanisms of single-strand templated DNA repair (SSTR) are inadequately understood, constraining rational improvements to precision editing. Here we study SSTR at CRISPR/Cas12a-induced DNA double-strand breaks (DSBs) in the eukaryotic model green microalga Chlamydomonas reinhardtii. We demonstrate that ssODNs physically incorporate into the genome during SSTR at Cas12a-induced DSBs. This process is genetically independent of the Rad51-dependent homologous recombination and Fanconi anemia pathways, is strongly antagonized by non-homologous end-joining, and is mediated almost entirely by the alternative end-joining enzyme polymerase θ. These findings suggest differences in SSTR between C. reinhardtii and animals. Our work illustrates the promising potentially of C. reinhardtii as a model organism for studying nuclear DNA repair.
Collapse
Affiliation(s)
- Aron Ferenczi
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Yen Peng Chew
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Erika Kroll
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | | | - Andrew Hudson
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| |
Collapse
|
15
|
Hussmann JA, Ling J, Ravisankar P, Yan J, Cirincione A, Xu A, Simpson D, Yang D, Bothmer A, Cotta-Ramusino C, Weissman JS, Adamson B. Mapping the genetic landscape of DNA double-strand break repair. Cell 2021; 184:5653-5669.e25. [PMID: 34672952 PMCID: PMC9074467 DOI: 10.1016/j.cell.2021.10.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/31/2021] [Accepted: 09/29/2021] [Indexed: 12/20/2022]
Abstract
Cells repair DNA double-strand breaks (DSBs) through a complex set of pathways critical for maintaining genomic integrity. To systematically map these pathways, we developed a high-throughput screening approach called Repair-seq that measures the effects of thousands of genetic perturbations on mutations introduced at targeted DNA lesions. Using Repair-seq, we profiled DSB repair products induced by two programmable nucleases (Cas9 and Cas12a) in the presence or absence of oligonucleotides for homology-directed repair (HDR) after knockdown of 476 genes involved in DSB repair or associated processes. The resulting data enabled principled, data-driven inference of DSB end joining and HDR pathways. Systematic interrogation of this data uncovered unexpected relationships among DSB repair genes and demonstrated that repair outcomes with superficially similar sequence architectures can have markedly different genetic dependencies. This work provides a foundation for mapping DNA repair pathways and for optimizing genome editing across diverse modalities.
Collapse
Affiliation(s)
- Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jia Ling
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Purnima Ravisankar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Jun Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ann Cirincione
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Albert Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danny Simpson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Dian Yang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | | | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Britt Adamson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
16
|
Ghanta KS, Chen Z, Mir A, Dokshin GA, Krishnamurthy PM, Yoon Y, Gallant J, Xu P, Zhang XO, Ozturk AR, Shin M, Idrizi F, Liu P, Gneid H, Edraki A, Lawson ND, Rivera-Pérez JA, Sontheimer EJ, Watts JK, Mello CC. 5'-Modifications improve potency and efficacy of DNA donors for precision genome editing. eLife 2021; 10:e72216. [PMID: 34665130 PMCID: PMC8568340 DOI: 10.7554/elife.72216] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/09/2021] [Indexed: 12/22/2022] Open
Abstract
Nuclease-directed genome editing is a powerful tool for investigating physiology and has great promise as a therapeutic approach to correct mutations that cause disease. In its most precise form, genome editing can use cellular homology-directed repair (HDR) pathways to insert information from an exogenously supplied DNA-repair template (donor) directly into a targeted genomic location. Unfortunately, particularly for long insertions, toxicity and delivery considerations associated with repair template DNA can limit HDR efficacy. Here, we explore chemical modifications to both double-stranded and single-stranded DNA-repair templates. We describe 5'-terminal modifications, including in its simplest form the incorporation of triethylene glycol (TEG) moieties, that consistently increase the frequency of precision editing in the germlines of three animal models (Caenorhabditis elegans, zebrafish, mice) and in cultured human cells.
Collapse
Affiliation(s)
- Krishna S Ghanta
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Aamir Mir
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Gregoriy A Dokshin
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | | | - Yeonsoo Yoon
- Department of Pediatrics, Division of Genes and Development, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Judith Gallant
- Department of Pediatrics, Division of Genes and Development, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Ping Xu
- Department of Pediatrics, Division of Genes and Development, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Ahmet Rasit Ozturk
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Masahiro Shin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Feston Idrizi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Hassan Gneid
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Alireza Edraki
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Nathan D Lawson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jaime A Rivera-Pérez
- Department of Pediatrics, Division of Genes and Development, University of Massachusetts Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
- Howard Hughes Medical Institute, University of Massachusetts Medical SchoolWorcesterUnited States
| |
Collapse
|
17
|
Schubert MS, Thommandru B, Woodley J, Turk R, Yan S, Kurgan G, McNeill MS, Rettig GR. Optimized design parameters for CRISPR Cas9 and Cas12a homology-directed repair. Sci Rep 2021; 11:19482. [PMID: 34593942 PMCID: PMC8484621 DOI: 10.1038/s41598-021-98965-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas proteins are RNA-guided nucleases used to introduce double-stranded breaks (DSBs) at targeted genomic loci. DSBs are repaired by endogenous cellular pathways such as non-homologous end joining (NHEJ) and homology-directed repair (HDR). Providing an exogenous DNA template during repair allows for the intentional, precise incorporation of a desired mutation via the HDR pathway. However, rates of repair by HDR are often slow compared to the more rapid but less accurate NHEJ-mediated repair. Here, we describe comprehensive design considerations and optimized methods for highly efficient HDR using single-stranded oligodeoxynucleotide (ssODN) donor templates for several CRISPR-Cas systems including S.p. Cas9, S.p. Cas9 D10A nickase, and A.s. Cas12a delivered as ribonucleoprotein (RNP) complexes. Features relating to guide RNA selection, donor strand preference, and incorporation of blocking mutations in the donor template to prevent re-cleavage were investigated and were implemented in a novel online tool for HDR donor template design. These findings allow for high frequencies of precise repair utilizing HDR in multiple mammalian cell lines. Tool availability: https://www.idtdna.com/HDR.
Collapse
Affiliation(s)
- Mollie S Schubert
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Bernice Thommandru
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Jessica Woodley
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Rolf Turk
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Shuqi Yan
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Gavin Kurgan
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Matthew S McNeill
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Garrett R Rettig
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA.
| |
Collapse
|
18
|
Sizova I, Kelterborn S, Verbenko V, Kateriya S, Hegemann P. Chlamydomonas POLQ is necessary for CRISPR/Cas9-mediated gene targeting. G3 (BETHESDA, MD.) 2021; 11:jkab114. [PMID: 33836052 PMCID: PMC8495919 DOI: 10.1093/g3journal/jkab114] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
The use of CRISPR/Cas endonucleases has revolutionized gene editing techniques for research on Chlamydomonas reinhardtii. To better utilize the CRISPR/Cas system, it is essential to develop a more comprehensive understanding of the DNA repair pathways involved in genome editing. In this study, we have analyzed contributions from canonical KU80/KU70-dependent nonhomologous end-joining (cNHEJ) and DNA polymerase theta (POLQ)-mediated end joining on SpCas9-mediated untemplated mutagenesis and homology-directed repair (HDR)/gene inactivation in Chlamydomonas. Using CRISPR/SpCas9 technology, we generated DNA repair-defective mutants ku80, ku70, polQ for gene targeting experiments. Our results show that untemplated repair of SpCas9-induced double strand breaks results in mutation spectra consistent with an involvement of both KU80/KU70 and POLQ. In addition, the inactivation of POLQ was found to negatively affect HDR of the inactivated paromomycin-resistant mut-aphVIII gene when donor single-stranded oligos were used. Nevertheless, mut-aphVIII was still repaired by homologous recombination in these mutants. POLQ inactivation suppressed random integration of transgenes co-transformed with the donor ssDNA. KU80 deficiency did not affect these events but instead was surprisingly found to stimulate HDR/gene inactivation. Our data suggest that in Chlamydomonas, POLQ is the main contributor to CRISPR/Cas-induced HDR and random integration of transgenes, whereas KU80/KU70 potentially plays a secondary role. We expect our results will lead to improvement of genome editing in C. reinhardtii and can be used for future development of algal biotechnology.
Collapse
Affiliation(s)
- Irina Sizova
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Simon Kelterborn
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
| | - Valeriy Verbenko
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Suneel Kateriya
- Laboratory of Optobiology School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Peter Hegemann
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
| |
Collapse
|
19
|
Li S, Zhang C, Li J, Yan L, Wang N, Xia L. Present and future prospects for wheat improvement through genome editing and advanced technologies. PLANT COMMUNICATIONS 2021; 2:100211. [PMID: 34327324 PMCID: PMC8299080 DOI: 10.1016/j.xplc.2021.100211] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/15/2021] [Accepted: 06/03/2021] [Indexed: 05/03/2023]
Abstract
Wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) is one of the most important staple food crops in the world. Despite the fact that wheat production has significantly increased over the past decades, future wheat production will face unprecedented challenges from global climate change, increasing world population, and water shortages in arid and semi-arid lands. Furthermore, excessive applications of diverse fertilizers and pesticides are exacerbating environmental pollution and ecological deterioration. To ensure global food and ecosystem security, it is essential to enhance the resilience of wheat production while minimizing environmental pollution through the use of cutting-edge technologies. However, the hexaploid genome and gene redundancy complicate advances in genetic research and precision gene modifications for wheat improvement, thus impeding the breeding of elite wheat cultivars. In this review, we first introduce state-of-the-art genome-editing technologies in crop plants, especially wheat, for both functional genomics and genetic improvement. We then outline applications of other technologies, such as GWAS, high-throughput genotyping and phenotyping, speed breeding, and synthetic biology, in wheat. Finally, we discuss existing challenges in wheat genome editing and future prospects for precision gene modifications using advanced genome-editing technologies. We conclude that the combination of genome editing and other molecular breeding strategies will greatly facilitate genetic improvement of wheat for sustainable global production.
Collapse
Affiliation(s)
- Shaoya Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Chen Zhang
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Jingying Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Lei Yan
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Ning Wang
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Lanqin Xia
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| |
Collapse
|
20
|
Zhang X, Li T, Ou J, Huang J, Liang P. Homology-based repair induced by CRISPR-Cas nucleases in mammalian embryo genome editing. Protein Cell 2021; 13:316-335. [PMID: 33945139 PMCID: PMC9008090 DOI: 10.1007/s13238-021-00838-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/16/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in genome editing, especially CRISPR-Cas nucleases, have revolutionized both laboratory research and clinical therapeutics. CRISPR-Cas nucleases, together with the DNA damage repair pathway in cells, enable both genetic diversification by classical non-homologous end joining (c-NHEJ) and precise genome modification by homology-based repair (HBR). Genome editing in zygotes is a convenient way to edit the germline, paving the way for animal disease model generation, as well as human embryo genome editing therapy for some life-threatening and incurable diseases. HBR efficiency is highly dependent on the DNA donor that is utilized as a repair template. Here, we review recent progress in improving CRISPR-Cas nuclease-induced HBR in mammalian embryos by designing a suitable DNA donor. Moreover, we want to provide a guide for producing animal disease models and correcting genetic mutations through CRISPR-Cas nuclease-induced HBR in mammalian embryos. Finally, we discuss recent developments in precise genome-modification technology based on the CRISPR-Cas system.
Collapse
Affiliation(s)
- Xiya Zhang
- Center for Reproductive Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, 510630, China
| | - Tao Li
- Center for Reproductive Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, 510630, China
| | - Jianping Ou
- Center for Reproductive Medicine, the Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, 510630, China.
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Puping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| |
Collapse
|
21
|
Bloh K, Rivera-Torres N. A Consensus Model of Homology-Directed Repair Initiated by CRISPR/Cas Activity. Int J Mol Sci 2021; 22:3834. [PMID: 33917142 PMCID: PMC8067812 DOI: 10.3390/ijms22083834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/31/2021] [Accepted: 04/05/2021] [Indexed: 12/26/2022] Open
Abstract
The mechanism of action of ssODN-directed gene editing has been a topic of discussion within the field of CRISPR gene editing since its inception. Multiple comparable, but distinct, pathways have been discovered for DNA repair both with and without a repair template oligonucleotide. We have previously described the ExACT pathway for oligo-driven DNA repair, which consisted of a two-step DNA synthesis-driven repair catalyzed by the simultaneous binding of the repair oligonucleotide (ssODN) upstream and downstream of the double-strand break. In order to better elucidate the mechanism of ExACT-based repair, we have challenged the assumptions of the pathway with those outlines in other similar non-ssODN-based DNA repair mechanisms. This more comprehensive iteration of the ExACT pathway better described the many different ways where DNA repair can occur in the presence of a repair oligonucleotide after CRISPR cleavage, as well as how these previously distinct pathways can overlap and lead to even more unique repair outcomes.
Collapse
Affiliation(s)
- Kevin Bloh
- Gene Editing Institute, Helen F. Graham Cancer Center & Research Institute, ChristianaCare, 4701 Ogletown-Stanton Road, Newark, DE 19710, USA;
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19710, USA
| | - Natalia Rivera-Torres
- Gene Editing Institute, Helen F. Graham Cancer Center & Research Institute, ChristianaCare, 4701 Ogletown-Stanton Road, Newark, DE 19710, USA;
| |
Collapse
|
22
|
Cooper SE, Schwartzentruber J, Bello E, Coomber EL, Bassett AR. Screening for functional transcriptional and splicing regulatory variants with GenIE. Nucleic Acids Res 2021; 48:e131. [PMID: 33152068 PMCID: PMC7736817 DOI: 10.1093/nar/gkaa960] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/22/2020] [Accepted: 10/08/2020] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified numerous genetic loci underlying human diseases, but a fundamental challenge remains to accurately identify the underlying causal genes and variants. Here, we describe an arrayed CRISPR screening method, Genome engineering-based Interrogation of Enhancers (GenIE), which assesses the effects of defined alleles on transcription or splicing when introduced in their endogenous genomic locations. We use this sensitive assay to validate the activity of transcriptional enhancers and splice regulatory elements in human induced pluripotent stem cells (hiPSCs), and develop a software package (rgenie) to analyse the data. We screen the 99% credible set of Alzheimer's disease (AD) GWAS variants identified at the clusterin (CLU) locus to identify a subset of likely causal variants, and employ GenIE to understand the impact of specific mutations on splicing efficiency. We thus establish GenIE as an efficient tool to rapidly screen for the role of transcribed variants on gene expression.
Collapse
Affiliation(s)
- Sarah E Cooper
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,OpenTargets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jeremy Schwartzentruber
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,OpenTargets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Erica Bello
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,OpenTargets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Eve L Coomber
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Andrew R Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,OpenTargets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| |
Collapse
|
23
|
Perisse IV, Fan Z, Singina GN, White KL, Polejaeva IA. Improvements in Gene Editing Technology Boost Its Applications in Livestock. Front Genet 2021; 11:614688. [PMID: 33603767 PMCID: PMC7885404 DOI: 10.3389/fgene.2020.614688] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 12/18/2022] Open
Abstract
Accelerated development of novel CRISPR/Cas9-based genome editing techniques provides a feasible approach to introduce a variety of precise modifications in the mammalian genome, including introduction of multiple edits simultaneously, efficient insertion of long DNA sequences into specific targeted loci as well as performing nucleotide transitions and transversions. Thus, the CRISPR/Cas9 tool has become the method of choice for introducing genome alterations in livestock species. The list of new CRISPR/Cas9-based genome editing tools is constantly expanding. Here, we discuss the methods developed to improve efficiency and specificity of gene editing tools as well as approaches that can be employed for gene regulation, base editing, and epigenetic modifications. Additionally, advantages and disadvantages of two primary methods used for the production of gene-edited farm animals: somatic cell nuclear transfer (SCNT or cloning) and zygote manipulations will be discussed. Furthermore, we will review agricultural and biomedical applications of gene editing technology.
Collapse
Affiliation(s)
- Iuri Viotti Perisse
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Zhiqiang Fan
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Galina N. Singina
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, Russia
| | - Kenneth L. White
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Irina A. Polejaeva
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| |
Collapse
|
24
|
Désaulniers K, Ortiz L, Dufour C, Claudel A, Plourde MB, Merindol N, Berthoux L. Editing of the TRIM5 Gene Decreases the Permissiveness of Human T Lymphocytic Cells to HIV-1. Viruses 2020; 13:E24. [PMID: 33375604 PMCID: PMC7824555 DOI: 10.3390/v13010024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/20/2020] [Accepted: 12/22/2020] [Indexed: 01/08/2023] Open
Abstract
Tripartite-motif-containing protein 5 isoform α (TRIM5α) is a cytoplasmic antiretroviral effector upregulated by type I interferons (IFN-I). We previously showed that two points mutations, R332G/R335G, in the retroviral capsid-binding region confer human TRIM5α the capacity to target and strongly restrict HIV-1 upon overexpression of the mutated protein. Here, we used clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-mediated homology-directed repair (HDR) to introduce these two mutations in the endogenous human TRIM5 gene. We found 6 out of 47 isolated cell clones containing at least one HDR-edited allele. One clone (clone 6) had both alleles containing R332G, but only one of the two alleles containing R335G. Upon challenge with an HIV-1 vector, clone 6 was significantly less permissive compared to unmodified cells, whereas the cell clones with monoallelic modifications were only slightly less permissive. Following interferon (IFN)-β treatment, inhibition of HIV-1 infection in clone 6 was significantly enhanced (~40-fold inhibition). TRIM5α knockdown confirmed that HIV-1 was inhibited by the edited TRIM5 gene products. Quantification of HIV-1 reverse transcription products showed that inhibition occurred through the expected mechanism. In conclusion, we demonstrate the feasibility of potently inhibiting a viral infection through the editing of innate effector genes. Our results also emphasize the importance of biallelic modification in order to reach significant levels of inhibition by TRIM5α.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Lionel Berthoux
- Department of Medical Biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada; (K.D.); (L.O.); (C.D.); (A.C.); (M.B.P.); (N.M.)
| |
Collapse
|
25
|
Lau CH, Tin C, Suh Y. CRISPR-based strategies for targeted transgene knock-in and gene correction. Fac Rev 2020; 9:20. [PMID: 33659952 PMCID: PMC7886068 DOI: 10.12703/r/9-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The last few years have seen tremendous advances in CRISPR-mediated genome editing. Great efforts have been made to improve the efficiency, specificity, editing window, and targeting scope of CRISPR/Cas9-mediated transgene knock-in and gene correction. In this article, we comprehensively review recent progress in CRISPR-based strategies for targeted transgene knock-in and gene correction in both homology-dependent and homology-independent approaches. We cover homology-directed repair (HDR), synthesis-dependent strand annealing (SDSA), microhomology-mediated end joining (MMEJ), and homology-mediated end joining (HMEJ) pathways for a homology-dependent strategy and alternative DNA repair pathways such as non-homologous end joining (NHEJ), base excision repair (BER), and mismatch repair (MMR) for a homology-independent strategy. We also discuss base editing and prime editing that enable direct conversion of nucleotides in genomic DNA without damaging the DNA or requiring donor DNA. Notably, we illustrate the key mechanisms and design principles for each strategy, providing design guidelines for multiplex, flexible, scarless gene insertion and replacement at high efficiency and specificity. In addition, we highlight next-generation base editors that provide higher editing efficiency, fewer undesired by-products, and broader targeting scope.
Collapse
Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Chung Tin
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| |
Collapse
|
26
|
Meitlis I, Allenspach EJ, Bauman BM, Phan IQ, Dabbah G, Schmitt EG, Camp ND, Torgerson TR, Nickerson DA, Bamshad MJ, Hagin D, Luthers CR, Stinson JR, Gray J, Lundgren I, Church JA, Butte MJ, Jordan MB, Aceves SS, Schwartz DM, Milner JD, Schuval S, Skoda-Smith S, Cooper MA, Starita LM, Rawlings DJ, Snow AL, James RG. Multiplexed Functional Assessment of Genetic Variants in CARD11. Am J Hum Genet 2020; 107:1029-1043. [PMID: 33202260 PMCID: PMC7820631 DOI: 10.1016/j.ajhg.2020.10.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 10/27/2020] [Indexed: 12/28/2022] Open
Abstract
Genetic testing has increased the number of variants identified in disease genes, but the diagnostic utility is limited by lack of understanding variant function. CARD11 encodes an adaptor protein that expresses dominant-negative and gain-of-function variants associated with distinct immunodeficiencies. Here, we used a "cloning-free" saturation genome editing approach in a diploid cell line to simultaneously score 2,542 variants for decreased or increased function in the region of CARD11 associated with immunodeficiency. We also described an exon-skipping mechanism for CARD11 dominant-negative activity. The classification of reported clinical variants was sensitive (94.6%) and specific (88.9%), which rendered the data immediately useful for interpretation of seven coding and splicing variants implicated in immunodeficiency found in our clinic. This approach is generalizable for variant interpretation in many other clinically actionable genes, in any relevant cell type.
Collapse
Affiliation(s)
- Iana Meitlis
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Eric J Allenspach
- Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Bradly M Bauman
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Isabelle Q Phan
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Gina Dabbah
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Erica G Schmitt
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, MO 63130, USA
| | - Nathan D Camp
- Seattle Children's Research Institute, Seattle, WA 98101, USA
| | | | - Deborah A Nickerson
- Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - David Hagin
- Allergy and Clinical Immunology Unit, Department of Medicine, Tel Aviv Sourasky Medical Center and Sackler Faculty of Medicine, University of Tel Aviv, Tel Aviv 62919, Israel
| | - Christopher R Luthers
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Jeffrey R Stinson
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Jessica Gray
- Divisions of Immunobiology, and Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Joseph A Church
- Department of Pediatrics, Keck School of Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Manish J Butte
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California Los Angeles, Los Angeles, CA 90404, USA
| | - Mike B Jordan
- Divisions of Immunobiology, and Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Seema S Aceves
- Division of Allergy Immunology, Departments of Pediatrics and Medicine, University of California, San Diego, and Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Joshua D Milner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Susan Schuval
- Department of Pediatrics, Stonybrook University, Stony Brook, NY 11794, USA
| | - Suzanne Skoda-Smith
- Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, MO 63130, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - David J Rawlings
- Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Richard G James
- Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA 98195, USA.
| |
Collapse
|
27
|
Ma L, Ruan J, Song J, Wen L, Yang D, Zhao J, Xia X, Chen YE, Zhang J, Xu J. MiCas9 increases large size gene knock-in rates and reduces undesirable on-target and off-target indel edits. Nat Commun 2020; 11:6082. [PMID: 33247137 PMCID: PMC7695827 DOI: 10.1038/s41467-020-19842-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/29/2020] [Indexed: 01/09/2023] Open
Abstract
Gene editing nuclease represented by Cas9 efficiently generates DNA double strand breaks at the target locus, followed by repair through either the error-prone non-homologous end joining or the homology directed repair pathways. To improve Cas9's homology directed repair capacity, here we report the development of miCas9 by fusing a minimal motif consisting of thirty-six amino acids to spCas9. MiCas9 binds RAD51 through this fusion motif and enriches RAD51 at the target locus. In comparison to spCas9, miCas9 enhances double-stranded DNA mediated large size gene knock-in rates, systematically reduces off-target insertion and deletion events, maintains or increases single-stranded oligodeoxynucleotides mediated precise gene editing rates, and effectively reduces on-target insertion and deletion rates in knock-in applications. Furthermore, we demonstrate that this fusion motif can work as a "plug and play" module, compatible and synergistic with other Cas9 variants. MiCas9 and the minimal fusion motif may find broad applications in gene editing research and therapeutics.
Collapse
Affiliation(s)
- Linyuan Ma
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Jinxue Ruan
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Luan Wen
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Dongshan Yang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Jiangyang Zhao
- Research & Development, ATGC Inc., 100 E Lancaster Avenue, LIMR Building Lab129, Wynnewood, PA, 19096, USA
| | - Xiaofeng Xia
- Research & Development, ATGC Inc., 100 E Lancaster Avenue, LIMR Building Lab129, Wynnewood, PA, 19096, USA
| | - Y Eugene Chen
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA.
| | - Jifeng Zhang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA.
| | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical School, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
28
|
Kondrateva E, Demchenko A, Lavrov A, Smirnikhina S. An overview of currently available molecular Cas-tools for precise genome modification. Gene 2020; 769:145225. [PMID: 33059029 DOI: 10.1016/j.gene.2020.145225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/17/2022]
Abstract
CRISPR-Cas system was first mentioned in 1987, and over the years have been studied so active that now it becomes the state-of-the-art tool for genome editing. Its working principle is based on Cas nuclease ability to bind short RNA, which targets it to complementary DNA or RNA sequence for highly precise cleavage. This alone or together with donor DNA allows to modify targeted sequence in different ways. Considering the many limitations of using native CRISPR-Cas systems, scientists around the world are working on creating modified variants to improve their specificity and efficiency in different objects. In addition, the use of the Cas effectors' targeting function in complex systems with other proteins is a promising work direction, as a result of which new tools are created with features such as single base editing, editing DNA without break and donor DNA, activation and repression of transcription, epigenetic regulation, modifying of different repair pathways involvement etc. In this review, we decided to consider in detail exactly this issue of variants of Cas effectors, their modifications and fusion molecules, which improve DNA-targeting and expand the scope of Cas effectors.
Collapse
Affiliation(s)
- Ekaterina Kondrateva
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia.
| | - Anna Demchenko
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia
| | - Alexander Lavrov
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia
| | - Svetlana Smirnikhina
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia
| |
Collapse
|
29
|
CRISPR-Mediated Non-Viral Site-Specific Gene Integration and Expression in T Cells: Protocol and Application for T-Cell Therapy. Cancers (Basel) 2020; 12:cancers12061704. [PMID: 32604839 PMCID: PMC7352666 DOI: 10.3390/cancers12061704] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 01/03/2023] Open
Abstract
T cells engineered with chimeric antigen receptors (CARs) show great promise in the treatment of some cancers. Modifying T cells to express CARs generally relies on T-cell transduction using viral vectors carrying a transgene, resulting in semi-random DNA integration within the T-cell genome. While this approach has proven successful and is used in generating the Food and Drug Administration (FDA, USA) approved B-lymphocyte antigen CD19-specific CAR T cells, it is possible the transgene could integrate into a locus that would lead to malignant transformation of the engineered T cells. In addition, manufacturing viral vectors is time-consuming and expensive. One way to overcome these challenges is site-specific gene integration, which can be achieved through clustered regularly interspaced short palindromic repeat (CRISPR) mediated editing and non-viral DNA, which serves as a template for homology-directed repair (HDR). This non-viral gene editing approach provides a rapid, highly specific, and inexpensive way to engineer T cells. Here, we describe an optimized protocol for the site-specific knock-in of a large transgene in primary human T cells using non-viral double stranded DNA as a repair template. As proof-of-principle, we targeted the T-cell receptor alpha constant (TRAC) locus for insertion of a large transgene containing green fluorescence protein (GFP) and interleukin-15 (IL-15). To optimize the knock-in conditions we tested template DNA concentration, homology arm length, cell number, and knock-in efficiency over time. We then applied these established guidelines to target the TRAC or interleukin-13 (IL-13) locus for the knock-in of synthetic molecules, such as a CAR, bispecific T-cell engager (BiTE), and other transgenes. While integration efficiency depends on the targeted gene locus and selected transgene, this optimized protocol reliably generates the desired insertion at rates upwards of 20%. Thus, it should serve as a good starting point for investigators who are interested in knocking in transgenes into specific loci.
Collapse
|
30
|
Carvajal-Garcia J, Cho JE, Carvajal-Garcia P, Feng W, Wood RD, Sekelsky J, Gupta GP, Roberts SA, Ramsden DA. Mechanistic basis for microhomology identification and genome scarring by polymerase theta. Proc Natl Acad Sci U S A 2020; 117:8476-8485. [PMID: 32234782 PMCID: PMC7165422 DOI: 10.1073/pnas.1921791117] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
DNA polymerase theta mediates an end joining pathway (TMEJ) that repairs chromosome breaks. It requires resection of broken ends to generate long, 3' single-stranded DNA tails, annealing of complementary sequence segments (microhomologies) in these tails, followed by microhomology-primed synthesis sufficient to resolve broken ends. The means by which microhomologies are identified is thus a critical step in this pathway, but is not understood. Here we show microhomologies are identified by a scanning mechanism initiated from the 3' terminus and favoring bidirectional progression into flanking DNA, typically to a maximum of 15 nucleotides into each flank. Polymerase theta is frequently insufficiently processive to complete repair of breaks in microhomology-poor, AT-rich regions. Aborted synthesis leads to one or more additional rounds of microhomology search, annealing, and synthesis; this promotes complete repair in part because earlier rounds of synthesis generate microhomologies de novo that are sufficiently long that synthesis is more processive. Aborted rounds of synthesis are evident in characteristic genomic scars as insertions of 3 to 30 bp of sequence that is identical to flanking DNA ("templated" insertions). Templated insertions are present at higher levels in breast cancer genomes from patients with germline BRCA1/2 mutations, consistent with an addiction to TMEJ in these cancers. Our work thus describes the mechanism for microhomology identification and shows how it both mitigates limitations implicit in the microhomology requirement and generates distinctive genomic scars associated with pathogenic genome instability.
Collapse
Affiliation(s)
- Juan Carvajal-Garcia
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jang-Eun Cho
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Pablo Carvajal-Garcia
- Departamento de Ingeniería Geológica y Minera, Universidad Politécnica de Madrid, 28003 Madrid, Spain
| | - Wanjuan Feng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957
| | - Jeff Sekelsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164
| | - Dale A Ramsden
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| |
Collapse
|
31
|
|
32
|
Walton RT, Christie KA, Whittaker MN, Kleinstiver BP. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science 2020; 368:290-296. [PMID: 32217751 DOI: 10.1126/science.aba8853] [Citation(s) in RCA: 641] [Impact Index Per Article: 160.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/16/2020] [Indexed: 12/18/2022]
Abstract
Manipulation of DNA by CRISPR-Cas enzymes requires the recognition of a protospacer-adjacent motif (PAM), limiting target site recognition to a subset of sequences. To remove this constraint, we engineered variants of Streptococcus pyogenes Cas9 (SpCas9) to eliminate the NGG PAM requirement. We developed a variant named SpG that is capable of targeting an expanded set of NGN PAMs, and we further optimized this enzyme to develop a near-PAMless SpCas9 variant named SpRY (NRN and to a lesser extent NYN PAMs). SpRY nuclease and base-editor variants can target almost all PAMs, exhibiting robust activities on a wide range of sites with NRN PAMs in human cells and lower but substantial activity on those with NYN PAMs. Using SpG and SpRY, we generated previously inaccessible disease-relevant genetic variants, supporting the utility of high-resolution targeting across genome editing applications.
Collapse
Affiliation(s)
- Russell T Walton
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kathleen A Christie
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Madelynn N Whittaker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA. .,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
33
|
Kan Y, Hendrickson EA. Conversion Tract Analysis of Homology-Directed Genome Editing Using Oligonucleotide Donors. Methods Mol Biol 2020; 1999:131-144. [PMID: 31127573 DOI: 10.1007/978-1-4939-9500-4_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Homology-directed genome editing is the intentional alteration of an endogenous genetic locus using information from an exogenous homology donor. A conversion tract is defined as the amount of genetic information that is converted from the homology donor to a given strand of the targeted chromosomal locus. Because of this, conversion tract analysis retrospectively not only elucidates the mechanism of homology-directed genome editing but also provides valuable insights on the conversion efficiency of every nucleotide in the homology donor. Here we describe a blue fluorescent protein-to-green fluorescent protein conversion system that can be conveniently used to measure the efficiency and analyze the lengths of conversion tracts of homology-directed genome editing using oligonucleotide donors in mammalian cells.
Collapse
Affiliation(s)
| | - Eric A Hendrickson
- BMBB Department, University of Minnesota Medical School, Minneapolis, MN, USA.
| |
Collapse
|
34
|
Li Y, Li X, Qu J, Luo D, Hu Z. Cas9 Mediated Correction of β-catenin Mutation and Restoring the Expression of Protein Phosphorylation in Colon Cancer HCT-116 Cells Decrease Cell Proliferation in vitro and Hamper Tumor Growth in Mice in vivo. Onco Targets Ther 2020; 13:17-29. [PMID: 32021251 PMCID: PMC6954092 DOI: 10.2147/ott.s225556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
Purpose Colorectal cancer (CRC) is one of the major contributors to cancer mortality and morbidity. Finding strategies to fight against CRC is urgently required. Mutations in driver genes of APC or β-catenin play an important role in the occurrence and progression of CRC. In the present study, we jointly apply CRISPR/Cas9-sgRNA system and Single-stranded oligodeoxynucleotide (ssODN) as templates to correct a heterozygous ΔTCT deletion mutation of β-catenin present in a colon cancer cell line HCT-116. This method provides a potential strategy in gene therapy for cancer. Methods A Cas9/β-catenin-sgRNA-eGFP co-expression vector was constructed and co-transfected with ssODN into HCT-116 cells. Mutation-corrected single-cell clones were sorted by FACS and judged by TA cloning and DNA sequencing. Effects of CRISPR/Cas9-mediated correction were tested by real-time quantitative PCR, Western blotting, CCK8, EDU dyeing and cell-plated clones. Moreover, the growth of cell clones derived tumors was analyzed at nude mice xenografts. Results CRISPR/Cas9-mediated β-catenin mutation correction resulted in the presence of TCT sequence and the re-expression of phosphorylation β-catenin at Ser45, which restored the normal function of phosphorylation β-catenin including reduction of the transportation of nuclear β-catenin and the expression of downstream c-myc, survivin. Significantly reduced cell growth was observed in β-catenin mutation-corrected cells. Mice xenografted with mutation-corrected HCT-116 cells showed significantly smaller tumor size than uncorrected xenografts. Conclusion The data of this study documented that correction of the driven mutation by the combination of CRISPR/Cas9 and ssODN could greatly remedy the biological behavior of the cancer cell line, suggesting a potential application of this strategy in gene therapy of cancer.
Collapse
Affiliation(s)
- Yanlan Li
- Translational Medicine Institute, the First People's Hospital of Chenzhou Affiliated to University of South China, Hunan 432000, People's Republic of China.,Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hunan 421001, People's Republic of China
| | - Xiangning Li
- Translational Medicine Institute, the First People's Hospital of Chenzhou Affiliated to University of South China, Hunan 432000, People's Republic of China.,National & Local Joint Engineering Laboratory for High-Through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, Hunan 432000, People's Republic of China
| | - Jiayao Qu
- Translational Medicine Institute, the First People's Hospital of Chenzhou Affiliated to University of South China, Hunan 432000, People's Republic of China.,National & Local Joint Engineering Laboratory for High-Through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, Hunan 432000, People's Republic of China
| | - Dixian Luo
- Translational Medicine Institute, the First People's Hospital of Chenzhou Affiliated to University of South China, Hunan 432000, People's Republic of China.,National & Local Joint Engineering Laboratory for High-Through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, Hunan 432000, People's Republic of China
| | - Zheng Hu
- Translational Medicine Institute, the First People's Hospital of Chenzhou Affiliated to University of South China, Hunan 432000, People's Republic of China.,National & Local Joint Engineering Laboratory for High-Through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, Hunan 432000, People's Republic of China
| |
Collapse
|
35
|
Li S, Xia L. Precise gene replacement in plants through CRISPR/Cas genome editing technology: current status and future perspectives. ABIOTECH 2020; 1:58-73. [PMID: 36305005 PMCID: PMC9590512 DOI: 10.1007/s42994-019-00009-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/08/2019] [Indexed: 12/01/2022]
Abstract
CRISPR/Cas, as a simple, versatile, robust and cost-effective system for genome manipulation, has dominated the genome editing field over the past few years. The application of CRISPR/Cas in crop improvement is particularly important in the context of global climate change, as well as diverse agricultural, environmental and ecological challenges. Various CRISPR/Cas toolboxes have been developed and allow for targeted mutagenesis at specific genome loci, transcriptome regulation and epigenome editing, base editing, and precise targeted gene/allele replacement or tagging in plants. In particular, precise replacement of an existing allele with an elite allele in a commercial variety through homology-directed repair (HDR) is a holy grail in genome editing for crop improvement as it has been very difficult, laborious and time-consuming to introgress the elite alleles into commercial varieties without any linkage drag from parental lines within a few generations in crop breeding practice. However, it still remains very challenging in crop plants. This review intends to provide an informative summary of the latest development and breakthroughs in gene replacement using CRISPR/Cas technology, with a focus on achievements, potential mechanisms and future perspectives in plant biological science as well as crop improvement.
Collapse
Affiliation(s)
- Shaoya Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
| | - Lanqin Xia
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
| |
Collapse
|
36
|
Sansbury BM, Hewes AM, Kmiec EB. Understanding the diversity of genetic outcomes from CRISPR-Cas generated homology-directed repair. Commun Biol 2019; 2:458. [PMID: 31840103 PMCID: PMC6898364 DOI: 10.1038/s42003-019-0705-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023] Open
Abstract
As CRISPR-Cas systems advance toward clinical application, it is essential to identify all the outcomes of gene-editing activity in human cells. Reports highlighting the remarkable success of homology-directed repair (HDR) in the treatment of inherited diseases may inadvertently underreport the collateral activity of this remarkable technology. We are utilizing an in vitro gene-editing system in which a CRISPR-Cas complex provides the double-stranded cleavage and a mammalian cell-free extract provides the enzymatic activity to promote non-homologous end joining, micro-homology mediated end joining, and homology-directed repair. Here, we detail the broad spectrum of gene-editing reaction outcomes utilizing Cas9 and Cas12a in combination with single-stranded donor templates of the sense and nonsense polarity. This system offers the opportunity to see the range of outcomes of gene-editing reactions in an unbiased fashion, detailing the distribution of DNA repair outcomes as a function of a set of genetic tools.
Collapse
Affiliation(s)
- Brett M. Sansbury
- Gene Editing Institute, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE USA
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE USA
| | - Amanda M. Hewes
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE USA
| | - Eric B. Kmiec
- Gene Editing Institute, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE USA
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE USA
| |
Collapse
|
37
|
Advances in genome editing through control of DNA repair pathways. Nat Cell Biol 2019; 21:1468-1478. [PMID: 31792376 DOI: 10.1038/s41556-019-0425-z] [Citation(s) in RCA: 221] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 10/25/2019] [Indexed: 02/06/2023]
Abstract
Eukaryotic cells deploy overlapping repair pathways to resolve DNA damage. Advancements in genome editing take advantage of these pathways to produce permanent genetic changes. Despite recent improvements, genome editing can produce diverse outcomes that can introduce risks in clinical applications. Although homology-directed repair is attractive for its ability to encode precise edits, it is particularly difficult in human cells. Here we discuss the DNA repair pathways that underlie genome editing and strategies to favour various outcomes.
Collapse
|
38
|
Park SH, Lee CM, Dever DP, Davis TH, Camarena J, Srifa W, Zhang Y, Paikari A, Chang AK, Porteus MH, Sheehan VA, Bao G. Highly efficient editing of the β-globin gene in patient-derived hematopoietic stem and progenitor cells to treat sickle cell disease. Nucleic Acids Res 2019; 47:7955-7972. [PMID: 31147717 PMCID: PMC6735704 DOI: 10.1093/nar/gkz475] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/14/2019] [Accepted: 05/17/2019] [Indexed: 12/14/2022] Open
Abstract
Sickle cell disease (SCD) is a monogenic disorder that affects millions worldwide. Allogeneic hematopoietic stem cell transplantation is the only available cure. Here, we demonstrate the use of CRISPR/Cas9 and a short single-stranded oligonucleotide template to correct the sickle mutation in the β-globin gene in hematopoietic stem and progenitor cells (HSPCs) from peripheral blood or bone marrow of patients with SCD, with 24.5 ± 7.6% efficiency without selection. Erythrocytes derived from gene-edited cells showed a marked reduction of sickle cells, with the level of normal hemoglobin (HbA) increased to 25.3 ± 13.9%. Gene-corrected SCD HSPCs retained the ability to engraft when transplanted into non-obese diabetic (NOD)-SCID-gamma (NSG) mice with detectable levels of gene correction 16-19 weeks post-transplantation. We show that, by using a high-fidelity SpyCas9 that maintained the same level of on-target gene modification, the off-target effects including chromosomal rearrangements were significantly reduced. Taken together, our results demonstrate efficient gene correction of the sickle mutation in both peripheral blood and bone marrow-derived SCD HSPCs, a significant reduction in sickling of red blood cells, engraftment of gene-edited SCD HSPCs in vivo and the importance of reducing off-target effects; all are essential for moving genome editing based SCD treatment into clinical practice.
Collapse
Affiliation(s)
- So Hyun Park
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Timothy H Davis
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Waracharee Srifa
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Yankai Zhang
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alireza Paikari
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alicia K Chang
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Vivien A Sheehan
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| |
Collapse
|
39
|
Bollen Y, Post J, Koo BK, Snippert HJG. How to create state-of-the-art genetic model systems: strategies for optimal CRISPR-mediated genome editing. Nucleic Acids Res 2019; 46:6435-6454. [PMID: 29955892 PMCID: PMC6061873 DOI: 10.1093/nar/gky571] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/14/2018] [Indexed: 12/24/2022] Open
Abstract
Model systems with defined genetic modifications are powerful tools for basic research and translational disease modelling. Fortunately, generating state-of-the-art genetic model systems is becoming more accessible to non-geneticists due to advances in genome editing technologies. As a consequence, solely relying on (transient) overexpression of (mutant) effector proteins is no longer recommended since scientific standards increasingly demand genetic modification of endogenous loci. In this review, we provide up-to-date guidelines with respect to homology-directed repair (HDR)-mediated editing of mammalian model systems, aimed at assisting researchers in designing an efficient genome editing strategy.
Collapse
Affiliation(s)
- Yannik Bollen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands.,Medical Cell BioPhysics, MIRA Institute, University of Twente, Enschede, The Netherlands
| | - Jasmin Post
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, The Netherlands.,Oncode Institute, The Netherlands
| |
Collapse
|
40
|
Maizels N, Davis L. Initiation of homologous recombination at DNA nicks. Nucleic Acids Res 2019; 46:6962-6973. [PMID: 29986051 PMCID: PMC6101574 DOI: 10.1093/nar/gky588] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/04/2018] [Indexed: 12/14/2022] Open
Abstract
Discontinuities in only a single strand of the DNA duplex occur frequently, as a result of DNA damage or as intermediates in essential nuclear processes and DNA repair. Nicks are the simplest of these lesions: they carry clean ends bearing 3′-hydroxyl groups that can undergo ligation or prime new DNA synthesis. In contrast, single-strand breaks also interrupt only one DNA strand, but they carry damaged ends that require clean-up before subsequent steps in repair. Despite their apparent simplicity, nicks can have significant consequences for genome stability. The availability of enzymes that can introduce a nick almost anywhere in a large genome now makes it possible to systematically analyze repair of nicks. Recent experiments demonstrate that nicks can initiate recombination via pathways distinct from those active at double-strand breaks (DSBs). Recombination at targeted DNA nicks can be very efficient, and because nicks are intrinsically less mutagenic than DSBs, nick-initiated gene correction is useful for genome engineering and gene therapy. This review revisits some physiological examples of recombination at nicks, and outlines experiments that have demonstrated that nicks initiate homology-directed repair by distinctive pathways, emphasizing research that has contributed to our current mechanistic understanding of recombination at nicks in mammalian cells.
Collapse
Affiliation(s)
- Nancy Maizels
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Luther Davis
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195, USA
| |
Collapse
|
41
|
Harmsen T, Klaasen S, van de Vrugt H, Te Riele H. DNA mismatch repair and oligonucleotide end-protection promote base-pair substitution distal from a CRISPR/Cas9-induced DNA break. Nucleic Acids Res 2019; 46:2945-2955. [PMID: 29447381 PMCID: PMC5888797 DOI: 10.1093/nar/gky076] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 01/25/2018] [Indexed: 12/14/2022] Open
Abstract
Single-stranded oligodeoxyribonucleotide (ssODN)-mediated repair of CRISPR/Cas9-induced DNA double-strand breaks (DSB) can effectively be used to introduce small genomic alterations in a defined locus. Here, we reveal DNA mismatch repair (MMR) activity is crucial for efficient nucleotide substitution distal from the Cas9-induced DNA break when the substitution is instructed by the 3' half of the ssODN. Furthermore, protecting the ssODN 3' end with phosphorothioate linkages enhances MMR-dependent gene editing events. Our findings can be exploited to optimize efficiencies of nucleotide substitutions distal from the DSB and imply that oligonucleotide-mediated gene editing is effectuated by templated break repair.
Collapse
Affiliation(s)
- Tim Harmsen
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Sjoerd Klaasen
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Henri van de Vrugt
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Department of Clinical Genetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Hein Te Riele
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| |
Collapse
|
42
|
Skarnes WC, Pellegrino E, McDonough JA. Improving homology-directed repair efficiency in human stem cells. Methods 2019; 164-165:18-28. [PMID: 31216442 DOI: 10.1016/j.ymeth.2019.06.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 11/30/2022] Open
Abstract
The generation of induced pluripotent stem cell models of human disease requires efficient modification of one or both alleles depending on dominant or recessive inheritance of the disease. To faithfully recapitulate many disease variants, the introduction of a single base change is required. The introduction of additional silent mutations designed to prevent re-cutting of the modified allele by Cas9 is not an optimal strategy, particularly for non-coding variants. Here, we developed an improved protocol for efficient engineering of single nucleotide variants in human iPS cells. Using a fluorescent BFP->GFP assay to monitor the incorporation of a single base pair change, we optimized the protocol to achieve HDR in 70% of unselected human iPS cells. The additive effects of cold shock, a small molecule enhancer of HDR and chemically modified ssODN dramatically shift the bias of repair in favor of HDR, resulting in a seven-fold higher ratio of HDR to NHEJ from 0.5 to 3.7.
Collapse
Affiliation(s)
- William C Skarnes
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | | | | |
Collapse
|
43
|
Abstract
Abstract
The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-Cas systems for genome editing has transformed the way life science research is conducted and holds enormous potential for the treatment of disease as well as for many aspects of biotechnology. Here, I provide a personal perspective on the development of CRISPR-Cas9 for genome editing within the broader context of the field and discuss our work to discover novel Cas effectors and develop them into additional molecular tools. The initial demonstration of Cas9-mediated genome editing launched the development of many other technologies, enabled new lines of biological inquiry, and motivated a deeper examination of natural CRISPR-Cas systems, including the discovery of new types of CRISPR-Cas systems. These new discoveries in turn spurred further technological developments. I review these exciting discoveries and technologies as well as provide an overview of the broad array of applications of these technologies in basic research and in the improvement of human health. It is clear that we are only just beginning to unravel the potential within microbial diversity, and it is quite likely that we will continue to discover other exciting phenomena, some of which it may be possible to repurpose as molecular technologies. The transformation of mysterious natural phenomena to powerful tools, however, takes a collective effort to discover, characterize, and engineer them, and it has been a privilege to join the numerous researchers who have contributed to this transformation of CRISPR-Cas systems.
Collapse
|
44
|
Rees HA, Yeh WH, Liu DR. Development of hRad51-Cas9 nickase fusions that mediate HDR without double-stranded breaks. Nat Commun 2019; 10:2212. [PMID: 31101808 PMCID: PMC6525190 DOI: 10.1038/s41467-019-09983-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/04/2019] [Indexed: 12/20/2022] Open
Abstract
In mammalian cells, double-stranded DNA breaks (DSBs) are preferentially repaired through end-joining processes that generally lead to mixtures of insertions and deletions (indels) or other rearrangements at the cleavage site. In the presence of homologous DNA, homology-directed repair (HDR) can generate specific mutations, albeit typically with modest efficiency and a low ratio of HDR products:indels. Here, we develop hRad51 mutants fused to Cas9(D10A) nickase (RDN) that mediate HDR while minimizing indels. We use RDN to install disease-associated point mutations in HEK293T cells with comparable or better efficiency than Cas9 nuclease and a 2.7-to-53-fold higher ratio of desired HDR product:undesired byproducts. Across five different human cell types, RDN variants generally result in higher HDR:indel ratios and lower off-target activity than Cas9 nuclease, although HDR efficiencies remain strongly site- and cell type-dependent. RDN variants provide precision editing options in cell types amenable to HDR, especially when byproducts of DSBs must be minimized.
Collapse
Affiliation(s)
- Holly A Rees
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Wei-Hsi Yeh
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, 02115, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02142, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
| |
Collapse
|
45
|
Porter SN, Levine RM, Pruett-Miller SM. A Practical Guide to Genome Editing Using Targeted Nuclease Technologies. Compr Physiol 2019; 9:665-714. [PMID: 30873595 DOI: 10.1002/cphy.c180022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome engineering using programmable nucleases is a rapidly evolving technique that enables precise genetic manipulations within complex genomes. Although this technology first surfaced with the creation of meganucleases, zinc finger nucleases, and transcription activator-like effector nucleases, CRISPR-Cas9 has been the most widely adopted platform because of its ease of use. This comprehensive review presents a basic overview of genome engineering and discusses the major technological advances in the field. In addition to nucleases, we discuss CRISPR-derived base editors and epigenetic modifiers. We also delve into practical applications of these tools, including creating custom-edited cell and animal models as well as performing genetic screens. Finally, we discuss the potential for therapeutic applications and ethical considerations related to employing this technology in humans. © 2019 American Physiological Society. Compr Physiol 9:665-714, 2019.
Collapse
Affiliation(s)
- Shaina N Porter
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rachel M Levine
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| |
Collapse
|
46
|
Strategies for Efficient Genome Editing Using CRISPR-Cas9. Genetics 2019; 211:431-457. [PMID: 30504364 PMCID: PMC6366907 DOI: 10.1534/genetics.118.301775] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/29/2018] [Indexed: 02/07/2023] Open
Abstract
The targetable DNA endonuclease CRISPR-Cas9 has transformed analysis of biological processes by enabling robust genome editing in model and nonmodel organisms. Although rules directing Cas9 to its target DNA via a guide RNA are straightforward, wide variation occurs in editing efficiency and repair outcomes for both imprecise error-prone repair and precise templated repair. We found that imprecise and precise DNA repair from double-strand breaks (DSBs) is asymmetric, favoring repair in one direction. Using this knowledge, we designed RNA guides and repair templates that increased the frequency of imprecise insertions and deletions and greatly enhanced precise insertion of point mutations in Caenorhabditis elegans We also devised strategies to insert long (10 kb) exogenous sequences and incorporate multiple nucleotide substitutions at a considerable distance from DSBs. We expanded the repertoire of co-conversion markers appropriate for diverse nematode species. These selectable markers enable rapid identification of Cas9-edited animals also likely to carry edits in desired targets. Lastly, we explored the timing, location, frequency, sex dependence, and categories of DSB repair events by developing loci with allele-specific Cas9 targets that can be contributed during mating from either male or hermaphrodite germ cells. We found a striking difference in editing efficiency between maternally and paternally contributed genomes. Furthermore, imprecise repair and precise repair from exogenous repair templates occur with high frequency before and after fertilization. Our strategies enhance Cas9-targeting efficiency, lend insight into the timing and mechanisms of DSB repair, and establish guidelines for achieving predictable precise and imprecise repair outcomes with high frequency.
Collapse
|
47
|
van de Vrugt HJ, Harmsen T, Riepsaame J, Alexantya G, van Mil SE, de Vries Y, Bin Ali R, Huijbers IJ, Dorsman JC, Wolthuis RMF, Te Riele H. Effective CRISPR/Cas9-mediated correction of a Fanconi anemia defect by error-prone end joining or templated repair. Sci Rep 2019; 9:768. [PMID: 30683899 PMCID: PMC6347620 DOI: 10.1038/s41598-018-36506-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022] Open
Abstract
Fanconi anemia (FA) is a cancer predisposition syndrome characterized by congenital abnormalities, bone marrow failure, and hypersensitivity to aldehydes and crosslinking agents. For FA patients, gene editing holds promise for therapeutic applications aimed at functionally restoring mutated genes in hematopoietic stem cells. However, intrinsic FA DNA repair defects may obstruct gene editing feasibility. Here, we report on the CRISPR/Cas9-mediated correction of a disruptive mutation in Fancf. Our experiments revealed that gene editing could effectively restore Fancf function via error-prone end joining resulting in a 27% increased survival in the presence of mitomycin C. In addition, templated gene correction could be achieved after double strand or single strand break formation. Although templated gene editing efficiencies were low (≤6%), FA corrected embryonic stem cells acquired a strong proliferative advantage over non-corrected cells, even without imposing genotoxic stress. Notably, Cas9 nickase activity resulted in mono-allelic gene editing and avoidance of undesired mutagenesis. In conclusion: DNA repair defects associated with FANCF deficiency do not prohibit CRISPR/Cas9 gene correction. Our data provide a solid basis for the application of pre-clinical models to further explore the potential of gene editing against FA, with the eventual aim to obtain therapeutic strategies against bone marrow failure.
Collapse
Affiliation(s)
- Henri J van de Vrugt
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. .,Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands.
| | - Tim Harmsen
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Joey Riepsaame
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Genome Engineering Oxford, Sir William Dunn School of Pathology, University of Oxford South Parks Road, OX1 3RE, Oxford, UK
| | - Georgina Alexantya
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Saskia E van Mil
- Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands
| | - Yne de Vries
- Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands
| | - Rahmen Bin Ali
- Mouse Clinic for Cancer and Aging research (MCCA) Transgenic Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Ivo J Huijbers
- Mouse Clinic for Cancer and Aging research (MCCA) Transgenic Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Josephine C Dorsman
- Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands
| | - Rob M F Wolthuis
- Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands
| | - Hein Te Riele
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. .,Section of Oncogenetics, Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam University Medical Centers, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands.
| |
Collapse
|
48
|
Que Q, Chen Z, Kelliher T, Skibbe D, Dong S, Chilton MD. Plant DNA Repair Pathways and Their Applications in Genome Engineering. Methods Mol Biol 2019; 1917:3-24. [PMID: 30610624 DOI: 10.1007/978-1-4939-8991-1_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Remarkable progress in the development of technologies for sequence-specific modification of primary DNA sequences has enabled the precise engineering of crops with novel characteristics. These programmable sequence-specific modifiers include site-directed nucleases (SDNs) and base editors (BEs). Currently, these genome editing machineries can be targeted to specific chromosomal locations to induce sequence changes. However, the sequence mutation outcomes are often greatly influenced by the type of DNA damage being generated, the status of host DNA repair machinery, and the presence and structure of DNA repair donor molecule. The outcome of sequence modification from repair of DNA double-strand breaks (DSBs) is often uncontrollable, resulting in unpredictable sequence insertions or deletions of various sizes. For base editing, the precision of intended edits is much higher, but the efficiency can vary greatly depending on the type of BE used or the activity of the endogenous DNA repair systems. This article will briefly review the possible DNA repair pathways present in the plant cells commonly used for generating edited variants for genome engineering applications. We will discuss the potential use of DNA repair mechanisms for developing and improving methodologies to enhance genome engineering efficiency and to direct DNA repair processes toward the desired outcomes.
Collapse
Affiliation(s)
- Qiudeng Que
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA.
| | - Zhongying Chen
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Tim Kelliher
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - David Skibbe
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Shujie Dong
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Mary-Dell Chilton
- Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| |
Collapse
|
49
|
Bruntraeger M, Byrne M, Long K, Bassett AR. Editing the Genome of Human Induced Pluripotent Stem Cells Using CRISPR/Cas9 Ribonucleoprotein Complexes. Methods Mol Biol 2019; 1961:153-183. [PMID: 30912046 DOI: 10.1007/978-1-4939-9170-9_11] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Genome editing using the CRISPR/Cas9 system has rapidly established itself as an essential tool in the genetic manipulation of many organisms, including human cell lines. Its application to human induced pluripotent stem cells (hiPSCs) allows for the generation of isogenic cell pairs that differ in a single genetic lesion, and therefore the identification and characterization of causal genetic variants. We describe a simple, effective approach to perform delicate manipulations of the genome of hiPSCs through delivery of Cas9 RNPs along with ssDNA oligonucleotide repair templates that can generate mutations in up to 98% of single cell clones and introduce single nucleotide changes at an efficiency of up to 40%. We describe our use of a T7 endonuclease assay to identify active guide RNAs, and a high-throughput sequencing genotyping strategy that allows the identification of correctly edited clones. We also present our experiences of generating single nucleotide changes at 15 sites, which show considerable variability between both guides and target sites in the efficiency at which such changes can be introduced.
Collapse
Affiliation(s)
| | - Meg Byrne
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kathleen Long
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Andrew R Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| |
Collapse
|
50
|
Ran Y, Patron N, Kay P, Wong D, Buchanan M, Cao Y, Sawbridge T, Davies JP, Mason J, Webb SR, Spangenberg G, Ainley WM, Walsh TA, Hayden MJ. Zinc finger nuclease-mediated precision genome editing of an endogenous gene in hexaploid bread wheat (Triticum aestivum) using a DNA repair template. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:2088-2101. [PMID: 29734518 PMCID: PMC6230953 DOI: 10.1111/pbi.12941] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/03/2018] [Accepted: 04/17/2018] [Indexed: 05/07/2023]
Abstract
Sequence-specific nucleases have been used to engineer targeted genome modifications in various plants. While targeted gene knockouts resulting in loss of function have been reported with relatively high rates of success, targeted gene editing using an exogenously supplied DNA repair template and site-specific transgene integration has been more challenging. Here, we report the first application of zinc finger nuclease (ZFN)-mediated, nonhomologous end-joining (NHEJ)-directed editing of a native gene in allohexaploid bread wheat to introduce, via a supplied DNA repair template, a specific single amino acid change into the coding sequence of acetohydroxyacid synthase (AHAS) to confer resistance to imidazolinone herbicides. We recovered edited wheat plants having the targeted amino acid modification in one or more AHAS homoalleles via direct selection for resistance to imazamox, an AHAS-inhibiting imidazolinone herbicide. Using a cotransformation strategy based on chemical selection for an exogenous marker, we achieved a 1.2% recovery rate of edited plants having the desired amino acid change and a 2.9% recovery of plants with targeted mutations at the AHAS locus resulting in a loss-of-function gene knockout. The latter results demonstrate a broadly applicable approach to introduce targeted modifications into native genes for nonselectable traits. All ZFN-mediated changes were faithfully transmitted to the next generation.
Collapse
Affiliation(s)
- Yidong Ran
- Genovo Biotechnology Co. LtdTianjinChina
| | | | - Pippa Kay
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Debbie Wong
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Margaret Buchanan
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Ying‐Ying Cao
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
| | - Tim Sawbridge
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
| | | | - John Mason
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
| | | | - German Spangenberg
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
| | | | | | - Matthew J. Hayden
- Department of Economic Development, Jobs, Transport and ResourcesCentre for AgriBioscienceAgriculture Victoria ResearchAgriBioBundooraVic.Australia
- School of Applied BiologyLa Trobe UniversityBundooraVic.Australia
| |
Collapse
|