1
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Vora DS, Bhandari SM, Sundar D. DNA shape features improve prediction of CRISPR/Cas9 activity. Methods 2024; 226:120-126. [PMID: 38641083 DOI: 10.1016/j.ymeth.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/27/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
The CRISPR/Cas9 genome editing technology has transformed basic and translational research in biology and medicine. However, the advances are hindered by off-target effects and a paucity in the knowledge of the mechanism of the Cas9 protein. Machine learning models have been proposed for the prediction of Cas9 activity at unintended sites, yet feature engineering plays a major role in the outcome of the predictors. This study evaluates the improvement in the performance of similar predictors upon inclusion of epigenetic and DNA shape feature groups in the conventionally used sequence-based Cas9 target and off-target datasets. The approach involved the utilization of neural networks trained on a diverse range of parameters, allowing us to systematically assess the performance increase for the meticulously designed datasets- (i) sequence only, (ii) sequence and epigenetic features, and (iii) sequence, epigenetic and DNA shape feature datasets. The addition of DNA shape information significantly improved predictive performance, evaluated by Akaike and Bayesian information criteria. The evaluation of individual feature importance by permutation and LIME-based methods also indicates that not only sequence features like mismatches and nucleotide composition, but also base pairing parameters like opening and stretch, that are indicative of distortion in the DNA-RNA hybrid in the presence of mismatches, influence model outcomes.
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Affiliation(s)
- Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India.
| | - Sakshi Manoj Bhandari
- Department of Mathematics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India; School of Artificial Intelligence, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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2
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Longo GMC, Sayols S, Kotini AG, Heinen S, Möckel MM, Beli P, Roukos V. Linking CRISPR-Cas9 double-strand break profiles to gene editing precision with BreakTag. Nat Biotechnol 2024:10.1038/s41587-024-02238-8. [PMID: 38740992 DOI: 10.1038/s41587-024-02238-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Cas9 can cleave DNA in both blunt and staggered configurations, resulting in distinct editing outcomes, but what dictates the type of Cas9 incisions is largely unknown. In this study, we developed BreakTag, a versatile method for profiling Cas9-induced DNA double-strand breaks (DSBs) and identifying the determinants of Cas9 incisions. Overall, we assessed cleavage by SpCas9 at more than 150,000 endogenous on-target and off-target sites targeted by approximately 3,500 single guide RNAs. We found that approximately 35% of SpCas9 DSBs are staggered, and the type of incision is influenced by DNA:gRNA complementarity and the use of engineered Cas9 variants. A machine learning model shows that Cas9 incision is dependent on the protospacer sequence and that human genetic variation impacts the configuration of Cas9 cuts and the DSB repair outcome. Matched datasets of Cas9 and engineered variant incisions with repair outcomes show that Cas9-mediated staggered breaks are linked with precise, templated and predictable single-nucleotide insertions, demonstrating that a scission-based gRNA design can be used to correct clinically relevant pathogenic single-nucleotide deletions.
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Affiliation(s)
| | - Sergi Sayols
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Andriana G Kotini
- Department of Biology, Medical School, University of Patras, Patras, Greece
| | - Sabine Heinen
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
- Johannes Gutenberg University (JGU), Mainz, Germany
| | - Vassilis Roukos
- Institute of Molecular Biology (IMB), Mainz, Germany.
- Department of Biology, Medical School, University of Patras, Patras, Greece.
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3
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Lemmens M, Dorsheimer L, Zeller A, Dietz-Baum Y. Non-clinical safety assessment of novel drug modalities: Genome safety perspectives on viral-, nuclease- and nucleotide-based gene therapies. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 896:503767. [PMID: 38821669 DOI: 10.1016/j.mrgentox.2024.503767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/08/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
Gene therapies have emerged as promising treatments for various conditions including inherited diseases as well as cancer. Ensuring their safe clinical application requires the development of appropriate safety testing strategies. Several guidelines have been provided by health authorities to address these concerns. These guidelines state that non-clinical testing should be carried out on a case-by-case basis depending on the modality. This review focuses on the genome safety assessment of frequently used gene therapy modalities, namely Adeno Associated Viruses (AAVs), Lentiviruses, designer nucleases and mRNAs. Important safety considerations for these modalities, amongst others, are vector integrations into the patient genome (insertional mutagenesis) and off-target editing. Taking into account the constraints of in vivo studies, health authorities endorse the development of novel approach methodologies (NAMs), which are innovative in vitro strategies for genotoxicity testing. This review provides an overview of NAMs applied to viral and CRISPR/Cas9 safety, including next generation sequencing-based methods for integration site analysis and off-target editing. Additionally, NAMs to evaluate the oncogenicity risk arising from unwanted genomic modifications are discussed. Thus, a range of promising techniques are available to support the safe development of gene therapies. Thorough validation, comparisons and correlations with clinical outcomes are essential to identify the most reliable safety testing strategies. By providing a comprehensive overview of these NAMs, this review aims to contribute to a better understanding of the genome safety perspectives of gene therapies.
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Affiliation(s)
| | - Lena Dorsheimer
- Research and Development, Preclinical Safety, Sanofi, Industriepark Hoechst, Frankfurt am Main 65926, Germany.
| | - Andreas Zeller
- Pharmaceutical Sciences, pRED Innovation Center Basel, Hoffmann-La Roche Ltd, Basel 4070, Switzerland
| | - Yasmin Dietz-Baum
- Research and Development, Preclinical Safety, Sanofi, Industriepark Hoechst, Frankfurt am Main 65926, Germany
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4
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Bischof J, Hierl M, Koller U. Emerging Gene Therapeutics for Epidermolysis Bullosa under Development. Int J Mol Sci 2024; 25:2243. [PMID: 38396920 PMCID: PMC10889532 DOI: 10.3390/ijms25042243] [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: 12/21/2023] [Revised: 02/01/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
The monogenetic disease epidermolysis bullosa (EB) is characterised by the formation of extended blisters and lesions on the patient's skin upon minimal mechanical stress. Causal for this severe condition are genetic mutations in genes, leading to the functional impairment, reduction, or absence of the encoded protein within the skin's basement membrane zone connecting the epidermis to the underlying dermis. The major burden of affected families justifies the development of long-lasting and curative therapies operating at the genomic level. The landscape of causal therapies for EB is steadily expanding due to recent breakthroughs in the gene therapy field, providing promising outcomes for patients suffering from this severe disease. Currently, two gene therapeutic approaches show promise for EB. The clinically more advanced gene replacement strategy was successfully applied in severe EB forms, leading to a ground-breaking in vivo gene therapy product named beremagene geperpavec (B-VEC) recently approved from the US Food and Drug Administration (FDA). In addition, the continuous innovations in both designer nucleases and gene editing technologies enable the efficient and potentially safe repair of mutations in EB in a potentially permanent manner, inspiring researchers in the field to define and reach new milestones in the therapy of EB.
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Affiliation(s)
- Johannes Bischof
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (J.B.); (M.H.)
| | - Markus Hierl
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (J.B.); (M.H.)
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria; (J.B.); (M.H.)
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5
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Lopes R, Prasad MK. Beyond the promise: evaluating and mitigating off-target effects in CRISPR gene editing for safer therapeutics. Front Bioeng Biotechnol 2024; 11:1339189. [PMID: 38390600 PMCID: PMC10883050 DOI: 10.3389/fbioe.2023.1339189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/29/2023] [Indexed: 02/24/2024] Open
Abstract
Over the last decade, CRISPR has revolutionized drug development due to its potential to cure genetic diseases that currently do not have any treatment. CRISPR was adapted from bacteria for gene editing in human cells in 2012 and, remarkably, only 11 years later has seen it's very first approval as a medicine for the treatment of sickle cell disease and transfusion-dependent beta-thalassemia. However, the application of CRISPR systems is associated with unintended off-target and on-target alterations (including small indels, and structural variations such as translocations, inversions and large deletions), which are a source of risk for patients and a vital concern for the development of safe therapies. In recent years, a wide range of methods has been developed to detect unwanted effects of CRISPR-Cas nuclease activity. In this review, we summarize the different methods for off-target assessment, discuss their strengths and limitations, and highlight strategies to improve the safety of CRISPR systems. Finally, we discuss their relevance and application for the pre-clinical risk assessment of CRISPR therapeutics within the current regulatory context.
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Affiliation(s)
- Rui Lopes
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Centre Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Megana K Prasad
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Centre Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
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6
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Störtz F, Mak JK, Minary P. piCRISPR: Physically informed deep learning models for CRISPR/Cas9 off-target cleavage prediction. ARTIFICIAL INTELLIGENCE IN THE LIFE SCIENCES 2023; 3:None. [PMID: 38047242 PMCID: PMC10316064 DOI: 10.1016/j.ailsci.2023.100075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/02/2023] [Accepted: 04/30/2023] [Indexed: 12/05/2023]
Abstract
CRISPR/Cas programmable nuclease systems have become ubiquitous in the field of gene editing. With progressing development, applications in in vivo therapeutic gene editing are increasingly within reach, yet limited by possible adverse side effects from unwanted edits. Recent years have thus seen continuous development of off-target prediction algorithms trained on in vitro cleavage assay data gained from immortalised cell lines. It has been shown that in contrast to experimental epigenetic features, computed physically informed features are so far underutilised despite bearing considerably larger correlation with cleavage activity. Here, we implement state-of-the-art deep learning algorithms and feature encodings for off-target prediction with emphasis on physically informed features that capture the biological environment of the cleavage site, hence terming our approach piCRISPR. Features were gained from the large, diverse crisprSQL off-target cleavage dataset. We find that our best-performing models highlight the importance of sequence context and chromatin accessibility for cleavage prediction and compare favourably with literature standard prediction performance. We further show that our novel, environmentally sensitive features are crucial to accurate prediction on sequence-identical locus pairs, making them highly relevant for clinical guide design. The source code and trained models can be found ready to use at github.com/florianst/picrispr.
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Affiliation(s)
- Florian Störtz
- Department of Computer Science, University of Oxford, Parks Road, Oxford OX1 3QD, UK
| | - Jeffrey K. Mak
- Department of Computer Science, University of Oxford, Parks Road, Oxford OX1 3QD, UK
| | - Peter Minary
- Department of Computer Science, University of Oxford, Parks Road, Oxford OX1 3QD, UK
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7
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Molugu K, Khajanchi N, Lazzarotto CR, Tsai SQ, Saha K. Trichostatin A for Efficient CRISPR-Cas9 Gene Editing of Human Pluripotent Stem Cells. CRISPR J 2023; 6:473-485. [PMID: 37676985 PMCID: PMC10611976 DOI: 10.1089/crispr.2023.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/31/2023] [Indexed: 09/09/2023] Open
Abstract
Genome-edited human-induced pluripotent stem cells (iPSCs) have broad applications in disease modeling, drug discovery, and regenerative medicine. Despite the development of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system, the gene editing process is inefficient and can take several weeks to months to generate edited iPSC clones. We developed a strategy to improve the efficiency of the iPSC gene editing process via application of a small-molecule, trichostatin A (TSA), a Class I and II histone deacetylase inhibitor. We observed that TSA decreased global chromatin condensation and further resulted in increased gene-editing efficiency of iPSCs by twofold to fourfold while concurrently ensuring no increased off-target effects. The edited iPSCs could be clonally expanded while maintaining genomic integrity and pluripotency. The rapid generation of therapeutically relevant gene-edited iPSCs could be enabled by these findings.
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Affiliation(s)
- Kaivalya Molugu
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Namita Khajanchi
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Biomedical and Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Cicera R. Lazzarotto
- Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shengdar Q. Tsai
- Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Krishanu Saha
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; St Jude Children's Research Hospital, Memphis, Tennessee, USA
- Department of Biomedical and Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and St Jude Children's Research Hospital, Memphis, Tennessee, USA
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8
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Kulcsár PI, Tálas A, Ligeti Z, Tóth E, Rakvács Z, Bartos Z, Krausz SL, Welker Á, Végi VL, Huszár K, Welker E. A cleavage rule for selection of increased-fidelity SpCas9 variants with high efficiency and no detectable off-targets. Nat Commun 2023; 14:5746. [PMID: 37717069 PMCID: PMC10505190 DOI: 10.1038/s41467-023-41393-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/04/2023] [Indexed: 09/18/2023] Open
Abstract
Streptococcus pyogenes Cas9 (SpCas9) has been employed as a genome engineering tool with a promising potential within therapeutics. However, its off-target effects present major safety concerns for applications requiring high specificity. Approaches developed to date to mitigate this effect, including any of the increased-fidelity (i.e., high-fidelity) SpCas9 variants, only provide efficient editing on a relatively small fraction of targets without detectable off-targets. Upon addressing this problem, we reveal a rather unexpected cleavability ranking of target sequences, and a cleavage rule that governs the on-target and off-target cleavage of increased-fidelity SpCas9 variants but not that of SpCas9-NG or xCas9. According to this rule, for each target, an optimal variant with matching fidelity must be identified for efficient cleavage without detectable off-target effects. Based on this insight, we develop here an extended set of variants, the CRISPRecise set, with increased fidelity spanning across a wide range, with differences in fidelity small enough to comprise an optimal variant for each target, regardless of its cleavability ranking. We demonstrate efficient editing with maximum specificity even on those targets that have not been possible in previous studies.
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Affiliation(s)
- Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zsófia Rakvács
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zsuzsa Bartos
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Sarah Laura Krausz
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Biospiral-2006 Ltd, Szeged, Hungary
- School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - Ágnes Welker
- Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Budapest, Hungary
- Gene Design Ltd, Szeged, Hungary
| | - Vanessza Laura Végi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Biospiral-2006 Ltd, Szeged, Hungary
| | - Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Gene Design Ltd, Szeged, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary.
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9
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Tian R, Cao C, He D, Dong D, Sun L, Liu J, Chen Y, Wang Y, Huang Z, Li L, Jin Z, Huang Z, Xie H, Zhao T, Zhong C, Hong Y, Hu Z. Massively parallel CRISPR off-target detection enables rapid off-target prediction model building. MED 2023; 4:478-492.e6. [PMID: 37279759 DOI: 10.1016/j.medj.2023.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 04/16/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND CRISPR (clustered regularly interspaced short palindromic repeats) genome editing holds tremendous potential in clinical translation. However, the off-target effect has always been a major concern. METHODS Here, we have developed a novel sensitive and specific off-target detection method, AID-seq (adaptor-mediated off-target identification by sequencing), that can comprehensively and faithfully detect the low-frequency off targets generated by different CRISPR nucleases (including Cas9 and Cas12a). FINDINGS Based on AID-seq, we developed a pooled strategy to simultaneously identify the on/off targets of multiple gRNAs, as well as using mixed human and human papillomavirus (HPV) genomes to screen the most efficient and safe targets from 416 HPV gRNA candidates for antiviral therapy. Moreover, we used the pooled strategy with 2,069 single-guide RNAs (sgRNAs) at a pool size of about 500 to profile the properties of our newly discovered CRISPR, FrCas9. Importantly, we successfully built an off-target detection model using these off-target data via the CRISPR-Net deep learning method (area under the receiver operating characteristic curve [AUROC] = 0.97, area under the precision recall curve [AUPRC] = 0.29). CONCLUSIONS To our knowledge, AID-seq is the most sensitive and specific in vitro off-target detection method to date. And the pooled AID-seq strategy can be used as a rapid and high-throughput platform to select the best sgRNAs and characterize the properties of new CRISPRs. FUNDING This work was supported by The National Natural Science Foundation of China (grant nos. 32171465 and 82102392), the General Program of Natural Science Foundation of Guangdong Province of China (grant no. 2021A1515012438), Guangdong Basic and Applied Basic Research Foundation (grant no. 2020A1515110170), and the National Ten Thousand Plan-Young Top Talents of China (grant no. 80000-41180002).
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Affiliation(s)
- Rui Tian
- Generulor Co., Ltd., Zhuhai 519000, Guangdong, China.
| | - Chen Cao
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Dan He
- Department of Neurology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China
| | - Dirong Dong
- Department of Gynecologic Oncology, Women and Children's Hospital Affiliated to Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China
| | - Lili Sun
- Department of Gynecologic Oncology, Women and Children's Hospital Affiliated to Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China
| | - Jiashuo Liu
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Ye Chen
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yuyan Wang
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zheying Huang
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Lifang Li
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zhuang Jin
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zhaoyue Huang
- Department of Gynecological Oncology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Hongxian Xie
- Generulor Co., Ltd., Zhuhai 519000, Guangdong, China
| | - Tingting Zhao
- Generulor Co., Ltd., Zhuhai 519000, Guangdong, China
| | - Chaoyue Zhong
- Generulor Co., Ltd., Zhuhai 519000, Guangdong, China
| | - Yongfeng Hong
- Generulor Co., Ltd., Zhuhai 519000, Guangdong, China
| | - Zheng Hu
- Department of Gynecologic Oncology, Women and Children's Hospital Affiliated to Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China; Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China; Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China; Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China.
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10
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Marchetti F, Cardoso R, Chen CL, Douglas GR, Elloway J, Escobar PA, Harper T, Heflich RH, Kidd D, Lynch AM, Myers MB, Parsons BL, Salk JJ, Settivari RS, Smith-Roe SL, Witt KL, Yauk CL, Young R, Zhang S, Minocherhomji S. Error-corrected next generation sequencing - Promises and challenges for genotoxicity and cancer risk assessment. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108466. [PMID: 37643677 DOI: 10.1016/j.mrrev.2023.108466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/12/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
Error-corrected Next Generation Sequencing (ecNGS) is rapidly emerging as a valuable, highly sensitive and accurate method for detecting and characterizing mutations in any cell type, tissue or organism from which DNA can be isolated. Recent mutagenicity and carcinogenicity studies have used ecNGS to quantify drug-/chemical-induced mutations and mutational spectra associated with cancer risk. ecNGS has potential applications in genotoxicity assessment as a new readout for traditional models, for mutagenesis studies in 3D organotypic cultures, and for detecting off-target effects of gene editing tools. Additionally, early data suggest that ecNGS can measure clonal expansion of mutations as a mechanism-agnostic early marker of carcinogenic potential and can evaluate mutational load directly in human biomonitoring studies. In this review, we discuss promising applications, challenges, limitations, and key data initiatives needed to enable regulatory testing and adoption of ecNGS - including for advancing safety assessment, augmenting weight-of-evidence for mutagenicity and carcinogenicity mechanisms, identifying early biomarkers of cancer risk, and managing human health risk from chemical exposures.
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Affiliation(s)
| | | | - Connie L Chen
- Health and Environmental Sciences Institute, Washington, DC, USA.
| | | | - Joanne Elloway
- Safety Sciences, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | - Tod Harper
- Amgen Research, Amgen Inc, Thousand Oaks, CA, USA
| | - Robert H Heflich
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | - Darren Kidd
- Labcorp Early Development Laboratories Limited, Harrogate, North Yorkshire, UK
| | | | - Meagan B Myers
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | - Barbara L Parsons
- US Food and Drug Administration/National Center for Toxicological Research, Jefferson, AR, USA
| | | | | | | | - Kristine L Witt
- NIEHS, Division of the National Toxicology Program, Research Triangle Park, NC, USA
| | | | - Robert Young
- MilliporeSigma, Rockville, MD, USA; Current: Consultant, Bethesda, MD, USA
| | | | - Sheroy Minocherhomji
- Amgen Research, Amgen Inc, Thousand Oaks, CA, USA; Current: Eli Lilly and Company, Indianapolis, IN, USA
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11
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Zou RS, Liu Y, Gaido OER, Konig MF, Mog BJ, Shen LL, Aviles-Vazquez F, Marin-Gonzalez A, Ha T. Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq. Nat Methods 2023; 20:706-713. [PMID: 37024653 PMCID: PMC10172116 DOI: 10.1038/s41592-023-01840-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/06/2023] [Indexed: 04/08/2023]
Abstract
Discovery of off-target CRISPR-Cas activity in patient-derived cells and animal models is crucial for genome editing applications, but currently exhibits low sensitivity. We demonstrate that inhibition of DNA-dependent protein kinase catalytic subunit accumulates the repair protein MRE11 at CRISPR-Cas-targeted sites, enabling high-sensitivity mapping of off-target sites to positions of MRE11 binding using chromatin immunoprecipitation followed by sequencing. This technique, termed DISCOVER-Seq+, discovered up to fivefold more CRISPR off-target sites in immortalized cell lines, primary human cells and mice compared with previous methods. We demonstrate applicability to ex vivo knock-in of a cancer-directed transgenic T cell receptor in primary human T cells and in vivo adenovirus knock-out of cardiovascular risk gene PCSK9 in mice. Thus, DISCOVER-Seq+ is, to our knowledge, the most sensitive method to-date for discovering off-target genome editing in vivo.
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Affiliation(s)
- Roger S Zou
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yang Liu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Oscar E Reyes Gaido
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Maximilian F Konig
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian J Mog
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leo L Shen
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Franklin Aviles-Vazquez
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alberto Marin-Gonzalez
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Taekjip Ha
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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12
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Guo C, Ma X, Gao F, Guo Y. Off-target effects in CRISPR/Cas9 gene editing. Front Bioeng Biotechnol 2023; 11:1143157. [PMID: 36970624 PMCID: PMC10034092 DOI: 10.3389/fbioe.2023.1143157] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Gene editing stands for the methods to precisely make changes to a specific nucleic acid sequence. With the recent development of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, gene editing has become efficient, convenient and programmable, leading to promising translational studies and clinical trials for both genetic and non-genetic diseases. A major concern in the applications of the CRISPR/Cas9 system is about its off-target effects, namely the deposition of unexpected, unwanted, or even adverse alterations to the genome. To date, many methods have been developed to nominate or detect the off-target sites of CRISPR/Cas9, which laid the basis for the successful upgrades of CRISPR/Cas9 derivatives with enhanced precision. In this review, we summarize these technological advancements and discuss about the current challenges in the management of off-target effects for future gene therapy.
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Affiliation(s)
- Congting Guo
- School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Institute of Cardiovascular Sciences, Beijing, China
| | - Xiaoteng Ma
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Fei Gao
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
- *Correspondence: Fei Gao, ; Yuxuan Guo,
| | - Yuxuan Guo
- School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Institute of Cardiovascular Sciences, Beijing, China
- Ministry of Education Key Laboratory of Molecular Cardiovascular Science, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
- *Correspondence: Fei Gao, ; Yuxuan Guo,
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13
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Wang H, Wang Y, Luo Z, Lin X, Liu M, Wu F, Shao H, Zhang W. Advances in Off-Target Detection for CRISPR-Based Genome Editing. Hum Gene Ther 2023; 34:112-128. [PMID: 36453226 DOI: 10.1089/hum.2022.198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based genome editing system exhibits marked potential for both gene editing and gene therapy, and its continuous improvement contributes to its great clinical potential. However, the largest hindrance to its application in clinical practice is the presence of off-target effects (OTEs). Thus, in addition to continuous optimization of the CRISPR system to reduce and eventually eliminate OTEs, further development of unbiased genome-wide detection of OTEs is key for its successful clinical application. This article summarizes detection strategies for OTEs of different CRISPR systems, to provide detailed guidance for the detection of OTEs in CRISPR-based genome editing.
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Affiliation(s)
- Haozheng Wang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and.,Department of Pharmacy, Meizhou People's Hospital, Meizhou, People's Republic of China
| | - Yangmin Wang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Zhongtao Luo
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Xinjian Lin
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Meilin Liu
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Fenglin Wu
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Hongwei Shao
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Wenfeng Zhang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
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14
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Brooks IR, Sheriff A, Moran D, Wang J, Jacków J. Challenges of Gene Editing Therapies for Genodermatoses. Int J Mol Sci 2023; 24:2298. [PMID: 36768619 PMCID: PMC9916788 DOI: 10.3390/ijms24032298] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Genodermatoses encompass a wide range of inherited skin diseases, many of which are monogenic. Genodermatoses range in severity and result in early-onset cancers or life-threatening damage to the skin, and there are few curative options. As such, there is a clinical need for single-intervention treatments with curative potential. Here, we discuss the nascent field of gene editing for the treatment of genodermatoses, exploring CRISPR-Cas9 and homology-directed repair, base editing, and prime editing tools for correcting pathogenic mutations. We specifically focus on the optimisation of editing efficiency, the minimisation off-targets edits, and the tools for delivery for potential future therapies. Honing each of these factors is essential for translating gene editing therapies into the clinical setting. Therefore, the aim of this review article is to raise important considerations for investigators aiming to develop gene editing approaches for genodermatoses.
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Affiliation(s)
| | | | | | | | - Joanna Jacków
- St John’s Institute of Dermatology, King’s College London, London SE1 9RT, UK
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15
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Tao J, Bauer DE, Chiarle R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat Commun 2023; 14:212. [PMID: 36639728 PMCID: PMC9838544 DOI: 10.1038/s41467-023-35886-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas gene editing has revolutionized experimental molecular biology over the past decade and holds great promise for the treatment of human genetic diseases. Here we review the development of CRISPR-Cas9/Cas12/Cas13 nucleases, DNA base editors, prime editors, and RNA base editors, focusing on the assessment and improvement of their editing precision and safety, pushing the limit of editing specificity and efficiency. We summarize the capabilities and limitations of each CRISPR tool from DNA editing to RNA editing, and highlight the opportunities for future improvements and applications in basic research, as well as the therapeutic and clinical considerations for their use in patients.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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16
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Kwon J, Kim M, Hwang W, Jo A, Hwang GH, Jung M, Kim UG, Cui G, Kim H, Eom JH, Hur JK, Lee J, Kim Y, Kim JS, Bae S, Lee JK. Extru-seq: a method for predicting genome-wide Cas9 off-target sites with advantages of both cell-based and in vitro approaches. Genome Biol 2023; 24:4. [PMID: 36627653 PMCID: PMC9832775 DOI: 10.1186/s13059-022-02842-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
We present a novel genome-wide off-target prediction method named Extru-seq and compare it with cell-based (GUIDE-seq), in vitro (Digenome-seq), and in silico methods using promiscuous guide RNAs with large numbers of valid off-target sites. Extru-seq demonstrates a high validation rate and retention of information about the intracellular environment, both beneficial characteristics of cell-based methods. Extru-seq also shows a low miss rate and could easily be performed in clinically relevant cell types with little optimization, which are major positive features of the in vitro methods. In summary, Extru-seq shows beneficial features of cell-based and in vitro methods.
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Affiliation(s)
| | | | - Woochang Hwang
- Department of Pre-Medicine, College of Medicine, Hanyang University, Seoul, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
| | - Anna Jo
- Toolgen, Seoul, Republic of Korea
| | - Gue-Ho Hwang
- Department of Chemistry, Hanyang University, Seoul, Republic of Korea
| | | | | | - Gang Cui
- Department of Ophthalmology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Heonseok Kim
- Department of Medicine, Division of Oncology, Stanford University, Stanford, USA
| | - Joon-Ho Eom
- National Institute of Food and Drug Safety Evaluation, Cheongju, Republic of Korea
| | - Junho K Hur
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
- Department of Genetics, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Junwon Lee
- Department of Ophthalmology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, Republic of Korea
| | - Sangsu Bae
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
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17
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Enabling Precision Medicine with CRISPR-Cas Genome Editing Technology: A Translational Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1396:315-339. [DOI: 10.1007/978-981-19-5642-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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18
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Kwon J, Kim M, Bae S, Jo A, Kim Y, Lee JK. TAPE-seq is a cell-based method for predicting genome-wide off-target effects of prime editor. Nat Commun 2022; 13:7975. [PMID: 36581624 PMCID: PMC9800413 DOI: 10.1038/s41467-022-35743-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Prime editors (PEs) are powerful tools that widen the possibilities for sequence modifications during genome editing. Although methods based on the analysis of Cas9 nuclease or nickase activity have been used to predict genome-wide off-target activities of PEs, no tool that directly uses PEs for this purpose has been reported yet. In this study, we present a cell-based assay, named TAgmentation of Prime Editor sequencing (TAPE-seq), that provides genome-wide off-target candidates for PEs. TAPE-seq analyses are successfully performed using many different versions of PEs. The TAPE-seq predictions are compared with results from two other off-site prediction methods, Cas9 nuclease-based GUIDE-seq and Cas9 nickase-based Digenome-seq (nDigenome-seq). TAPE-seq shows a lower miss rate, and a higher area under the receiver operating characteristic curve compared to the other methods. TAPE-seq also identified valid off-target sites that were missed by the other methods.
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Affiliation(s)
| | | | | | - Anna Jo
- grid.410909.5Toolgen, Seoul, Republic of Korea
| | - Youngho Kim
- grid.410909.5Toolgen, Seoul, Republic of Korea
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19
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Yu Z, Lu Z, Li J, Wang Y, Wu P, Li Y, Zhou Y, Li B, Zhang H, Liu Y, Ma L. PEAC-seq adopts Prime Editor to detect CRISPR off-target and DNA translocation. Nat Commun 2022; 13:7545. [PMID: 36509752 PMCID: PMC9744820 DOI: 10.1038/s41467-022-35086-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022] Open
Abstract
CRISPR technology holds significant promise for biological studies and gene therapies because of its high flexibility and efficiency when applied in mammalian cells. But endonuclease (e.g., Cas9) potentially generates undesired edits; thus, there is an urgent need to comprehensively identify off-target sites so that the genotoxicities can be accurately assessed. To date, it is still challenging to streamline the entire process to specifically label and efficiently enrich the cleavage sites from unknown genomic locations. Here we develop PEAC-seq, in which we adopt the Prime Editor to insert a sequence-optimized tag to the editing sites and enrich the tagged regions with site-specific primers for high throughput sequencing. Moreover, we demonstrate that PEAC-seq could identify DNA translocations, which are more genotoxic but usually overlooked by other off-target detection methods. As PEAC-seq does not rely on exogenous oligodeoxynucleotides to label the editing site, we also conduct in vivo off-target identification as proof of concept. In summary, PEAC-seq provides a comprehensive and streamlined strategy to identify CRISPR off-targeting sites in vitro and in vivo, as well as DNA translocation events. This technique further diversified the toolkit to evaluate the genotoxicity of CRISPR applications in research and clinics.
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Affiliation(s)
- Zhenxing Yu
- grid.8547.e0000 0001 0125 2443Fudan University, 220 Handan Road, 201100 Shanghai, China ,grid.494629.40000 0004 8008 9315Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, 600 Dunyu Road, 310030 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China
| | - Zhike Lu
- grid.494629.40000 0004 8008 9315Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, 600 Dunyu Road, 310030 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China
| | - Jingjing Li
- grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, 600 Dunyu Road, 310030 Hangzhou, Zhejiang China ,grid.33199.310000 0004 0368 7223Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, Hubei China
| | - Yingying Wang
- grid.8547.e0000 0001 0125 2443Fudan University, 220 Handan Road, 201100 Shanghai, China ,grid.494629.40000 0004 8008 9315Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, 600 Dunyu Road, 310030 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China
| | - Panfeng Wu
- grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, 600 Dunyu Road, 310030 Hangzhou, Zhejiang China ,grid.49470.3e0000 0001 2331 6153Department of Tissue and Embryology, School of Basic Medical Sciences, Wuhan University, 115 Donghu Road, 430071 Wuhan, Hubei China
| | - Yini Li
- grid.8547.e0000 0001 0125 2443Fudan University, 220 Handan Road, 201100 Shanghai, China ,grid.494629.40000 0004 8008 9315Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, 600 Dunyu Road, 310030 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China
| | - Yangfan Zhou
- grid.494629.40000 0004 8008 9315Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, 600 Dunyu Road, 310030 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China
| | - Bailun Li
- grid.494629.40000 0004 8008 9315Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, 600 Dunyu Road, 310030 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China
| | - Heng Zhang
- grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, 600 Dunyu Road, 310030 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China
| | - Yingzheng Liu
- grid.494629.40000 0004 8008 9315Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, 600 Dunyu Road, 310030 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China
| | - Lijia Ma
- grid.494629.40000 0004 8008 9315Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, 600 Dunyu Road, 310030 Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024 Hangzhou, Zhejiang China
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20
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Yamada N, Aruga A. Analysis of Off-target Effects and Risk Assessment Leading from Preclinical to Clinical Trials of Gene-edited Therapeutic Products. Ther Innov Regul Sci 2022; 57:538-551. [PMID: 36434373 DOI: 10.1007/s43441-022-00481-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Concerns about off-target effects (OTEs) of genomic DNA cleavages by gene-editing enzymes have been raised, especially for OTEs that go undetected due to technical limitations. Since no explicit guidelines have been in place for risk assessment of OTEs, the regulatory authorities' concept of an acceptable evaluation scheme for OTEs in the investigational drug application (IND) has not been clear. Here, we clarify the regulatory expectations by examining reports on OTE evaluations of leading gene-editing products that have achieved IND clearance. METHODS We collected and analyzed the gene-editing products that have entered clinical trials by searching on ClinicalTrials.gov and EU-Clinical-Trial-Registries, and related reports for OTE evaluations from Google Scholar, PubMed, and the developers' websites. RESULTS We found a common two-step verification method used for different products at the preclinical stage. First, numerous potential off-target loci (POLs) are listed with state-of-the-art high-sensitivity detection methods and theoretical screens; Second, these OTEs are checked by amplicon sequencing of the POLs after treatment by enzymes in in vitro models close to clinical use conditions. Only the OTEs that can be detected and verified are addressed in the risk assessment in the translational phase from preclinical to clinical study. DISCUSSION Here, we describe a clear scheme for risk assessment of OTEs at the key translational phase, based on the common features in protocols for gene-editing products that were cleared for use in clinical trials. This report will provide a guide for those newly attempting to conduct clinical development in this field.
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21
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Wienert B, Cromer MK. CRISPR nuclease off-target activity and mitigation strategies. Front Genome Ed 2022; 4:1050507. [PMID: 36439866 PMCID: PMC9685173 DOI: 10.3389/fgeed.2022.1050507] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
The discovery of CRISPR has allowed site-specific genomic modification to become a reality and this technology is now being applied in a number of human clinical trials. While this technology has demonstrated impressive efficacy in the clinic to date, there remains the potential for unintended on- and off-target effects of CRISPR nuclease activity. A variety of in silico-based prediction tools and empirically derived experimental methods have been developed to identify the most common unintended effect-small insertions and deletions at genomic sites with homology to the guide RNA. However, large-scale aberrations have recently been reported such as translocations, inversions, deletions, and even chromothripsis. These are more difficult to detect using current workflows indicating a major unmet need in the field. In this review we summarize potential sequencing-based solutions that may be able to detect these large-scale effects even at low frequencies of occurrence. In addition, many of the current clinical trials using CRISPR involve ex vivo isolation of a patient's own stem cells, modification, and re-transplantation. However, there is growing interest in direct, in vivo delivery of genome editing tools. While this strategy has the potential to address disease in cell types that are not amenable to ex vivo manipulation, in vivo editing has only one desired outcome-on-target editing in the cell type of interest. CRISPR activity in unintended cell types (both on- and off-target) is therefore a major safety as well as ethical concern in tissues that could enable germline transmission. In this review, we have summarized the strengths and weaknesses of current editing and delivery tools and potential improvements to off-target and off-tissue CRISPR activity detection. We have also outlined potential mitigation strategies that will ensure that the safety of CRISPR keeps pace with efficacy, a necessary requirement if this technology is to realize its full translational potential.
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Affiliation(s)
- Beeke Wienert
- Graphite Bio, Inc., South San Francisco, CA, United States
| | - M. Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States,Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA, United States,*Correspondence: M. Kyle Cromer,
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22
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Vora DS, Verma Y, Sundar D. A Machine Learning Approach to Identify the Importance of Novel Features for CRISPR/Cas9 Activity Prediction. Biomolecules 2022; 12:1123. [PMID: 36009017 PMCID: PMC9405635 DOI: 10.3390/biom12081123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
The reprogrammable CRISPR/Cas9 genome editing tool's growing popularity is hindered by unwanted off-target effects. Efforts have been directed toward designing efficient guide RNAs as well as identifying potential off-target threats, yet factors that determine efficiency and off-target activity remain obscure. Based on sequence features, previous machine learning models performed poorly on new datasets, thus there is a need for the incorporation of novel features. The binding energy estimation of the gRNA-DNA hybrid as well as the Cas9-gRNA-DNA hybrid allowed generating better performing machine learning models for the prediction of Cas9 activity. The analysis of feature contribution towards the model output on a limited dataset indicated that energy features played a determining role along with the sequence features. The binding energy features proved essential for the prediction of on-target activity and off-target sites. The plateau, in the performance on unseen datasets, of current machine learning models could be overcome by incorporating novel features, such as binding energy, among others. The models are provided on GitHub (GitHub Inc., San Francisco, CA, USA).
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Affiliation(s)
- Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Yugesh Verma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
- Yardi School of Artificial Intelligence, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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23
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Pan X, Qu K, Yuan H, Xiang X, Anthon C, Pashkova L, Liang X, Han P, Corsi GI, Xu F, Liu P, Zhong J, Zhou Y, Ma T, Jiang H, Liu J, Wang J, Jessen N, Bolund L, Yang H, Xu X, Church GM, Gorodkin J, Lin L, Luo Y. Massively targeted evaluation of therapeutic CRISPR off-targets in cells. Nat Commun 2022; 13:4049. [PMID: 35831290 PMCID: PMC9279339 DOI: 10.1038/s41467-022-31543-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Methods for sensitive and high-throughput evaluation of CRISPR RNA-guided nucleases (RGNs) off-targets (OTs) are essential for advancing RGN-based gene therapies. Here we report SURRO-seq for simultaneously evaluating thousands of therapeutic RGN OTs in cells. SURRO-seq captures RGN-induced indels in cells by pooled lentiviral OTs libraries and deep sequencing, an approach comparable and complementary to OTs detection by T7 endonuclease 1, GUIDE-seq, and CIRCLE-seq. Application of SURRO-seq to 8150 OTs from 110 therapeutic RGNs identifies significantly detectable indels in 783 OTs, of which 37 OTs are found in cancer genes and 23 OTs are further validated in five human cell lines by targeted amplicon sequencing. Finally, SURRO-seq reveals that thermodynamically stable wobble base pair (rG•dT) and free binding energy strongly affect RGN specificity. Our study emphasizes the necessity of thoroughly evaluating therapeutic RGN OTs to minimize inevitable off-target effects.
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Affiliation(s)
- Xiaoguang Pan
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Kunli Qu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biology, Copenhagen University, Copenhagen, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Hao Yuan
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xi Xiang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Liubov Pashkova
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Xue Liang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Giulia I Corsi
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Fengping Xu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Research, BGI-Shenzhen, Shenzhen, China
| | - Ping Liu
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Jiayan Zhong
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Yan Zhou
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Tao Ma
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Hui Jiang
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Junnian Liu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Jian Wang
- BGI-Research, BGI-Shenzhen, Shenzhen, China
| | - Niels Jessen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Huanming Yang
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Xun Xu
- BGI-Research, BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China
| | - George M Church
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- BGI-Research, BGI-Shenzhen, Shenzhen, China.
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
- IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
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24
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Abstract
The rapid development of CRISPR-Cas genome editing tools has greatly changed the way to conduct research and holds tremendous promise for clinical applications. During genome editing, CRISPR-Cas enzymes induce DNA breaks at the target sites and subsequently the DNA repair pathways are recruited to generate diverse editing outcomes. Besides off-target cleavage, unwanted editing outcomes including chromosomal structural variations and exogenous DNA integrations have recently raised concerns for clinical safety. To eliminate these unwanted editing byproducts, we need to explore the underlying mechanisms for the formation of diverse editing outcomes from the perspective of DNA repair. Here, we describe the involved DNA repair pathways in sealing Cas enzyme-induced DNA double-stranded breaks and discuss the origins and effects of unwanted editing byproducts on genome stability. Furthermore, we propose the potential risk of inhibiting DNA repair pathways to enhance gene editing. The recent combined studies of DNA repair and CRISPR-Cas editing provide a framework for further optimizing genome editing to enhance editing safety.
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25
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Ravendran S, Hernández SS, König S, Bak RO. CRISPR/Cas-Based Gene Editing Strategies for DOCK8 Immunodeficiency Syndrome. Front Genome Ed 2022; 4:793010. [PMID: 35373187 PMCID: PMC8969908 DOI: 10.3389/fgeed.2022.793010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/14/2022] [Indexed: 12/17/2022] Open
Abstract
Defects in the DOCK8 gene causes combined immunodeficiency termed DOCK8 immunodeficiency syndrome (DIDS). DIDS previously belonged to the disease category of autosomal recessive hyper IgE syndrome (AR-HIES) but is now classified as a combined immunodeficiency (CID). This genetic disorder induces early onset of susceptibility to severe recurrent viral and bacterial infections, atopic diseases and malignancy resulting in high morbidity and mortality. This pathological state arises from impairment of actin polymerization and cytoskeletal rearrangement, which induces improper immune cell migration-, survival-, and effector functions. Owing to the severity of the disease, early allogenic hematopoietic stem cell transplantation is recommended even though it is associated with risk of unintended adverse effects, the need for compatible donors, and high expenses. So far, no alternative therapies have been developed, but the monogenic recessive nature of the disease suggests that gene therapy may be applied. The advent of the CRISPR/Cas gene editing system heralds a new era of possibilities in precision gene therapy, and positive results from clinical trials have already suggested that the tool may provide definitive cures for several genetic disorders. Here, we discuss the potential application of different CRISPR/Cas-mediated genetic therapies to correct the DOCK8 gene. Our findings encourage the pursuit of CRISPR/Cas-based gene editing approaches, which may constitute more precise, affordable, and low-risk definitive treatment options for DOCK8 deficiency.
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26
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Fu R, He W, Dou J, Villarreal OD, Bedford E, Wang H, Hou C, Zhang L, Wang Y, Ma D, Chen Y, Gao X, Depken M, Xu H. Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity. Nat Commun 2022; 13:474. [PMID: 35078987 PMCID: PMC8789861 DOI: 10.1038/s41467-022-28028-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/04/2022] [Indexed: 12/20/2022] Open
Abstract
The specificity of CRISPR/Cas9 genome editing is largely determined by the sequences of guide RNA (gRNA) and the targeted DNA, yet the sequence-dependent rules underlying off-target effects are not fully understood. To systematically explore the sequence determinants governing CRISPR/Cas9 specificity, here we describe a dual-target system to measure the relative cleavage rate between off- and on-target sequences (off-on ratios) of 1902 gRNAs on 13,314 synthetic target sequences, and reveal a set of sequence rules involving 2 factors in off-targeting: 1) a guide-intrinsic mismatch tolerance (GMT) independent of the mismatch context; 2) an "epistasis-like" combinatorial effect of multiple mismatches, which are associated with the free-energy landscape in R-loop formation and are explainable by a multi-state kinetic model. These sequence rules lead to the development of MOFF, a model-based predictor of Cas9-mediated off-target effects. Moreover, the "epistasis-like" combinatorial effect suggests a strategy of allele-specific genome editing using mismatched guides. With the aid of MOFF prediction, this strategy significantly improves the selectivity and expands the application domain of Cas9-based allele-specific editing, as tested in a high-throughput allele-editing screen on 18 cancer hotspot mutations.
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Affiliation(s)
- Rongjie Fu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Wei He
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Jinzhuang Dou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Oscar D Villarreal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Ella Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Helen Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Connie Hou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Liang Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Yalong Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Dacheng Ma
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
- Department of Chemistry, Rice University, Houston, TX, 77005, USA
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA
| | - Martin Depken
- Kavli Institute of NanoScience and Department of BionanoScience, Delft University of Technology, Delft, 2629HZ, the Netherlands
| | - Han Xu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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27
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Liang SQ, Liu P, Smith JL, Mintzer E, Maitland S, Dong X, Yang Q, Lee J, Haynes CM, Zhu LJ, Watts JK, Sontheimer EJ, Wolfe SA, Xue W. Genome-wide detection of CRISPR editing in vivo using GUIDE-tag. Nat Commun 2022; 13:437. [PMID: 35064134 PMCID: PMC8782884 DOI: 10.1038/s41467-022-28135-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Analysis of off-target editing is an important aspect of the development of safe nuclease-based genome editing therapeutics. in vivo assessment of nuclease off-target activity has primarily been indirect (based on discovery in vitro, in cells or via computational prediction) or through ChIP-based detection of double-strand break (DSB) DNA repair factors, which can be cumbersome. Herein we describe GUIDE-tag, which enables one-step, off-target genome editing analysis in mouse liver and lung. The GUIDE-tag system utilizes tethering between the Cas9 nuclease and the DNA donor to increase the capture rate of nuclease-mediated DSBs and UMI incorporation via Tn5 tagmentation to avoid PCR bias. These components can be delivered as SpyCas9-mSA ribonucleoprotein complexes and biotin-dsDNA donor for in vivo editing analysis. GUIDE-tag enables detection of off-target sites where editing rates are ≥ 0.2%. UDiTaS analysis utilizing the same tagmented genomic DNA detects low frequency translocation events with off-target sites and large deletions in vivo. The SpyCas9-mSA and biotin-dsDNA system provides a method to capture DSB loci in vivo in a variety of tissues with a workflow that is amenable to analysis of gross genomic alterations that are associated with genome editing.
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Affiliation(s)
- Shun-Qing Liang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jordan L Smith
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Esther Mintzer
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Stacy Maitland
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Xiaolong Dong
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Qiyuan Yang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Cole M Haynes
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
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28
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Zhu D, Wang J, Yang D, Xi J, Li J. High-Throughput Profiling of Cas12a Orthologues and Engineered Variants for Enhanced Genome Editing Activity. Int J Mol Sci 2021; 22:ijms222413301. [PMID: 34948095 PMCID: PMC8706968 DOI: 10.3390/ijms222413301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas12a (formerly Cpf1), an RNA-guided endonuclease of the Class II Type V-A CRISPR system, provides a promising tool for genome engineering. Over 10 Cas12a orthologues have been identified and employed for gene editing in human cells. However, the functional diversity among emerging Cas12a orthologues remains poorly explored. Here, we report a high-throughput comparative profiling of editing activities across 16 Cas12a orthologues in human cells by constructing genome-integrated, self-cleaving, paired crRNA–target libraries containing >40,000 guide RNAs. Three Cas12a candidates exhibited promising potential owing to their compact structures and editing efficiency comparable with those of AsCas12a and LbCas12a, which are well characterized. We generated three arginine substitution variants (3Rv) via structure-guided protein engineering: BsCas12a-3Rv (K155R/N512R/K518R), PrCas12a-3Rv (E162R/N519R/K525R), and Mb3Cas12a-3Rv (D180R/N581R/K587R). All three Cas12a variants showed enhanced editing activities and expanded targeting ranges (NTTV, NTCV, and TRTV) compared with the wild-type Cas12a effectors. The base preference analysis among the three Cas12a variants revealed that PrCas12a-3Rv shows the highest activity at target sites with canonical PAM TTTV and non-canonical PAM TTCV, while Mb3Cas12a-3Rv exhibits recognition features distinct from the others by accommodating for more nucleotide A at position −3 for PAM TATV and at position −4 for PAM ATCV. Thus, the expanded Cas12a toolbox and an improved understanding of Cas12a activities should facilitate their use in genome engineering.
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Affiliation(s)
| | | | | | - Jianzhong Xi
- Correspondence: (J.X.); (J.L.); Tel.: +86-10-6276-0698 (J.X.); +86-10-6275-6627 (J.L.)
| | - Juan Li
- Correspondence: (J.X.); (J.L.); Tel.: +86-10-6276-0698 (J.X.); +86-10-6275-6627 (J.L.)
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29
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Kuzin A, Redler B, Onuska J, Slesarev A. RGEN-seq for highly sensitive amplification-free screen of off-target sites of gene editors. Sci Rep 2021; 11:23600. [PMID: 34880355 PMCID: PMC8654851 DOI: 10.1038/s41598-021-03160-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/29/2021] [Indexed: 11/24/2022] Open
Abstract
Sensitive detection of off-target sites produced by gene editing nucleases is crucial for developing reliable gene therapy platforms. Although several biochemical assays for the characterization of nuclease off-target effects have been recently published, significant technical and methodological issues still remain. Of note, existing methods rely on PCR amplification, tagging, and affinity purification which can introduce bias, contaminants, sample loss through handling, etc. Here we describe a sensitive, PCR-free next-generation sequencing method (RGEN-seq) for unbiased detection of double-stranded breaks generated by RNA-guided CRISPR-Cas9 endonuclease. Through use of novel sequencing adapters, the RGEN-Seq method saves time, simplifies workflow, and removes genomic coverage bias and gaps associated with PCR and/or other enrichment procedures. RGEN-seq is fully compatible with existing off-target detection software; moreover, the unbiased nature of RGEN-seq offers a robust foundation for relating assigned DNA cleavage scores to propensity for off-target mutations in cells. A detailed comparison of RGEN-seq with other off-target detection methods is provided using a previously characterized set of guide RNAs.
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Affiliation(s)
- Alexander Kuzin
- MilliporeSigma, 14920 Broschart Road, Rockville, MD, 20850, USA
| | - Brendan Redler
- MilliporeSigma, 14920 Broschart Road, Rockville, MD, 20850, USA
| | - Jaya Onuska
- MilliporeSigma, 14920 Broschart Road, Rockville, MD, 20850, USA
| | - Alexei Slesarev
- MilliporeSigma, 14920 Broschart Road, Rockville, MD, 20850, USA.
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30
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Niu R, Peng J, Zhang Z, Shang X. R-CRISPR: A Deep Learning Network to Predict Off-Target Activities with Mismatch, Insertion and Deletion in CRISPR-Cas9 System. Genes (Basel) 2021; 12:1878. [PMID: 34946828 PMCID: PMC8702036 DOI: 10.3390/genes12121878] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein 9 (Cas9) system is a groundbreaking gene-editing tool, which has been widely adopted in biomedical research. However, the guide RNAs in CRISPR-Cas9 system may induce unwanted off-target activities and further affect the practical application of the technique. Most existing in silico prediction methods that focused on off-target activities possess limited predictive precision and remain to be improved. Hence, it is necessary to propose a new in silico prediction method to address this problem. In this work, a deep learning framework named R-CRISPR is presented, which devises an encoding scheme to encode gRNA-target sequences into binary matrices, a convolutional neural network as feature extractor, and a recurrent neural network to predict off-target activities with mismatch, insertion, or deletion. It is demonstrated that R-CRISPR surpasses six mainstream prediction methods with a significant improvement on mismatch-only datasets verified by GUIDE-seq. Compared with the state-of-art prediction methods, R-CRISPR also achieves competitive performance on datasets with mismatch, insertion, and deletion. Furthermore, experiments show that data concatenate could influence the quality of training data, and investigate the optimal combination of datasets.
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Affiliation(s)
| | | | | | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi’an 710072, China; (R.N.); (J.P.); (Z.Z.)
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31
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Vicente MM, Chaves-Ferreira M, Jorge JMP, Proença JT, Barreto VM. The Off-Targets of Clustered Regularly Interspaced Short Palindromic Repeats Gene Editing. Front Cell Dev Biol 2021; 9:718466. [PMID: 34604217 PMCID: PMC8484971 DOI: 10.3389/fcell.2021.718466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/09/2021] [Indexed: 12/26/2022] Open
Abstract
The repurposing of the CRISPR/Cas bacterial defense system against bacteriophages as simple and flexible molecular tools has revolutionized the field of gene editing. These tools are now widely used in basic research and clinical trials involving human somatic cells. However, a global moratorium on all clinical uses of human germline editing has been proposed because the technology still lacks the required efficacy and safety. Here we focus on the approaches developed since 2013 to decrease the frequency of unwanted mutations (the off-targets) during CRISPR-based gene editing.
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Affiliation(s)
- Manuel M Vicente
- DNA Breaks Group, NOVA Medical School (NMS), Centro de Estudos de Doenças Crónicas (CEDOC), NOVA University of Lisbon, Lisbon, Portugal
| | - Miguel Chaves-Ferreira
- DNA Breaks Group, NOVA Medical School (NMS), Centro de Estudos de Doenças Crónicas (CEDOC), NOVA University of Lisbon, Lisbon, Portugal
| | - João M P Jorge
- DNA Breaks Group, NOVA Medical School (NMS), Centro de Estudos de Doenças Crónicas (CEDOC), NOVA University of Lisbon, Lisbon, Portugal
| | - João T Proença
- DNA Breaks Group, NOVA Medical School (NMS), Centro de Estudos de Doenças Crónicas (CEDOC), NOVA University of Lisbon, Lisbon, Portugal
| | - Vasco M Barreto
- DNA Breaks Group, NOVA Medical School (NMS), Centro de Estudos de Doenças Crónicas (CEDOC), NOVA University of Lisbon, Lisbon, Portugal
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32
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Atkins A, Chung CH, Allen AG, Dampier W, Gurrola TE, Sariyer IK, Nonnemacher MR, Wigdahl B. Off-Target Analysis in Gene Editing and Applications for Clinical Translation of CRISPR/Cas9 in HIV-1 Therapy. Front Genome Ed 2021; 3:673022. [PMID: 34713260 PMCID: PMC8525399 DOI: 10.3389/fgeed.2021.673022] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/21/2021] [Indexed: 12/26/2022] Open
Abstract
As genome-editing nucleases move toward broader clinical applications, the need to define the limits of their specificity and efficiency increases. A variety of approaches for nuclease cleavage detection have been developed, allowing a full-genome survey of the targeting landscape and the detection of a variety of repair outcomes for nuclease-induced double-strand breaks. Each approach has advantages and disadvantages relating to the means of target-site capture, target enrichment mechanism, cellular environment, false discovery, and validation of bona fide off-target cleavage sites in cells. This review examines the strengths, limitations, and origins of the different classes of off-target cleavage detection systems including anchored primer enrichment (GUIDE-seq), in situ detection (BLISS), in vitro selection libraries (CIRCLE-seq), chromatin immunoprecipitation (ChIP) (DISCOVER-Seq), translocation sequencing (LAM PCR HTGTS), and in vitro genomic DNA digestion (Digenome-seq and SITE-Seq). Emphasis is placed on the specific modifications that give rise to the enhanced performance of contemporary techniques over their predecessors and the comparative performance of techniques for different applications. The clinical relevance of these techniques is discussed in the context of assessing the safety of novel CRISPR/Cas9 HIV-1 curative strategies. With the recent success of HIV-1 and SIV-1 viral suppression in humanized mice and non-human primates, respectively, using CRISPR/Cas9, rigorous exploration of potential off-target effects is of critical importance. Such analyses would benefit from the application of the techniques discussed in this review.
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Affiliation(s)
- Andrew Atkins
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Alexander G. Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Theodore E. Gurrola
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ilker K. Sariyer
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States,*Correspondence: Brian Wigdahl
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33
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Huang H, Hu Y, Huang G, Ma S, Feng J, Wang D, Lin Y, Zhou J, Rong Z. Tag-seq: a convenient and scalable method for genome-wide specificity assessment of CRISPR/Cas nucleases. Commun Biol 2021; 4:830. [PMID: 34215845 PMCID: PMC8253812 DOI: 10.1038/s42003-021-02351-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/08/2021] [Indexed: 12/26/2022] Open
Abstract
Genome-wide identification of DNA double-strand breaks (DSBs) induced by CRISPR-associated protein (Cas) systems is vital for profiling the off-target events of Cas nucleases. However, current methods for off-target discovery are tedious and costly, restricting their widespread applications. Here we present an easy alternative method for CRISPR off-target detection by tracing the integrated oligonucleotide Tag using next-generation-sequencing (CRISPR-Tag-seq, or Tag-seq). Tag-seq enables rapid and convenient profiling of nuclease-induced DSBs by incorporating the optimized double-stranded oligodeoxynucleotide sequence (termed Tag), adapters, and PCR primers. Moreover, we employ a one-step procedure for library preparation in Tag-seq, which can be applied in the routine workflow of a molecular biology laboratory. We further show that Tag-seq successfully determines the cleavage specificity of SpCas9 variants and Cas12a/Cpf1 in a large-scale manner, and discover the integration sites of exogenous genes introduced by the Sleeping Beauty transposon. Our results demonstrate that Tag-seq is an efficient and scalable approach to genome-wide identification of Cas-nuclease-induced off-targets. Hongxin Huang and Yongfei Hu et al. develop Tag-seq, a streamlined sequencing method to examine off-target editing by CRISPR-Cas systems. The authors validate Tag-seq in multiple cell lines, demonstrating its broad utility and flexibility in identifying off-target genome editing.
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Affiliation(s)
- Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yongfei Hu
- Dermatology Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guanjie Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Shufeng Ma
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Jianqi Feng
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Dong Wang
- Dermatology Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China.
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, China.
| | - Zhili Rong
- Dermatology Hospital, Southern Medical University, Guangzhou, China. .,Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China. .,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
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34
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Accurate genomic variant detection in single cells with primary template-directed amplification. Proc Natl Acad Sci U S A 2021; 118:2024176118. [PMID: 34099548 PMCID: PMC8214697 DOI: 10.1073/pnas.2024176118] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Improvements in whole genome amplification (WGA) would enable new types of basic and applied biomedical research, including studies of intratissue genetic diversity that require more accurate single-cell genotyping. Here, we present primary template-directed amplification (PTA), an isothermal WGA method that reproducibly captures >95% of the genomes of single cells in a more uniform and accurate manner than existing approaches, resulting in significantly improved variant calling sensitivity and precision. To illustrate the types of studies that are enabled by PTA, we developed direct measurement of environmental mutagenicity (DMEM), a tool for mapping genome-wide interactions of mutagens with single living human cells at base-pair resolution. In addition, we utilized PTA for genome-wide off-target indel and structural variant detection in cells that had undergone CRISPR-mediated genome editing, establishing the feasibility for performing single-cell evaluations of biopsies from edited tissues. The improved precision and accuracy of variant detection with PTA overcomes the current limitations of accurate WGA, which is the major obstacle to studying genetic diversity and evolution at cellular resolution.
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35
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Park SJ, Jeong TY, Shin SK, Yoon DE, Lim SY, Kim SP, Choi J, Lee H, Hong JI, Ahn J, Seong JK, Kim K. Targeted mutagenesis in mouse cells and embryos using an enhanced prime editor. Genome Biol 2021; 22:170. [PMID: 34082781 PMCID: PMC8173820 DOI: 10.1186/s13059-021-02389-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/25/2021] [Indexed: 01/07/2023] Open
Abstract
Prime editors, novel genome-editing tools consisting of a CRISPR-Cas9 nickase and an engineered reverse transcriptase, can induce targeted mutagenesis. Nevertheless, much effort is required to optimize and improve the efficiency of prime-editing. Herein, we introduce two strategies to improve the editing efficiency using proximal dead sgRNA and chromatin-modulating peptides. We used enhanced prime-editing to generate Igf2 mutant mice with editing frequencies of up to 47% and observed germline transmission, no off-target effects, and a dwarf phenotype. This improved prime-editing method can be efficiently applied to cell research and to generate mouse models.
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Affiliation(s)
- Soo-Ji Park
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Tae Yeong Jeong
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Seung Kyun Shin
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Da Eun Yoon
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Soo-Yeon Lim
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sol Pin Kim
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Hyunji Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon, 34126, Republic of Korea
| | - Jeong-Im Hong
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Jinhee Ahn
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, 08826, Republic of Korea.
- Laboratory of Developmental Biology and Genomics, BK21 Program Plus for Advanced Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program for Bioinformatics, Program for Cancer Biology, BIO-MAX/N-Bio Institute, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
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36
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Gohil N, Bhattacharjee G, Lam NL, Perli SD, Singh V. CRISPR-Cas systems: Challenges and future prospects. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:141-151. [PMID: 33934835 DOI: 10.1016/bs.pmbts.2021.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The advancement gained over the past couple of decades in clustered regularly interspaced short palindromic repeats and CRISPR associated proteins (CRISPR-Cas) systems have revolutionized the field of synthetic biology, therapeutics, diagnostics and metabolic engineering. The technique has enabled the process of genome editing to be very precise, rapid, cost-effective and highly efficient which were the downfalls for the previously debuted zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN) technologies. However, despite its great potential, challenges including off-target activity, method of delivery, ethical and regulatory issues still remain unresolved for the CRISPR-Cas systems. In this chapter, we present and point out the obstacles faced in implementation of the CRISPR-Cas system along with its future prospects.
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Affiliation(s)
- Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Gargi Bhattacharjee
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Navya Lavina Lam
- The J. David Gladstone Institutes, San Francisco, CA, United States
| | - Samuel D Perli
- The J. David Gladstone Institutes, San Francisco, CA, United States
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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37
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Kim D, Kang BC, Kim JS. Identifying genome-wide off-target sites of CRISPR RNA-guided nucleases and deaminases with Digenome-seq. Nat Protoc 2021; 16:1170-1192. [PMID: 33462439 DOI: 10.1038/s41596-020-00453-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/22/2020] [Indexed: 01/29/2023]
Abstract
Digested genome sequencing (Digenome-seq) is a highly sensitive, easy-to-carry-out, cell-free method for experimentally identifying genome-wide off-target sites of programmable nucleases and deaminases (also known as base editors). Genomic DNA is digested in vitro using clustered regularly interspaced short palindromic repeats ribonucleoproteins (RNPs; plus DNA-modifying enzymes to cleave both strands of DNA at sites containing deaminated base products, in the case of base editors) and subjected to whole-genome sequencing (WGS) with a typical sequencing depth of 30×. A web-based program is available to map in vitro cleavage sites corresponding to on- and off-target sites. Chromatin DNA, in parallel with histone-free genomic DNA, can also be used to account for the effects of chromatin structure on off-target nuclease activity. Digenome-seq is more sensitive and comprehensive than cell-based methods for identifying off-target sites. Unlike other cell-free methods, Digenome-seq does not involve enrichment of DNA ends through PCR amplification. The entire process other than WGS, which takes ~1-2 weeks, including purification and preparation of RNPs, digestion of genomic DNA and bioinformatic analysis after WGS, takes about several weeks.
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Affiliation(s)
- Daesik Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea
| | - Beum-Chang Kang
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, Republic of Korea.
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
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38
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Rybin MJ, Ramic M, Ricciardi NR, Kapranov P, Wahlestedt C, Zeier Z. Emerging Technologies for Genome-Wide Profiling of DNA Breakage. Front Genet 2021; 11:610386. [PMID: 33584810 PMCID: PMC7873462 DOI: 10.3389/fgene.2020.610386] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022] Open
Abstract
Genome instability is associated with myriad human diseases and is a well-known feature of both cancer and neurodegenerative disease. Until recently, the ability to assess DNA damage-the principal driver of genome instability-was limited to relatively imprecise methods or restricted to studying predefined genomic regions. Recently, new techniques for detecting DNA double strand breaks (DSBs) and single strand breaks (SSBs) with next-generation sequencing on a genome-wide scale with single nucleotide resolution have emerged. With these new tools, efforts are underway to define the "breakome" in normal aging and disease. Here, we compare the relative strengths and weaknesses of these technologies and their potential application to studying neurodegenerative diseases.
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Affiliation(s)
- Matthew J Rybin
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, United States.,Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Melina Ramic
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, United States.,Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Natalie R Ricciardi
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, United States.,Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Philipp Kapranov
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, China
| | - Claes Wahlestedt
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, United States.,Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Zane Zeier
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, United States.,Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, United States
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39
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Störtz F, Minary P. crisprSQL: a novel database platform for CRISPR/Cas off-target cleavage assays. Nucleic Acids Res 2021; 49:D855-D861. [PMID: 33084893 PMCID: PMC7778913 DOI: 10.1093/nar/gkaa885] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/23/2020] [Accepted: 10/17/2020] [Indexed: 12/20/2022] Open
Abstract
With ongoing development of the CRISPR/Cas programmable nuclease system, applications in the area of in vivo therapeutic gene editing are increasingly within reach. However, non-negligible off-target effects remain a major concern for clinical applications. Even though a multitude of off-target cleavage datasets have been published, a comprehensive, transparent overview tool has not yet been established. Here, we present crisprSQL (http://www.crisprsql.com), an interactive and bioinformatically enhanced collection of CRISPR/Cas9 off-target cleavage studies aimed at enriching the fields of cleavage profiling, gene editing safety analysis and transcriptomics. The current version of crisprSQL contains cleavage data from 144 guide RNAs on 25,632 guide-target pairs from human and rodent cell lines, with interaction-specific references to epigenetic markers and gene names. The first curated database of this standard, it promises to enhance safety quantification research, inform experiment design and fuel development of computational off-target prediction algorithms.
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Affiliation(s)
- Florian Störtz
- Department of Computer Science, University of Oxford, Parks Road, Oxford OX1 3QD, UK
| | - Peter Minary
- Department of Computer Science, University of Oxford, Parks Road, Oxford OX1 3QD, UK
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40
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Bao XR, Pan Y, Lee CM, Davis TH, Bao G. Tools for experimental and computational analyses of off-target editing by programmable nucleases. Nat Protoc 2021; 16:10-26. [PMID: 33288953 PMCID: PMC8049448 DOI: 10.1038/s41596-020-00431-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022]
Abstract
Genome editing using programmable nucleases is revolutionizing life science and medicine. Off-target editing by these nucleases remains a considerable concern, especially in therapeutic applications. Here we review tools developed for identifying potential off-target editing sites and compare the ability of these tools to properly analyze off-target effects. Recent advances in both in silico and experimental tools for off-target analysis have generated remarkably concordant results for sites with high off-target editing activity. However, no single tool is able to accurately predict low-frequency off-target editing, presenting a bottleneck in therapeutic genome editing, because even a small number of cells with off-target editing can be detrimental. Therefore, we recommend that at least one in silico tool and one experimental tool should be used together to identify potential off-target sites, and amplicon-based next-generation sequencing (NGS) should be used as the gold standard assay for assessing the true off-target effects at these candidate sites. Future work to improve off-target analysis includes expanding the true off-target editing dataset to evaluate new experimental techniques and to train machine learning algorithms; performing analysis using the particular genome of the cells in question rather than the reference genome; and applying novel NGS techniques to improve the sensitivity of amplicon-based off-target editing quantification.
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Affiliation(s)
- X Robert Bao
- ILISATech, Houston, TX, USA
- Arsenal Biosciences, South San Francisco, CA, USA
| | - Yidan Pan
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Ciaran M Lee
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Timothy H Davis
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA.
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41
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Ballarino R, Bouwman BAM, Crosetto N. Genome-Wide CRISPR Off-Target DNA Break Detection by the BLISS Method. Methods Mol Biol 2021; 2162:261-281. [PMID: 32926388 DOI: 10.1007/978-1-0716-0687-2_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced palindromic repeat (CRISPR) systems are revolutionizing many areas of biology and medicine, where they are increasingly utilized as therapeutic tools for correcting disease-causing mutations. From a clinical perspective, unintended off-target (OT) DNA double-strand break (DSB) induction by CRISPR nucleases represents a major concern. Therefore, in recent years considerable effort has been dedicated to developing methods for assessing the OT activity of CRISPR nucleases, which in turn can be used to guide engineering of nucleases with minimal OT activity. Here we describe a detailed protocol for quantifying OT DSBs genome-wide in cultured cells transfected with CRISPR enzymes, based on the breaks labeling in situ and sequencing (BLISS) method that we have previously developed. CRISPR-BLISS is versatile and scalable, and allows assessment of multiple guide RNAs in different cell types and time points following cell transfection or transduction.
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Affiliation(s)
- Roberto Ballarino
- Science for Life Laboratory (SciLifeLab), Research Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Britta A M Bouwman
- Science for Life Laboratory (SciLifeLab), Research Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nicola Crosetto
- Science for Life Laboratory (SciLifeLab), Research Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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42
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An unbiased method for evaluating the genome-wide specificity of base editors in rice. Nat Protoc 2020; 16:431-457. [PMID: 33349703 DOI: 10.1038/s41596-020-00423-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022]
Abstract
Base editors can achieve targeted genomic base conversion. However, the off-target issue is one of the major concerns in their application. Whole-genome sequencing (WGS) at the individual level can provide direct information on genome-wide specificity, but it is difficult to distinguish true off-target single-nucleotide variants (SNVs) induced by base editors from background variation. Here we describe an unbiased WGS method for evaluating the specificity of base editors in rice. In this protocol, we describe the experimental design and provide details of vector construction, rice transformation and tissue culture, as well as a comprehensive WGS data analysis pipeline for overcoming two related core problems in various plant species: high background mutation rates and the heterogeneity of examined populations. Using this protocol, researchers can straightforwardly and accurately assess the genome-wide specificity of base editors and other genome editing tools in 12-15 weeks.
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43
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Blattner G, Cavazza A, Thrasher AJ, Turchiano G. Gene Editing and Genotoxicity: Targeting the Off-Targets. Front Genome Ed 2020; 2:613252. [PMID: 34713236 PMCID: PMC8525370 DOI: 10.3389/fgeed.2020.613252] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/20/2020] [Indexed: 12/26/2022] Open
Abstract
Gene editing technologies show great promise for application to human disease as a result of rapid developments in targeting tools notably based on ZFN, TALEN, and CRISPR-Cas systems. Precise modification of a DNA sequence is now possible in mature human somatic cells including stem and progenitor cells with increasing degrees of efficiency. At the same time new technologies are required to evaluate their safety and genotoxicity before widespread clinical application can be confidently implemented. A number of methodologies have now been developed in an attempt to predict expected and unexpected modifications occurring during gene editing. This review surveys the techniques currently available as state of the art, highlighting benefits and limitations, and discusses approaches that may achieve sufficient accuracy and predictability for application in clinical settings.
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Affiliation(s)
| | | | | | - Giandomenico Turchiano
- Infection, Immunity and Inflammation Research and Teaching Department, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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44
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Chaudhari HG, Penterman J, Whitton HJ, Spencer SJ, Flanagan N, Lei Zhang MC, Huang E, Khedkar AS, Toomey JM, Shearer CA, Needham AW, Ho TW, Kulman JD, Cradick T, Kernytsky A. Evaluation of Homology-Independent CRISPR-Cas9 Off-Target Assessment Methods. CRISPR J 2020; 3:440-453. [PMID: 33346710 PMCID: PMC7757695 DOI: 10.1089/crispr.2020.0053] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The ability to alter genomes specifically by CRISPR-Cas gene editing has revolutionized biological research, biotechnology, and medicine. Broad therapeutic application of this technology, however, will require thorough preclinical assessment of off-target editing by homology-based prediction coupled with reliable methods for detecting off-target editing. Several off-target site nomination assays exist, but careful comparison is needed to ascertain their relative strengths and weaknesses. In this study, HEK293T cells were treated with Streptococcus pyogenes Cas9 and eight guide RNAs with varying levels of predicted promiscuity in order to compare the performance of three homology-independent off-target nomination methods: the cell-based assay, GUIDE-seq, and the biochemical assays CIRCLE-seq and SITE-seq. The three methods were benchmarked by sequencing 75,000 homology-nominated sites using hybrid capture followed by high-throughput sequencing, providing the most comprehensive assessment of such methods to date. The three methods performed similarly in nominating sequence-confirmed off-target sites, but with large differences in the total number of sites nominated. When combined with homology-dependent nomination methods and confirmation by sequencing, all three off-target nomination methods provide a comprehensive assessment of off-target activity. GUIDE-seq's low false-positive rate and the high correlation of its signal with observed editing highlight its suitability for nominating off-target sites for ex vivo CRISPR-Cas therapies.
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Affiliation(s)
- Hemangi G. Chaudhari
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - Jon Penterman
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - Holly J. Whitton
- TScan Therapeutics, Waltham, Massachusetts, USA; and San Francisco, California 94102, USA
| | - Sarah J. Spencer
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - Nicole Flanagan
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - Maria C. Lei Zhang
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - Elaine Huang
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - Aditya S. Khedkar
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - J. Mike Toomey
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - Courtney A. Shearer
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - Alexander W. Needham
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - Tony W. Ho
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - John D. Kulman
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
| | - T.J. Cradick
- Excision BioTherapeutics, San Francisco, California 94102, USA
| | - Andrew Kernytsky
- CRISPR Therapeutics, Inc., Cambridge, Massachusetts, USA; San Francisco, California 94102, USA
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45
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Yan J, Xue D, Chuai G, Gao Y, Zhang G, Liu Q. Benchmarking and integrating genome-wide CRISPR off-target detection and prediction. Nucleic Acids Res 2020; 48:11370-11379. [PMID: 33137817 PMCID: PMC7672467 DOI: 10.1093/nar/gkaa930] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022] Open
Abstract
Systematic evaluation of genome-wide Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) off-target profiles is a fundamental step for the successful application of the CRISPR system to clinical therapies. Many experimental techniques and in silico tools have been proposed for detecting and predicting genome-wide CRISPR off-target profiles. These techniques and tools, however, have not been systematically benchmarked. A comprehensive benchmark study and an integrated strategy that takes advantage of the currently available tools to improve predictions of genome-wide CRISPR off-target profiles are needed. We focused on the specificity of the traditional CRISPR SpCas9 system for gene knockout. First, we benchmarked 10 available genome-wide off-target cleavage site (OTS) detection techniques with the published OTS detection datasets. Second, taking the datasets generated from OTS detection techniques as the benchmark datasets, we benchmarked 17 available in silico genome-wide OTS prediction tools to evaluate their genome-wide CRISPR off-target prediction performances. Finally, we present the first one-stop integrated Genome-Wide Off-target cleavage Search platform (iGWOS) that was specifically designed for the optimal genome-wide OTS prediction by integrating the available OTS prediction algorithms with an AdaBoost ensemble framework.
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Affiliation(s)
- Jifang Yan
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Dongyu Xue
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Guohui Chuai
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yuli Gao
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Gongchen Zhang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qi Liu
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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Bouwman BAM, Agostini F, Garnerone S, Petrosino G, Gothe HJ, Sayols S, Moor AE, Itzkovitz S, Bienko M, Roukos V, Crosetto N. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc 2020; 15:3894-3941. [PMID: 33139954 DOI: 10.1038/s41596-020-0397-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023]
Abstract
sBLISS (in-suspension breaks labeling in situ and sequencing) is a versatile and widely applicable method for identification of endogenous and induced DNA double-strand breaks (DSBs) in any cell type that can be brought into suspension. sBLISS provides genome-wide profiles of the most consequential DNA lesion implicated in a variety of pathological, but also physiological, processes. In sBLISS, after in situ labeling, DSB ends are linearly amplified, followed by next-generation sequencing and DSB landscape analysis. Here, we present a step-by-step experimental protocol for sBLISS, as well as a basic computational analysis. The main advantages of sBLISS are (i) the suspension setup, which renders the protocol user-friendly and easily scalable; (ii) the possibility of adapting it to a high-throughput or single-cell workflow; and (iii) its flexibility and its applicability to virtually every cell type, including patient-derived cells, organoids, and isolated nuclei. The wet-lab protocol can be completed in 1.5 weeks and is suitable for researchers with intermediate expertise in molecular biology and genomics. For the computational analyses, basic-to-intermediate bioinformatics expertise is required.
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Affiliation(s)
- Britta A M Bouwman
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Federico Agostini
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Silvano Garnerone
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Sergi Sayols
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Nicola Crosetto
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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Newman A, Starrs L, Burgio G. Cas9 Cuts and Consequences; Detecting, Predicting, and Mitigating CRISPR/Cas9 On- and Off-Target Damage: Techniques for Detecting, Predicting, and Mitigating the On- and off-target Effects of Cas9 Editing. Bioessays 2020; 42:e2000047. [PMID: 32643177 DOI: 10.1002/bies.202000047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/12/2020] [Indexed: 12/12/2022]
Abstract
Large deletions and genomic re-arrangements are increasingly recognized as common products of double-strand break repair at Clustered Regularly Interspaced, Short Palindromic Repeats - CRISPR associated protein 9 (CRISPR/Cas9) on-target sites. Together with well-known off-target editing products from Cas9 target misrecognition, these are important limitations, that need to be addressed. Rigorous assessment of Cas9-editing is necessary to ensure validity of observed phenotypes in Cas9-edited cell-lines and model organisms. Here the mechanisms of Cas9 specificity, and strategies to assess and mitigate unwanted effects of Cas9 editing are reviewed; covering guide-RNA design, RNA modifications, Cas9 modifications, control of Cas9 activity; computational prediction for off-targets, and experimental methods for detecting Cas9 cleavage. Although recognition of the prevalence of on- and off-target effects of Cas9 editing has increased in recent years, broader uptake across the gene editing community will be important in determining the specificity of Cas9 across diverse applications and organisms.
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Affiliation(s)
- Anthony Newman
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
| | - Lora Starrs
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
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48
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Zhou L, Li R, Zhang R, Peng R, Chen K, Gao P, Zhang J, Zhang R, Li J. Utilizing CRISPR/Cas9 technology to prepare lymphoblastoid cell lines harboring genetic mutations for generating quality control materials in genetic testing. J Clin Lab Anal 2020; 34:e23256. [PMID: 32118319 PMCID: PMC7370731 DOI: 10.1002/jcla.23256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/01/2020] [Accepted: 02/04/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND To meet the requirements of the rapidly progressing genetic testing technologies in clinical laboratories, assuring the quality of genetic tests by utilizing appropriate quality control materials is of paramount importance. The CRISPR/Cas9 technology was used to prepare quality control materials because genome-edited human cell lines are one of the major resources for quality control materials. METHODS In this study, in vitro transcribed sgRNA were transfected into a Cas9-expressing lymphoblastoid cell line (LCL)-by electroporation-to simulate the SEA-type deletion observed in α-thalassemia. The edited positive cell line was screened and identified by polymerase chain reaction (PCR) followed by Sanger sequencing. The whole-genome sequencing was also performed to show evidence of predicted mutation. RESULTS The results showed that electroporation of the in vitro transcribed gRNAs into stable Cas9-expressing LCL was a more efficient gene-editing technique as compared to plasmid-mediated transfection, and that the positive rates could reach up to 35.9%. The predominance of indel sizes relative to the predicted deletion length was clustered between 10 and 0 bp. The results of whole-genome sequencing also demonstrated the existence of SEA-type deletion of α-thalassemia. CONCLUSIONS Gene-editing based on Cas9-expressing LCL by electroporation of sgRNA was a more efficient approach to introduce mutations for generating quality control materials for genetic testing. The edited lymphoblastoid cell lines were feasible to serve as quality control materials in genetic testing.
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Affiliation(s)
- Li Zhou
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Rui Li
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Runling Zhang
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Rongxue Peng
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Kun Chen
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Peng Gao
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Jiawei Zhang
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Rui Zhang
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Jinming Li
- National Center for Clinical LaboratoriesBeijing HospitalNational Center of GerontologyBeijingChina
- Graduate SchoolPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
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49
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CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity. Nat Biotechnol 2020; 38:1317-1327. [PMID: 32541958 PMCID: PMC7652380 DOI: 10.1038/s41587-020-0555-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
Current methods can illuminate the genome-wide activity of CRISPR-Cas9 nucleases, but are not easily scalable to the throughput needed to fully understand the principles that govern Cas9 specificity. Here we describe ‘circularization for high-throughput analysis of nuclease genome-wide effects by sequencing’ (CHANGE-seq), a scalable, automatable tagmentation-based method for measuring the genome-wide activity of Cas9 in vitro. We applied CHANGE-seq to 110 sgRNA targets across 13 therapeutically relevant loci in human primary T-cells and identified 201,934 off-target sites, enabling the training of a machine learning model to predict off-target activity. Comparing matched genome-wide off-target, chromatin modification and accessibility, and transcriptional data, we found that cellular off-target activity was two to four times more likely to occur near active promoters, enhancers, and transcribed regions. Finally, CHANGE-seq analysis of 6 targets across 8 individual genomes revealed that human single-nucleotide variation had significant effects on activity at ~15.2% of off-target sites analyzed. CHANGE-seq is a simplified, sensitive, and scalable approach to understanding the specificity of genome editors.
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50
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On-Target CRISPR/Cas9 Activity Can Cause Undesigned Large Deletion in Mouse Zygotes. Int J Mol Sci 2020; 21:ijms21103604. [PMID: 32443745 PMCID: PMC7279260 DOI: 10.3390/ijms21103604] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
Genome engineering has been tremendously affected by the appearance of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9)-based approach. Initially discovered as an adaptive immune system for prokaryotes, the method has rapidly evolved over the last decade, overtaking multiple technical challenges and scientific tasks and becoming one of the most effective, reliable, and easy-to-use technologies for precise genomic manipulations. Despite its undoubtable advantages, CRISPR/Cas9 technology cannot ensure absolute accuracy and predictability of genomic editing results. One of the major concerns, especially for clinical applications, is mutations resulting from error-prone repairs of CRISPR/Cas9-induced double-strand DNA breaks. In some cases, such error-prone repairs can cause unpredicted and unplanned large genomic modifications within the CRISPR/Cas9 on-target site. Here we describe the largest, to the best of our knowledge, undesigned on-target deletion with a size of ~293 kb that occurred after the cytoplasmic injection of CRISPR/Cas9 system components into mouse zygotes and speculate about its origin. We suppose that deletion occurred as a result of the truncation of one of the ends of a double-strand break during the repair.
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