1
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Liu Y, Binda CS, Berkhout B, Das AT. CRISPR-Cas attack of HIV-1 proviral DNA can cause unintended deletion of surrounding cellular DNA. J Virol 2023; 97:e0133423. [PMID: 37982648 PMCID: PMC10734527 DOI: 10.1128/jvi.01334-23] [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: 08/28/2023] [Accepted: 10/23/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Although HIV replication can be effectively inhibited by antiretroviral therapy, this does not result in a cure as the available drugs do not inactivate the integrated HIV-1 DNA in infected cells. Consequently, HIV-infected individuals need lifelong therapy to prevent viral rebound. Several preclinical studies indicate that CRISPR-Cas gene-editing systems can be used to achieve permanent inactivation of the viral DNA. It was previously shown that this inactivation was due to small inactivating mutations at the targeted sites in the HIV genome and to excision or inversion of the viral DNA fragment between two target sites. We, here, demonstrate that CRISPR-Cas treatment also causes large unintended deletions, which can include surrounding chromosomal sequences. As the loss of chromosomal sequences may cause oncogenic transformation of the cell, such unintended large deletions form a potential safety risk in clinical application of this antiviral application and possibly all CRISPR-Cas gene-editing approaches.
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Affiliation(s)
- Ye Liu
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Caroline S. Binda
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Ben Berkhout
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Atze T. Das
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
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2
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Ghasemi HI, Bacal J, Yoon AC, Tavasoli KU, Cruz C, Vu JT, Gardner BM, Richardson CD. Interstrand crosslinking of homologous repair template DNA enhances gene editing in human cells. Nat Biotechnol 2023; 41:1398-1404. [PMID: 36849829 PMCID: PMC10460463 DOI: 10.1038/s41587-022-01654-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 12/22/2022] [Indexed: 03/01/2023]
Abstract
We describe a strategy to boost the efficiency of gene editing via homology-directed repair (HDR) by covalently modifying the template DNA with interstrand crosslinks. Crosslinked templates (xHDRTs) increase Cas9-mediated editing efficiencies by up to fivefold in K562, HEK293T, U2OS, iPS and primary T cells. Increased editing from xHDRTs is driven by events on the template molecule and requires ataxia telangiectasia and Rad3-related (ATR) kinase and components of the Fanconi anemia pathway.
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Affiliation(s)
- Hannah I Ghasemi
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Julien Bacal
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Amanda C Yoon
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Katherine U Tavasoli
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Carmen Cruz
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Jonathan T Vu
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Brooke M Gardner
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Chris D Richardson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
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3
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Liu Y, Cottle WT, Ha T. Mapping cellular responses to DNA double-strand breaks using CRISPR technologies. Trends Genet 2023; 39:560-574. [PMID: 36967246 PMCID: PMC11062594 DOI: 10.1016/j.tig.2023.02.015] [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: 09/22/2021] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/15/2023]
Abstract
DNA double-strand breaks (DSBs) are one of the most genotoxic DNA lesions, driving a range of pathological defects from cancers to immunodeficiencies. To combat genomic instability caused by DSBs, evolution has outfitted cells with an intricate protein network dedicated to the rapid and accurate repair of these lesions. Pioneering studies have identified and characterized many crucial repair factors in this network, while the advent of genome manipulation tools like clustered regularly interspersed short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) has reinvigorated interest in DSB repair mechanisms. This review surveys the latest methodological advances and biological insights gained by utilizing Cas9 as a precise 'damage inducer' for the study of DSB repair. We highlight rapidly inducible Cas9 systems that enable synchronized and efficient break induction. When combined with sequencing and genome-specific imaging approaches, inducible Cas9 systems greatly expand our capability to spatiotemporally characterize cellular responses to DSB at specific genomic coordinates, providing mechanistic insights that were previously unobtainable.
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Affiliation(s)
- Yang Liu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - W Taylor Cottle
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Howard Hughes Medical Institute, Baltimore, MD, USA.
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4
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Pallaseni A, Peets EM, Girling G, Crepaldi L, Kuzmin I, Raudvere U, Peterson H, Serçin Ö, Mardin BR, Kosicki M, Parts L. The interplay of DNA repair context with target sequence predictably biasses Cas9-generated mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546891. [PMID: 37425722 PMCID: PMC10326969 DOI: 10.1101/2023.06.28.546891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The genome engineering capability of the CRISPR/Cas system depends on the DNA repair machinery to generate the final outcome. Several genes can have an impact on mutations created, but their exact function and contribution to the result of the repair are not completely characterised. This lack of knowledge has limited the ability to comprehend and regulate the editing outcomes. Here, we measure how the absence of 21 repair genes changes the mutation outcomes of Cas9-generated cuts at 2,812 synthetic target sequences in mouse embryonic stem cells. Absence of key non-homologous end joining genes Lig4, Xrcc4, and Xlf abolished small insertions and deletions, while disabling key microhomology-mediated repair genes Nbn and Polq reduced frequency of longer deletions. Complex alleles of combined insertion and deletions were preferentially generated in the absence of Xrcc6. We further discover finer structure in the outcome frequency changes for single nucleotide insertions and deletions between large microhomologies that are differentially modulated by the knockouts. We use the knowledge of the reproducible variation across repair milieus to build predictive models of Cas9 editing results that outperform the current standards. This work improves our understanding of DNA repair gene function, and provides avenues for more precise modulation of CRISPR/Cas9-generated mutations.
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Affiliation(s)
- Ananth Pallaseni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elin Madli Peets
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Gareth Girling
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Luca Crepaldi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ivan Kuzmin
- Department of Computer Science, University of Tartu, Tartu, Estonia
| | - Uku Raudvere
- Department of Computer Science, University of Tartu, Tartu, Estonia
| | - Hedi Peterson
- Department of Computer Science, University of Tartu, Tartu, Estonia
| | - Özdemirhan Serçin
- BioMed X Institute (GmbH), Im Neuenheimer Feld 515, Heidelberg, Germany
| | - Balca R. Mardin
- BioMed X Institute (GmbH), Im Neuenheimer Feld 515, Heidelberg, Germany
| | - Michael Kosicki
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Leopold Parts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Computer Science, University of Tartu, Tartu, Estonia
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5
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Wettengel JM, Hansen-Palmus L, Yusova S, Rust L, Biswas S, Carson J, Ryu J, Bimber BN, Hennebold JD, Burwitz BJ. A Multifunctional and Highly Adaptable Reporter System for CRISPR/Cas Editing. Int J Mol Sci 2023; 24:8271. [PMID: 37175977 PMCID: PMC10179647 DOI: 10.3390/ijms24098271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/30/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
CRISPR/Cas systems are some of the most promising tools for therapeutic genome editing. The use of these systems is contingent on the optimal designs of guides and homology-directed repair (HDR) templates. While this design can be achieved in silico, validation and further optimization are usually performed with the help of reporter systems. Here, we describe a novel reporter system, termed BETLE, that allows for the fast, sensitive, and cell-specific detection of genome editing and template-specific HDR by encoding multiple reporter proteins in different open-reading frames. Out-of-frame non-homologous end joining (NHEJ) leads to the expression of either secretable NanoLuc luciferase, enabling a highly sensitive and low-cost analysis of editing, or fluorescent mTagBFP2, allowing for the enumeration and tissue-specific localization of genome-edited cells. BETLE includes a site to validate CRISPR/Cas systems for a sequence-of-interest, making it broadly adaptable. We evaluated BETLE using a defective moxGFP with a 39-base-pair deletion and showed spCas9, saCas9, and asCas12a editing as well as sequence-specific HDR and the repair of moxGFP in cell lines with single and multiple reporter integrants. Taken together, these data show that BETLE allows for the rapid detection and optimization of CRISPR/Cas genome editing and HDR in vitro and represents a state-of the art tool for future applications in vivo.
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Affiliation(s)
- Jochen M. Wettengel
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.M.W.)
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, 81675 München, Germany
| | - Lea Hansen-Palmus
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, 81675 München, Germany
| | - Sofiya Yusova
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.M.W.)
| | - Lauren Rust
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.M.W.)
| | - Sreya Biswas
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.M.W.)
| | - Julien Carson
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.M.W.)
| | - Junghyun Ryu
- Division of Reproductive & Developmental, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.R.)
| | - Benjamin N. Bimber
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jon D. Hennebold
- Division of Reproductive & Developmental, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.R.)
- Department of Obstetrics & Gynecology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Benjamin J. Burwitz
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA; (J.M.W.)
- Division of Pathobiology & Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
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6
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Park SH, Cao M, Pan Y, Davis TH, Saxena L, Deshmukh H, Fu Y, Treangen T, Sheehan VA, Bao G. Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing. SCIENCE ADVANCES 2022; 8:eabo7676. [PMID: 36269834 PMCID: PMC9586483 DOI: 10.1126/sciadv.abo7676] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/02/2022] [Indexed: 05/23/2023]
Abstract
Most genome editing analyses to date are based on quantifying small insertions and deletions. Here, we show that CRISPR-Cas9 genome editing can induce large gene modifications, such as deletions, insertions, and complex local rearrangements in different primary cells and cell lines. We analyzed large deletion events in hematopoietic stem and progenitor cells (HSPCs) using different methods, including clonal genotyping, droplet digital polymerase chain reaction, single-molecule real-time sequencing with unique molecular identifier, and long-amplicon sequencing assay. Our results show that large deletions of up to several thousand bases occur with high frequencies at the Cas9 on-target cut sites on the HBB (11.7 to 35.4%), HBG (14.3%), and BCL11A (13.2%) genes in HSPCs and the PD-1 (15.2%) gene in T cells. Our findings have important implications to advancing genome editing technologies for treating human diseases, because unintended large gene modifications may persist, thus altering the biological functions and reducing the available therapeutic alleles.
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Affiliation(s)
- So Hyun Park
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Mingming Cao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Yidan Pan
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Timothy H. Davis
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Lavanya Saxena
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | | | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Todd Treangen
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | | | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
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7
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Geng K, Merino LG, Wedemann L, Martens A, Sobota M, Sanchez YP, Søndergaard JN, White RJ, Kutter C. Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells. Genome Res 2022; 32:1876-1891. [PMID: 36180232 PMCID: PMC9712622 DOI: 10.1101/gr.276901.122] [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: 05/05/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022]
Abstract
The CRISPR-Cas9 system is widely used to permanently delete genomic regions via dual guide RNAs. Genomic rearrangements induced by CRISPR-Cas9 can occur, but continuous technical developments make it possible to characterize complex on-target effects. We combined an innovative droplet-based target enrichment approach with long-read sequencing and coupled it to a customized de novo sequence assembly. This approach enabled us to dissect the sequence content at kilobase scale within an on-target genomic locus. We here describe extensive genomic disruptions by Cas9, involving the allelic co-occurrence of a genomic duplication and inversion of the target region, as well as integrations of exogenous DNA and clustered interchromosomal DNA fragment rearrangements. Furthermore, we found that these genomic alterations led to functional aberrant DNA fragments and can alter cell proliferation. Our findings broaden the consequential spectrum of the Cas9 deletion system, reinforce the necessity of meticulous genomic validations, and introduce a data-driven workflow enabling detailed dissection of the on-target sequence content with superior resolution.
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Affiliation(s)
- Keyi Geng
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Lara G Merino
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Linda Wedemann
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Aniek Martens
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Małgorzata Sobota
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Yerma P Sanchez
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Jonas Nørskov Søndergaard
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Robert J White
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Claudia Kutter
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
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8
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Processing DNA lesions during mitosis to prevent genomic instability. Biochem Soc Trans 2022; 50:1105-1118. [PMID: 36040211 PMCID: PMC9444068 DOI: 10.1042/bst20220049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022]
Abstract
Failure of cells to process toxic double-strand breaks (DSBs) constitutes a major intrinsic source of genome instability, a hallmark of cancer. In contrast with interphase of the cell cycle, canonical repair pathways in response to DSBs are inactivated in mitosis. Although cell cycle checkpoints prevent transmission of DNA lesions into mitosis under physiological condition, cancer cells frequently display mitotic DNA lesions. In this review, we aim to provide an overview of how mitotic cells process lesions that escape checkpoint surveillance. We outline mechanisms that regulate the mitotic DNA damage response and the different types of lesions that are carried over to mitosis, with a focus on joint DNA molecules arising from under-replication and persistent recombination intermediates, as well as DNA catenanes. Additionally, we discuss the processing pathways that resolve each of these lesions in mitosis. Finally, we address the acute and long-term consequences of unresolved mitotic lesions on cellular fate and genome stability.
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9
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Cisneros-Aguirre M, Lopezcolorado FW, Tsai LJ, Bhargava R, Stark JM. The importance of DNAPKcs for blunt DNA end joining is magnified when XLF is weakened. Nat Commun 2022; 13:3662. [PMID: 35760797 PMCID: PMC9237100 DOI: 10.1038/s41467-022-31365-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022] Open
Abstract
Canonical non-homologous end joining (C-NHEJ) factors can assemble into a long-range (LR) complex with DNA ends relatively far apart that contains DNAPKcs, XLF, XRCC4, LIG4, and the KU heterodimer and a short-range (SR) complex lacking DNAPKcs that has the ends positioned for ligation. Since the SR complex can form de novo, the role of the LR complex (i.e., DNAPKcs) for chromosomal EJ is unclear. We have examined EJ of chromosomal blunt DNA double-strand breaks (DSBs), and found that DNAPKcs is significantly less important than XLF for such EJ. However, weakening XLF via disrupting interaction interfaces causes a marked requirement for DNAPKcs, its kinase activity, and its ABCDE-cluster autophosphorylation sites for blunt DSB EJ. In contrast, other aspects of genome maintenance are sensitive to DNAPKcs kinase inhibition in a manner that is not further enhanced by XLF loss (i.e., suppression of homology-directed repair and structural variants, and IR-resistance). We suggest that DNAPKcs is required to position a weakened XLF in an LR complex that can transition into a functional SR complex for blunt DSB EJ, but also has distinct functions for other aspects of genome maintenance. DNAPKcs and its kinase activity are required for blunt DNA break end joining when the bridging factor XLF is weakened, but for homologous recombination and radiation resistance, the influence of DNAPKcs is not further enhanced with loss of XLF.
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Affiliation(s)
- Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Felicia Wednesday Lopezcolorado
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Linda Jillianne Tsai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Ragini Bhargava
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.,Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA. .,Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd, Duarte, CA 91010, USA.
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10
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Kosicki M, Allen F, Steward F, Tomberg K, Pan Y, Bradley A. Cas9-induced large deletions and small indels are controlled in a convergent fashion. Nat Commun 2022; 13:3422. [PMID: 35701408 PMCID: PMC9197861 DOI: 10.1038/s41467-022-30480-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 04/28/2022] [Indexed: 11/09/2022] Open
Abstract
Repair of Cas9-induced double-stranded breaks results primarily in formation of small insertions and deletions (indels), but can also cause potentially harmful large deletions. While mechanisms leading to the creation of small indels are relatively well understood, very little is known about the origins of large deletions. Using a library of clonal NGS-validated mouse embryonic stem cells deficient for 32 DNA repair genes, we have shown that large deletion frequency increases in cells impaired for non-homologous end joining and decreases in cells deficient for the central resection gene Nbn and the microhomology-mediated end joining gene Polq. Across deficient clones, increase in large deletion frequency was closely correlated with the increase in the extent of microhomology and the size of small indels, implying a continuity of repair processes across different genomic scales. Furthermore, by targeting diverse genomic sites, we identified examples of repair processes that were highly locus-specific, discovering a role for exonuclease Trex1. Finally, we present evidence that indel sizes increase with the overall efficiency of Cas9 mutagenesis. These findings may have impact on both basic research and clinical use of CRISPR-Cas9, in particular in conjunction with repair pathway modulation. CRISPR/Cas9 system has revolutionized science and therapy, but DNA damage it causes often goes beyond the desired ’precision editing’. Here, the authors identify general and target specific DNA repair pathways responsible for unwanted mutagenesis.
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Affiliation(s)
| | | | - Frances Steward
- The Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kärt Tomberg
- The Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Yangyang Pan
- The Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Allan Bradley
- The Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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11
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Hong J, Meng Z, Zhang Z, Su H, Fan Y, Huang R, Ding R, Zhang N, Li F, Wang S. Comprehensive Analysis of CRISPR-Cas9 Editing Outcomes in Yeast Xanthophyllomyces dendrorhous. CRISPR J 2022; 5:558-570. [PMID: 35506993 DOI: 10.1089/crispr.2021.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
DNA repair after Cas9 cutting can result in deletions/insertions, genomic rearrangements, and rare nucleotide substitutions. However, most work has only focused on deletions/insertions resulting from repair after CRISPR-Cas9 action. Here, we comprehensively analyzed the editing outcomes induced by CRISPR-Cas9 treatment in yeast Xanthophyllomyces dendrorhous by Sanger and Illumina sequencing and identified diverse DNA repair patterns, including DNA deletions, interchromosomal translocations, and on-target nucleotide substitutions (point mutations). Some deletions were observed repeatedly, and others, especially large deletions, varied in size. Genome sequencing and structural variation analysis showed that the interchromosomal translocations happened between Cas9 target sites and the endogenous ADH4 promoter. In contrast to previous studies, analysis revealed that the on-target point mutations were not random. Importantly, these point mutations showed strong sequence dependence that is not consistent with previous work in Hela cells, where CRISPR-mediated substitutions were found to lack sequence dependence and conversion preferences. Finally, we found that the non-homologous end joining components Ku70, Ku80, Mre11, or RAD50, and the overlapping roles of non-essential DNA polymerases were necessary for the production of both point mutations and deletions. This work expands our knowledge of CRISPR-Cas9 mediated DNA repair.
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Affiliation(s)
- Jixuan Hong
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Ziyue Meng
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Zixi Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Hang Su
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Yuxuan Fan
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Ruilin Huang
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Ruirui Ding
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Ning Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Fuli Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Molecular and Microbial Engineering Group, Shandong Energy Institute, Qingdao, China
| | - Shi'an Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Molecular and Microbial Engineering Group, Shandong Energy Institute, Qingdao, China
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12
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Lopez A, Nichols Doyle R, Sandoval C, Nisson K, Yang V, Fregoso OI. Viral Modulation of the DNA Damage Response and Innate Immunity: Two Sides of the Same Coin. J Mol Biol 2022; 434:167327. [PMID: 34695379 PMCID: PMC9119581 DOI: 10.1016/j.jmb.2021.167327] [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: 09/01/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 11/29/2022]
Abstract
The DDR consists of multiple pathways that sense, signal, and respond to anomalous DNA. To promote efficient replication, viruses have evolved to engage and even modulate the DDR. In this review, we will discuss a select set of diverse viruses and the range of mechanisms they evolved to interact with the DDR and some of the subsequent cellular consequences. There is a dichotomy in that the DDR can be both beneficial for viruses yet antiviral. We will also review the connection between the DDR and innate immunity. Previously believed to be disparate cellular functions, more recent research is emerging that links these processes. Furthermore, we will discuss some discrepancies in the literature that we propose can be remedied by utilizing more consistent DDR-focused assays. By doing so, we hope to obtain a much clearer understanding of how broadly these mechanisms and phenotypes are conserved among all viruses. This is crucial for human health since understanding how viruses manipulate the DDR presents an important and tractable target for antiviral therapies.
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Affiliation(s)
- Andrew Lopez
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Randilea Nichols Doyle
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Carina Sandoval
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Karly Nisson
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Vivian Yang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Oliver I Fregoso
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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13
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CRISPR-Cas9 gene editing induced complex on-target outcomes in human cells. Exp Hematol 2022; 110:13-19. [PMID: 35304271 DOI: 10.1016/j.exphem.2022.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/24/2022]
Abstract
CRISPR-Cas9 is a powerful tool to edit the genome and holds great promise for gene therapy applications. Initial concerns of gene engineering focus on off-target effects. However, in addition to short indel mutations (often < 50 bp), an increasing number of studies have revealed complex on-target results after double-strand break repair by CRISPR-Cas9, such as large deletions, gene rearrangement, and loss of heterozygosity. These unintended mutations are potential safety concerns in clinical gene editing. Here, in this review, we summarize the significant findings of CRISPR-Cas9-induced on-target deleterious outcomes and discuss putative ways to achieve safe gene therapy.
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14
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van de Kooij B, van Attikum H. Genomic Reporter Constructs to Monitor Pathway-Specific Repair of DNA Double-Strand Breaks. Front Genet 2022; 12:809832. [PMID: 35237296 PMCID: PMC8884240 DOI: 10.3389/fgene.2021.809832] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/23/2021] [Indexed: 11/29/2022] Open
Abstract
Repair of DNA Double-Strand Breaks (DSBs) can be error-free or highly mutagenic, depending on which of multiple mechanistically distinct pathways repairs the break. Hence, DSB-repair pathway choice directly affects genome integrity, and it is therefore of interest to understand the parameters that direct repair towards a specific pathway. This has been intensively studied using genomic reporter constructs, in which repair of a site-specific DSB by the pathway of interest generates a quantifiable phenotype, generally the expression of a fluorescent protein. The current developments in genome editing with targetable nucleases like Cas9 have increased reporter usage and accelerated the generation of novel reporter constructs. Considering these recent advances, this review will discuss and compare the available DSB-repair pathway reporters, provide essential considerations to guide reporter choice, and give an outlook on potential future developments.
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15
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Yang F, Zhang H, Cai S, Imtiaz K, Li M, Wang M, Liu Y, Xue F, Zhang L, Gu F. Green Fluorescent Protein Tagged Polycistronic Reporter System Reveals Functional Editing Characteristics of CRISPR-Cas. CRISPR J 2022; 5:254-263. [PMID: 35085009 DOI: 10.1089/crispr.2021.0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The green fluorescent protein (GFP)-based reporter system has been widely harnessed as a quick quantitative activity assessment method for characterizing CRISPR-Cas via flow cytometry. However, due to the small size (738 nt) of the GFP coding sequence, the targeting sites for certain CRISPR-Cas are greatly restricted. To address this, here we developed a GFP tagged polycistronic reporter system to determine the activity of CRISPR-Cas in human cells. Specifically, the system contains the herpes simplex virus thymidine kinase (TK) gene, bacterial neomycin phosphotransferase (Neo) gene, and green fluorescent protein (GFP), named TNG gene, with a coding sequence of 2,577 nt. To investigate its performance, we generated a human cell line harboring the TNG expression cassette at the AAVS1 locus, and then we tested it with different Cas orthologs (SaCas9, St1Cas9, and AsCas12a). Our results demonstrated that using the TNG reporter system greatly expands the targeting site selection (3- to 13-fold) with CRISPR-Cas genome editing. The study therefore reports an additional method for the characterization of CRISPR-Cas technology.
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Affiliation(s)
- Fayu Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Hao Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Shuo Cai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Kiran Imtiaz
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Mingchun Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Mi Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Yingchun Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Feiqun Xue
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Lifang Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
| | - Feng Gu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P.R. China; and Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China.,Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai, P.R. China
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16
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Yoo KW, Yadav MK, Song Q, Atala A, Lu B. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3944-3957. [PMID: 35323942 PMCID: PMC9023269 DOI: 10.1093/nar/gkac186] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Kyung W Yoo
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC 27101, USA
| | - Manish Kumar Yadav
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC 27101, USA
| | - Qianqian Song
- Department of Cancer Biology, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC 27101, USA
| | - Baisong Lu
- To whom correspondence should be addressed. Tel: +1 336 713 7276; Fax: +1 336 713 7290;
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17
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Smirnov A, Battulin N. Concatenation of Transgenic DNA: Random or Orchestrated? Genes (Basel) 2021; 12:genes12121969. [PMID: 34946918 PMCID: PMC8701086 DOI: 10.3390/genes12121969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022] Open
Abstract
Generation of transgenic organisms by pronuclear microinjection has become a routine procedure. However, while the process of DNA integration in the genome is well understood, we still do not know much about the recombination between transgene molecules that happens in the first moments after DNA injection. Most of the time, injected molecules are joined together in head-to-tail tandem repeats-the so-called concatemers. In this review, we focused on the possible concatenation mechanisms and how they could be studied with genetic reporters tracking individual copies in concatemers. We also discuss various features of concatemers, including palindromic junctions and repeat-induced gene silencing (RIGS). Finally, we speculate how cooperation of DNA repair pathways creates a multicopy concatenated insert.
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Affiliation(s)
- Alexander Smirnov
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
| | - Nariman Battulin
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
- Institute of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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18
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Xu X, Liu C, Wang Y, Koivisto O, Zhou J, Shu Y, Zhang H. Nanotechnology-based delivery of CRISPR/Cas9 for cancer treatment. Adv Drug Deliv Rev 2021; 176:113891. [PMID: 34324887 DOI: 10.1016/j.addr.2021.113891] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023]
Abstract
CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats-associated protein 9) is a potent technology for gene-editing. Owing to its high specificity and efficiency, CRISPR/Cas9 is extensity used for human diseases treatment, especially for cancer, which involves multiple genetic alterations. Different concepts of cancer treatment by CRISPR/Cas9 are established. However, significant challenges remain for its clinical applications. The greatest challenge for CRISPR/Cas9 therapy is how to safely and efficiently deliver it to target sites in vivo. Nanotechnology has greatly contributed to cancer drug delivery. Here, we present the action mechanisms of CRISPR/Cas9, its application in cancer therapy and especially focus on the nanotechnology-based delivery of CRISPR/Cas9 for cancer gene editing and immunotherapy to pave the way for its clinical translation. We detail the difficult barriers for CRISIR/Cas9 delivery in vivo and discuss the relative solutions for encapsulation, target delivery, controlled release, cellular internalization, and endosomal escape.
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Affiliation(s)
- Xiaoyu Xu
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200031, China; Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland
| | - Chang Liu
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland
| | - Yonghui Wang
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland
| | - Oliver Koivisto
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland
| | - Junnian Zhou
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland; Experimental Hematology and Biochemistry Lab, Beijing Institute of Radiation Medicine, Beijing 100850, China; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Yilai Shu
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200031, China
| | - Hongbo Zhang
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland.
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19
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Benfatto S, Serçin Ö, Dejure FR, Abdollahi A, Zenke FT, Mardin BR. Uncovering cancer vulnerabilities by machine learning prediction of synthetic lethality. Mol Cancer 2021; 20:111. [PMID: 34454516 PMCID: PMC8401190 DOI: 10.1186/s12943-021-01405-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Synthetic lethality describes a genetic interaction between two perturbations, leading to cell death, whereas neither event alone has a significant effect on cell viability. This concept can be exploited to specifically target tumor cells. CRISPR viability screens have been widely employed to identify cancer vulnerabilities. However, an approach to systematically infer genetic interactions from viability screens is missing. METHODS Here we describe PAn-canceR Inferred Synthetic lethalities (PARIS), a machine learning approach to identify cancer vulnerabilities. PARIS predicts synthetic lethal (SL) interactions by combining CRISPR viability screens with genomics and transcriptomics data across hundreds of cancer cell lines profiled within the Cancer Dependency Map. RESULTS Using PARIS, we predicted 15 high confidence SL interactions within 549 DNA damage repair (DDR) genes. We show experimental validation of an SL interaction between the tumor suppressor CDKN2A, thymidine phosphorylase (TYMP) and the thymidylate synthase (TYMS), which may allow stratifying patients for treatment with TYMS inhibitors. Using genome-wide mapping of SL interactions for DDR genes, we unraveled a dependency between the aldehyde dehydrogenase ALDH2 and the BRCA-interacting protein BRIP1. Our results suggest BRIP1 as a potential therapeutic target in ~ 30% of all tumors, which express low levels of ALDH2. CONCLUSIONS PARIS is an unbiased, scalable and easy to adapt platform to identify SL interactions that should aid in improving cancer therapy with increased availability of cancer genomics data.
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Affiliation(s)
- Salvatore Benfatto
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Özdemirhan Serçin
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Francesca R Dejure
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Amir Abdollahi
- Division of Molecular and Translational Radiation Oncology, National Centre for Tumour Diseases (NCT), Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Frank T Zenke
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Balca R Mardin
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany.
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20
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Gillyard T, Davis J. DNA double-strand break repair in cancer: A path to achieving precision medicine. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:111-137. [PMID: 34507781 DOI: 10.1016/bs.ircmb.2021.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The assessment of DNA damage can be a significant diagnostic for precision medicine. DNA double strand break (DSBs) pathways in cancer are the primary targets in a majority of anticancer therapies, yet the molecular vulnerabilities that underlie each tumor can vary widely making the application of precision medicine challenging. Identifying and understanding these interindividual vulnerabilities enables the design of targeted DSB inhibitors along with evolving precision medicine approaches to selectively kill cancer cells with minimal side effects. A major challenge however, is defining exactly how to target unique differences in DSB repair pathway mechanisms. This review comprises a brief overview of the DSB repair mechanisms in cancer and includes results obtained with revolutionary advances such as CRISPR/Cas9 and machine learning/artificial intelligence, which are rapidly advancing not only our understanding of determinants of DSB repair choice, but also how it can be used to advance precision medicine. Scientific innovation in the methods used to diagnose and treat cancer is converging with advances in basic science and translational research. This revolution will continue to be a critical driver of precision medicine that will enable precise targeting of unique individual mechanisms. This review aims to lay the foundation for achieving this goal.
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Affiliation(s)
- Taneisha Gillyard
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, TN, United States
| | - Jamaine Davis
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, TN, United States.
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21
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Tatin X, Muggiolu G, Sauvaigo S, Breton J. Evaluation of DNA double-strand break repair capacity in human cells: Critical overview of current functional methods. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108388. [PMID: 34893153 DOI: 10.1016/j.mrrev.2021.108388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 02/05/2023]
Abstract
DNA double-strand breaks (DSBs) are highly deleterious lesions, responsible for mutagenesis, chromosomal translocation or cell death. DSB repair (DSBR) is therefore a critical part of the DNA damage response (DDR) to restore molecular and genomic integrity. In humans, this process is achieved through different pathways with various outcomes. The balance between DSB repair activities varies depending on cell types, tissues or individuals. Over the years, several methods have been developed to study variations in DSBR capacity. Here, we mainly focus on functional techniques, which provide dynamic information regarding global DSB repair proficiency or the activity of specific pathways. These methods rely on two kinds of approaches. Indirect techniques, such as pulse field gel electrophoresis (PFGE), the comet assay and immunofluorescence (IF), measure DSB repair capacity by quantifying the time-dependent decrease in DSB levels after exposure to a DNA-damaging agent. On the other hand, cell-free assays and reporter-based methods directly track the repair of an artificial DNA substrate. Each approach has intrinsic advantages and limitations and despite considerable efforts, there is currently no ideal method to quantify DSBR capacity. All techniques provide different information and can be regarded as complementary, but some studies report conflicting results. Parameters such as the type of biological material, the required equipment or the cost of analysis may also limit available options. Improving currently available methods measuring DSBR capacity would be a major step forward and we present direct applications in mechanistic studies, drug development, human biomonitoring and personalized medicine, where DSBR analysis may improve the identification of patients eligible for chemo- and radiotherapy.
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Affiliation(s)
- Xavier Tatin
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France; LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | | | - Sylvie Sauvaigo
- LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | - Jean Breton
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France.
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22
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Abstract
The use of genome editing tools is expanding our understanding of various human diseases by providing insight into gene-disease interactions. Despite the recognized role of toxicants in the development of human health issues and conditions, there is currently limited characterization of their mechanisms of action, and the application of CRISPR-based genome editing to the study of toxicants could help in the identification of novel gene-environment interactions. CRISPR-based functional screens enable identification of cellular mechanisms fundamental for response and susceptibility to a given toxicant. The aim of this review is to inform future directions in the application of CRISPR technologies in toxicological studies. We review and compare different types of CRISPR-based methods including pooled, anchored, combinatorial, and perturb-sequencing screens in vitro, in addition to pooled screenings in model organisms. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
- Amin Sobh
- Department of Medicine, University of Florida Health Cancer Center, University of Florida, Gainesville, Florida
| | - Max Russo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Christopher D Vulpe
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida
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23
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A reporter system for enriching CRISPR/Cas9 knockout cells in technically challenging settings like patient models. Sci Rep 2021; 11:12649. [PMID: 34135367 PMCID: PMC8209181 DOI: 10.1038/s41598-021-91760-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas9 represents a valuable tool to determine protein function, but technical hurdles limit its use in challenging settings such as cells unable to grow in vitro like primary leukemia cells and xenografts derived thereof (PDX). To enrich CRISPR/Cas9-edited cells, we improved a dual-reporter system and cloned the genomic target sequences of the gene of interest (GOI) upstream of an out-of-frame fluorochrome which was expressed only upon successful gene editing. To reduce rounds of in vivo passaging required for PDX leukemia growth, targets of 17 GOI were cloned in a row, flanked by an improved linker, and PDX cells were lentivirally transduced for stable expression. The reporter enriched scarce, successfully gene-edited PDX cells as high as 80%. Using the reporter, we show that KO of the SRC-family kinase LYN increased the response of PDX cells of B precursor cell ALL towards Vincristine, even upon heterozygous KO, indicating haploinsufficiency. In summary, our reporter system enables enriching KO cells in technically challenging settings and extends the use of gene editing to highly patient-related model systems.
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24
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Chen L, Gao H, Zhou B, Wang Y. Comprehensive optimization of a reporter assay toolbox for three distinct CRISPR-Cas systems. FEBS Open Bio 2021; 11:1965-1980. [PMID: 33999508 PMCID: PMC8255852 DOI: 10.1002/2211-5463.13198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022] Open
Abstract
The clustered, regularly interspaced, short palindromic repeats‐associated DNA nuclease (CRISPR‐Cas) protein system allows programmable gene editing through inducing double‐strand breaks. Reporter assays for DNA cleavage and DNA repair events play an important role in advancing the CRISPR technology and improving our understanding of the underlying molecular mechanisms. Here, we developed a series of reporter assays to probe mechanisms of action of various editing processes, including nonhomologous DNA end joining, homology‐directed repair and single‐strand annealing. With special target design, the reporter assays as an optimized toolbox can be used to take advantage of three distinct CRISPR‐Cas systems (Streptococcus pyogenes Cas9, Staphylococcus aureus Cas9 and Francisella novicida U112 Cpf1) and two different reporters (GFP and Gaussia luciferase). We further validated the Gaussia reporter assays using a series of small molecules, including NU7441, RI‐1 and Mirin, and showcased the use of a GFP reporter assay as an effective tool for enrichment of cells with edited genome.
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Affiliation(s)
- Li Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haoyuan Gao
- College of Life Sciences and Oceanography, Shenzhen University, China.,Department of Biology, Oberlin College, OH, USA
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yu Wang
- College of Life Sciences and Oceanography, Shenzhen University, China
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25
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Yin Z, Zhu L, Lv Z, Li M, Tang D. Persistent luminescence nanorods-based autofluorescence-free biosensor for prostate-specific antigen detection. Talanta 2021; 233:122563. [PMID: 34215059 DOI: 10.1016/j.talanta.2021.122563] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/10/2021] [Accepted: 05/24/2021] [Indexed: 02/08/2023]
Abstract
Persistent luminescent nanoparticles (PLNPs) are a class of materials with excellent optical properties, which can continue to emit light for a long time after removing the excitation light source. This feature enables PLNPs to be used for development of biological detection modes without autofluorescence background. In this study, we prepared Zn2GeO4: Mn2+, Pr3+ (ZGOMP) nanorods through a one-pot hydrothermal method. Using the pH-responsive luminescence behavior of ZGOMP, we developed an autofluorescence-free biosensor using ZGOMP as a probe and gluconic acid as a quencher to detect prostate-specific antigen (PSA). Hybridization chain reaction (HCR) and magnetic separation system were introduced in the design to achieve efficient signal amplification. Under the optimal conditions, the as-designed autofluorescence-free sensing platform showed high selectivity, and showed a good luminescence response to PSA within the linear range of 0.001-10 ng/mL at a detection limit of 0.64 pg/mL. The excellent analytical performance shows that the current strategy provides an effective platform for clinical sample analysis.
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Affiliation(s)
- Zipeng Yin
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province), Fujian Provincial Key Laboratory of Electrochemical Energy Storage Materials, State Key Laboratory of Photocatalysis on Energy and Environment, Department of Chemistry, Fuzhou University, Fuzhou, 350108, PR China
| | - Ling Zhu
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province), Fujian Provincial Key Laboratory of Electrochemical Energy Storage Materials, State Key Laboratory of Photocatalysis on Energy and Environment, Department of Chemistry, Fuzhou University, Fuzhou, 350108, PR China
| | - Zijian Lv
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province), Fujian Provincial Key Laboratory of Electrochemical Energy Storage Materials, State Key Laboratory of Photocatalysis on Energy and Environment, Department of Chemistry, Fuzhou University, Fuzhou, 350108, PR China
| | - Meijin Li
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province), Fujian Provincial Key Laboratory of Electrochemical Energy Storage Materials, State Key Laboratory of Photocatalysis on Energy and Environment, Department of Chemistry, Fuzhou University, Fuzhou, 350108, PR China.
| | - Dianping Tang
- Key Laboratory for Analytical Science of Food Safety and Biology (MOE & Fujian Province), Fujian Provincial Key Laboratory of Electrochemical Energy Storage Materials, State Key Laboratory of Photocatalysis on Energy and Environment, Department of Chemistry, Fuzhou University, Fuzhou, 350108, PR China.
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Lau CH, Tin C, Suh Y. CRISPR-based strategies for targeted transgene knock-in and gene correction. Fac Rev 2020; 9:20. [PMID: 33659952 PMCID: PMC7886068 DOI: 10.12703/r/9-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The last few years have seen tremendous advances in CRISPR-mediated genome editing. Great efforts have been made to improve the efficiency, specificity, editing window, and targeting scope of CRISPR/Cas9-mediated transgene knock-in and gene correction. In this article, we comprehensively review recent progress in CRISPR-based strategies for targeted transgene knock-in and gene correction in both homology-dependent and homology-independent approaches. We cover homology-directed repair (HDR), synthesis-dependent strand annealing (SDSA), microhomology-mediated end joining (MMEJ), and homology-mediated end joining (HMEJ) pathways for a homology-dependent strategy and alternative DNA repair pathways such as non-homologous end joining (NHEJ), base excision repair (BER), and mismatch repair (MMR) for a homology-independent strategy. We also discuss base editing and prime editing that enable direct conversion of nucleotides in genomic DNA without damaging the DNA or requiring donor DNA. Notably, we illustrate the key mechanisms and design principles for each strategy, providing design guidelines for multiplex, flexible, scarless gene insertion and replacement at high efficiency and specificity. In addition, we highlight next-generation base editors that provide higher editing efficiency, fewer undesired by-products, and broader targeting scope.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Chung Tin
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
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