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Mózner O, Moldvay J, Szabó KS, Vaskó D, Domján J, Ács D, Ligeti Z, Fehér C, Hirsch E, Puskás L, Stahl C, Frey M, Sarkadi B. Application of a Receptor-Binding-Domain-Based Simple Immunoassay for Assessing Humoral Immunity against Emerging SARS-CoV-2 Virus Variants. Biomedicines 2023; 11:3193. [PMID: 38137414 PMCID: PMC10740953 DOI: 10.3390/biomedicines11123193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
We have developed a simple, rapid, high-throughput RBD-based ELISA to assess the humoral immunity against emerging SARS-CoV-2 virus variants. The cDNAs of the His-tagged RBD proteins of the virus variants were stably engineered into HEK cells secreting the protein into the supernatant, and RBD purification was performed by Ni-chromatography and buffer exchange by membrane filtration. The simplified assay uses single dilutions of sera from finger-pricked native blood samples, purified RBD in 96-well plates, and a chromogenic dye for development. The results of this RBD-ELISA were confirmed to correlate with those of a commercial immunoassay measuring antibodies against the Wuhan strain, as well as direct virus neutralization assays assessing the cellular effects of the Wuhan and the Omicron (BA.5) variants. Here, we document the applicability of this ELISA to assess the variant-specific humoral immunity in vaccinated and convalescent patients, as well as to follow the time course of selective vaccination response. This simple and rapid assay, easily modified to detect humoral immunity against emerging SARS-CoV-2 virus variants, may help to assess the level of antiviral protection after vaccination or infection.
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Affiliation(s)
- Orsolya Mózner
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
- Doctoral School, Semmelweis University, 1085 Budapest, Hungary
- CelluVir Biotechnology Ltd., 1094 Budapest, Hungary
| | - Judit Moldvay
- CelluVir Biotechnology Ltd., 1094 Budapest, Hungary
- I. Department of Pulmonology, National Korányi Institute of Pulmonology, 1121 Budapest, Hungary
| | - Kata Sára Szabó
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
| | - Dorottya Vaskó
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Júlia Domján
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Dorottya Ács
- I. Department of Pulmonology, National Korányi Institute of Pulmonology, 1121 Budapest, Hungary
| | - Zoltán Ligeti
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
| | - Csaba Fehér
- Biorefinery Research Group, Department of Applied Biotechnology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | - Edit Hirsch
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary
| | | | - Cordula Stahl
- Steinbeis-Innovationszentrum Zellkulturtechnik, c/o University of Applied Sciences Mannheim, Paul-Wittsack-Str. 10, D-68163 Mannheim, Germany
| | - Manfred Frey
- Steinbeis-Innovationszentrum Zellkulturtechnik, c/o University of Applied Sciences Mannheim, Paul-Wittsack-Str. 10, D-68163 Mannheim, Germany
| | - Balázs Sarkadi
- Research Centre for Natural Sciences, 1117 Budapest, Hungary; (O.M.)
- Doctoral School, Semmelweis University, 1085 Budapest, Hungary
- CelluVir Biotechnology Ltd., 1094 Budapest, Hungary
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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3
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Huszár K, Welker Z, Györgypál Z, Tóth E, Ligeti Z, Kulcsár P, Dancsó J, Tálas A, Krausz S, Varga É, Welker E. Position-dependent sequence motif preferences of SpCas9 are largely determined by scaffold-complementary spacer motifs. Nucleic Acids Res 2023; 51:5847-5863. [PMID: 37140059 PMCID: PMC10287927 DOI: 10.1093/nar/gkad323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 04/04/2023] [Accepted: 05/02/2023] [Indexed: 05/05/2023] Open
Abstract
Streptococcus pyogenes Cas9 (SpCas9) nuclease exhibits considerable position-dependent sequence preferences. The reason behind these preferences is not well understood and is difficult to rationalise, since the protein establishes interactions with the target-spacer duplex in a sequence-independent manner. We revealed here that intramolecular interactions within the single guide RNA (sgRNA), between the spacer and the scaffold, cause most of these preferences. By using in cellulo and in vitro SpCas9 activity assays with systematically designed spacer and scaffold sequences and by analysing activity data from a large SpCas9 sequence library, we show that some long (>8 nucleotides) spacer motifs, that are complementary to the RAR unit of the scaffold, interfere with sgRNA loading, and that some motifs of more than 4 nucleotides, that are complementary to the SL1 unit, inhibit DNA binding and cleavage. Furthermore, we show that intramolecular interactions are present in the majority of the inactive sgRNA sequences of the library, suggesting that they are the most important intrinsic determinants of the activity of the SpCas9 ribonucleoprotein complex. We also found that in pegRNAs, sequences at the 3' extension of the sgRNA that are complementary to the SL2 unit are also inhibitory to prime editing, but not to the nuclease activity of SpCas9.
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Affiliation(s)
- Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Genetics, Doctoral School of Biology, Faculty of Science, Eötvös Loránd University, Budapest, H-1117, Hungary
- Gene Design Ltd, Szeged, Hungary
| | - Zsombor Welker
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Biospiral-2006 Ltd, Szeged, Hungary
| | - Zoltán Györgypál
- Biospiral-2006 Ltd, Szeged, Hungary
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Gene Design Ltd, Szeged, 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, Hungary
| | - Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - János Dancsó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- Biospiral-2006 Ltd, Szeged, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Sarah Laura Krausz
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
- School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - Éva Varga
- 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, 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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4
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Tóth E, Varga É, Kulcsár PI, Kocsis-Jutka V, Krausz SL, Nyeste A, Welker Z, Huszár K, Ligeti Z, Tálas A, Welker E. Improved LbCas12a variants with altered PAM specificities further broaden the genome targeting range of Cas12a nucleases. Nucleic Acids Res 2020; 48:3722-3733. [PMID: 32107556 PMCID: PMC7144938 DOI: 10.1093/nar/gkaa110] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 02/07/2020] [Accepted: 02/24/2020] [Indexed: 12/26/2022] Open
Abstract
The widespread use of Cas12a (formerly Cpf1) nucleases for genome engineering is limited by their requirement for a rather long TTTV protospacer adjacent motif (PAM) sequence. Here we have aimed to loosen these PAM constraints and have generated new PAM mutant variants of the four Cas12a orthologs that are active in mammalian and plant cells, by combining the mutations of their corresponding RR and RVR variants with altered PAM specificities. LbCas12a-RVRR showing the highest activity was selected for an in-depth characterization of its PAM preferences in mammalian cells, using a plasmid-based assay. The consensus PAM sequence of LbCas12a-RVRR resembles a TNTN motif, but also includes TACV, TTCV CTCV and CCCV. The D156R mutation in improved LbCas12a (impLbCas12a) was found to further increase the activity of that variant in a PAM-dependent manner. Due to the overlapping but still different PAM preferences of impLbCas12a and the recently reported enAsCas12a variant, they complement each other to provide increased efficiency for genome editing and transcriptome modulating applications.
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Affiliation(s)
- Eszter Tóth
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Éva Varga
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged H-6726, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
| | - Péter István Kulcsár
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged H-6726, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
| | - Virág Kocsis-Jutka
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,ProteoScientia Kft, Cserhátszentiván, H-3066, Hungary
| | - Sarah Laura Krausz
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Antal Nyeste
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary.,ProteoScientia Kft, Cserhátszentiván, H-3066, Hungary
| | | | - Krisztina Huszár
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Biospirál-2006 Kft., Szeged, H-6726, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged H-6726, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
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5
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Kulcsár PI, Tálas A, Tóth E, Nyeste A, Ligeti Z, Welker Z, Welker E. Blackjack mutations improve the on-target activities of increased fidelity variants of SpCas9 with 5'G-extended sgRNAs. Nat Commun 2020; 11:1223. [PMID: 32144253 PMCID: PMC7060260 DOI: 10.1038/s41467-020-15021-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/06/2020] [Indexed: 12/17/2022] Open
Abstract
Increased fidelity mutants of the SpCas9 nuclease constitute the most promising approach to mitigating its off-target effects. However, these variants are effective only in a restricted target space, and many of them are reported to work less efficiently when applied in clinically relevant, pre-assembled, ribonucleoprotein forms. The low tolerance to 5'-extended, 21G-sgRNAs contributes, to a great extent, to their decreased performance. Here, we report the generation of Blackjack SpCas9 variant that shows increased fidelity yet remain effective with 21G-sgRNAs. Introducing Blackjack mutations into previously reported increased fidelity variants make them effective with 21G-sgRNAs and increases their fidelity. Two "Blackjack" nucleases, eSpCas9-plus and SpCas9-HF1-plus are superior variants of eSpCas9 and SpCas9-HF1, respectively, possessing matching on-target activity and fidelity but retaining activity with 21G-sgRNAs. They facilitate the use of existing pooled sgRNA libraries with higher specificity and show similar activities whether delivered as plasmids or as pre-assembled ribonucleoproteins.
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Affiliation(s)
- Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary.
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720, Szeged, Hungary.
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
- School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Antal Nyeste
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720, Szeged, Hungary
- Gene Design Ltd, Szeged, H-6726, Hungary
| | | | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary.
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6
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Tóth E, Czene BC, Kulcsár PI, Krausz SL, Tálas A, Nyeste A, Varga É, Huszár K, Weinhardt N, Ligeti Z, Borsy AÉ, Fodor E, Welker E. Mb- and FnCpf1 nucleases are active in mammalian cells: activities and PAM preferences of four wild-type Cpf1 nucleases and of their altered PAM specificity variants. Nucleic Acids Res 2019; 46:10272-10285. [PMID: 30239882 PMCID: PMC6212782 DOI: 10.1093/nar/gky815] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/11/2018] [Indexed: 01/02/2023] Open
Abstract
Cpf1s, the RNA-guided nucleases of the class II clustered regularly interspaced short palindromic repeats system require a short motive called protospacer adjacent motif (PAM) to be present next to the targeted sequence for their activity. The TTTV PAM sequence of As- and LbCpf1 nucleases is relatively rare in the genome of higher eukaryotic organisms. Here, we show that two other Cpf1 nucleases, Fn- and MbCpf1, which have been reported to utilize a shorter, more frequently occurring PAM sequence (TTN) when tested in vitro, carry out efficient genome modification in mammalian cells. We found that all four Cpf1 nucleases showed similar activities and TTTV PAM preferences. Our approach also revealed that besides their activities their PAM preferences are also target dependent. To increase the number of the available targets for Fn- and MbCpf1 we generated their RVR and RR mutants with altered PAM specificity and compared them to the wild-type and analogous As- and LbCpf1 variants. The mutants gained new PAM specificities but retained their activity on targets with TTTV PAMs, redefining RR-Cpf1's PAM-specificities as TTYV/TCCV, respectively. These variants may become versatile substitutes for wild-type Cpf1s by providing an expanded range of targets for genome engineering applications.
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Affiliation(s)
- Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Bernadett C Czene
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Gene Design Kft., Szeged, H-6726, Hungary
| | - Péter I Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, H-6726, Hungary
| | - Sarah L Krausz
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Antal Nyeste
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Éva Varga
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Nóra Weinhardt
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, H-6726, Hungary.,Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, H-6726, Hungary
| | - Adrienn É Borsy
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Biospirál-2006 Kft., Szeged, H-6726, Hungary
| | - Elfrieda Fodor
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary.,Biospirál-2006 Kft., Szeged, H-6726, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
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7
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Tálas A, Kulcsár PI, Weinhardt N, Borsy A, Tóth E, Szebényi K, Krausz SL, Huszár K, Vida I, Sturm Á, Gordos B, Hoffmann OI, Bencsura P, Nyeste A, Ligeti Z, Fodor E, Welker E. A convenient method to pre-screen candidate guide RNAs for CRISPR/Cas9 gene editing by NHEJ-mediated integration of a 'self-cleaving' GFP-expression plasmid. DNA Res 2017; 24:609-621. [PMID: 28679166 PMCID: PMC5726473 DOI: 10.1093/dnares/dsx029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 06/07/2017] [Indexed: 12/20/2022] Open
Abstract
The efficacies of guide RNAs (gRNAs), the short RNA molecules that bind to and determine the sequence specificity of the Streptococcus pyogenes Cas9 nuclease, to mediate DNA cleavage vary dramatically. Thus, the selection of appropriate target sites, and hence spacer sequence, is critical for most applications. Here, we describe a simple, unparalleled method for experimentally pre-testing the efficiencies of various gRNAs targeting a gene. The method explores NHEJ-cloning, genomic integration of a GFP-expressing plasmid without homologous arms and linearized in-cell. The use of 'self-cleaving' GFP-plasmids containing universal gRNAs and corresponding targets alleviates cloning burdens when this method is applied. These universal gRNAs mediate efficient plasmid cleavage and are designed to avoid genomic targets in several model species. The method combines the advantages of the straightforward FACS detection provided by applying fluorescent reporter systems and of the PCR-based approaches being capable of testing targets in their genomic context, without necessitating any extra cloning steps. Additionally, we show that NHEJ-cloning can also be used in mammalian cells for targeted integration of donor plasmids up to 10 kb in size, with up to 30% efficiency, without any selection or enrichment.
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Affiliation(s)
- András Tálas
- School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- University of Szeged, Szeged, Hungary
| | - Nóra Weinhardt
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- University of Szeged, Szeged, Hungary
| | - Adrienn Borsy
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Kornélia Szebényi
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Sarah Laura Krausz
- School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - István Vida
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Organic Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ádám Sturm
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Bianka Gordos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Orsolya Ivett Hoffmann
- Animal Biotechnology Section, Ruminant Genome Biology Group, NARIC Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Petra Bencsura
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Antal Nyeste
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Elfrieda Fodor
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
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Kulcsár PI, Tálas A, Huszár K, Ligeti Z, Tóth E, Weinhardt N, Fodor E, Welker E. Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage. Genome Biol 2017; 18:190. [PMID: 28985763 PMCID: PMC6389135 DOI: 10.1186/s13059-017-1318-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/11/2017] [Indexed: 12/19/2022] Open
Abstract
Background The propensity for off-target activity of Streptococcus pyogenes Cas9 (SpCas9) has been considerably decreased by rationally engineered variants with increased fidelity (eSpCas9; SpCas9-HF1). However, a subset of targets still generate considerable off-target effects. To deal specifically with these targets, we generated new “Highly enhanced Fidelity” nuclease variants (HeFSpCas9s) containing mutations from both eSpCas9 and SpCas9-HF1 and examined these improved nuclease variants side by side to decipher the factors that affect their specificities and to determine the optimal nuclease for applications sensitive to off-target effects. Results These three increased-fidelity nucleases can routinely be used only with perfectly matching 20-nucleotide-long spacers, a matching 5′ G extension being more detrimental to their activities than a mismatching one. HeFSpCas9 exhibit substantially improved specificity for those targets for which eSpCas9 and SpCas9-HF1 have higher off-target propensity. The targets can also be ranked by their cleavability and off-target effects manifested by the increased fidelity nucleases. Furthermore, we show that the mutations in these variants may diminish the cleavage, but not the DNA-binding, of SpCas9s. Conclusions No single nuclease variant shows generally superior fidelity; instead, for highest specificity cleavage, each target needs to be matched with an appropriate high-fidelity nuclease. We provide here a framework for generating new nuclease variants for targets that currently have no matching optimal nuclease, and offer a simple means for identifying the optimal nuclease for targets in the absence of accurate target-ranking prediction tools. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1318-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,University of Szeged, Szeged, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,Gene Design Kft, Szeged, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Gene Design Kft, Szeged, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Nóra Weinhardt
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,University of Szeged, Szeged, Hungary
| | - Elfrieda Fodor
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary. .,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
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