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Jacobs R, Dogbey MD, Mnyandu N, Neves K, Barth S, Arbuthnot P, Maepa MB. AAV Immunotoxicity: Implications in Anti-HBV Gene Therapy. Microorganisms 2023; 11:2985. [PMID: 38138129 PMCID: PMC10745739 DOI: 10.3390/microorganisms11122985] [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: 11/03/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Hepatitis B virus (HBV) has afflicted humankind for decades and there is still no treatment that can clear the infection. The development of recombinant adeno-associated virus (rAAV)-based gene therapy for HBV infection has become important in recent years and research has made exciting leaps. Initial studies, mainly using mouse models, showed that rAAVs are non-toxic and induce minimal immune responses. However, several later studies demonstrated rAAV toxicity, which is inextricably associated with immunogenicity. This is a major setback for the progression of rAAV-based therapies toward clinical application. Research aimed at understanding the mechanisms behind rAAV immunity and toxicity has contributed significantly to the inception of approaches to overcoming these challenges. The target tissue, the features of the vector, and the vector dose are some of the determinants of AAV toxicity, with the latter being associated with the most severe adverse events. This review discusses our current understanding of rAAV immunogenicity, toxicity, and approaches to overcoming these hurdles. How this information and current knowledge about HBV biology and immunity can be harnessed in the efforts to design safe and effective anti-HBV rAAVs is discussed.
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Affiliation(s)
- Ridhwaanah Jacobs
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Infectious Diseases and Oncology Research Institute (IDORI), Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa
| | - Makafui Dennis Dogbey
- Medical Biotechnology and Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7700, South Africa; (M.D.D.)
| | - Njabulo Mnyandu
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Infectious Diseases and Oncology Research Institute (IDORI), Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa
| | - Keila Neves
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Infectious Diseases and Oncology Research Institute (IDORI), Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa
| | - Stefan Barth
- Medical Biotechnology and Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7700, South Africa; (M.D.D.)
- South African Research Chair in Cancer Biotechnology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7700, South Africa
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Infectious Diseases and Oncology Research Institute (IDORI), Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa
| | - Mohube Betty Maepa
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Infectious Diseases and Oncology Research Institute (IDORI), Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa
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2
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Yang ZX, Fu YW, Zhao JJ, Zhang F, Li SA, Zhao M, Wen W, Zhang L, Cheng T, Zhang JP, Zhang XB. Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1206-1220. [PMID: 36549468 PMCID: PMC11082263 DOI: 10.1016/j.gpb.2022.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 11/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
A series of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9) systems have been engineered for genome editing. The most widely used Cas9 is SpCas9 from Streptococcus pyogenes and SaCas9 from Staphylococcus aureus. However, a comparison of their detailed gene editing outcomes is still lacking. By characterizing the editing outcomes of 11 sites in human induced pluripotent stem cells (iPSCs) and K562 cells, we found that SaCas9 could edit the genome with greater efficiencies than SpCas9. We also compared the effects of spacer lengths of single-guide RNAs (sgRNAs; 18-21 nt for SpCas9 and 19-23 nt for SaCas9) and found that the optimal spacer lengths were 20 nt and 21 nt for SpCas9 and SaCas9, respectively. However, the optimal spacer length for a particular sgRNA was 18-21 nt for SpCas9 and 21-22 nt for SaCas9. Furthermore, SpCas9 exhibited a more substantial bias than SaCas9 for nonhomologous end-joining (NHEJ) +1 insertion at the fourth nucleotide upstream of the protospacer adjacent motif (PAM), indicating a characteristic of a staggered cut. Accordingly, editing with SaCas9 led to higher efficiencies of NHEJ-mediated double-stranded oligodeoxynucleotide (dsODN) insertion or homology-directed repair (HDR)-mediated adeno-associated virus serotype 6 (AAV6) donor knock-in. Finally, GUIDE-seq analysis revealed that SaCas9 exhibited significantly reduced off-target effects compared with SpCas9. Our work indicates the superior performance of SaCas9 to SpCas9 in transgene integration-based therapeutic gene editing and the necessity to identify the optimal spacer length to achieve desired editing results.
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Affiliation(s)
- Zhi-Xue Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Ya-Wen Fu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Juan-Juan Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Si-Ang Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Mei Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Wei Wen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China
| | - Jian-Ping Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
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3
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Maltseva EA, Vasil’eva IA, Moor NA, Kim DV, Dyrkheeva NS, Kutuzov MM, Vokhtantsev IP, Kulishova LM, Zharkov DO, Lavrik OI. Cas9 is mostly orthogonal to human systems of DNA break sensing and repair. PLoS One 2023; 18:e0294683. [PMID: 38019812 PMCID: PMC10686484 DOI: 10.1371/journal.pone.0294683] [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: 06/28/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
CRISPR/Cas9 system is а powerful gene editing tool based on the RNA-guided cleavage of target DNA. The Cas9 activity can be modulated by proteins involved in DNA damage signalling and repair due to their interaction with double- and single-strand breaks (DSB and SSB, respectively) generated by wild-type Cas9 or Cas9 nickases. Here we address the interplay between Streptococcus pyogenes Cas9 and key DNA repair factors, including poly(ADP-ribose) polymerase 1 (SSB/DSB sensor), its closest homolog poly(ADP-ribose) polymerase 2, Ku antigen (DSB sensor), DNA ligase I (SSB sensor), replication protein A (DNA duplex destabilizer), and Y-box binding protein 1 (RNA/DNA binding protein). None of those significantly affected Cas9 activity, while Cas9 efficiently shielded DSBs and SSBs from their sensors. Poly(ADP-ribosyl)ation of Cas9 detected for poly(ADP-ribose) polymerase 2 had no apparent effect on the activity. In cellulo, Cas9-dependent gene editing was independent of poly(ADP-ribose) polymerase 1. Thus, Cas9 can be regarded as an enzyme mostly orthogonal to the natural regulation of human systems of DNA break sensing and repair.
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Affiliation(s)
| | - Inna A. Vasil’eva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Nina A. Moor
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Daria V. Kim
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | - Mikhail M. Kutuzov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Ivan P. Vokhtantsev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Lilya M. Kulishova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Olga I. Lavrik
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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4
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Maghsoud Y, Jayasinghe-Arachchige VM, Kumari P, Cisneros GA, Liu J. Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects. J Chem Inf Model 2023; 63:6834-6850. [PMID: 37877218 DOI: 10.1021/acs.jcim.3c01284] [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] [Indexed: 10/26/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) technology is an RNA-guided targeted genome-editing tool using Cas family proteins. Two magnesium-dependent nuclease domains of the Cas9 enzyme, termed HNH and RuvC, are responsible for cleaving the target DNA (t-DNA) and nontarget DNA strands, respectively. The HNH domain is believed to determine the DNA cleavage activity of both endonuclease domains and is sensitive to complementary RNA-DNA base pairing. However, the underlying molecular mechanisms of CRISPR-Cas9, by which it rebukes or accepts mismatches, are poorly understood. Thus, investigation of the structure and dynamics of the catalytic state of Cas9 with either matched or mismatched t-DNA can provide insights into improving its specificity by reducing off-target cleavages. Here, we focus on a recently discovered catalytic-active form of the Streptococcus pyogenes Cas9 (SpCas9) and employ classical molecular dynamics and coupled quantum mechanics/molecular mechanics simulations to study two possible mechanisms of t-DNA cleavage reaction catalyzed by the HNH domain. Moreover, by designing a mismatched t-DNA structure called MM5 (C to G at the fifth position from the protospacer adjacent motif region), the impact of single-guide RNA (sgRNA) and t-DNA complementarity on the catalysis process was investigated. Based on these simulations, our calculated binding affinities, minimum energy paths, and analysis of catalytically important residues provide atomic-level details of the differences between matched and mismatched cleavage reactions. In addition, several residues exhibit significant differences in their catalytic roles for the two studied systems, including K253, K263, R820, K896, and K913.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Vindi M Jayasinghe-Arachchige
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Pratibha Kumari
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
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5
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Barghouth PG, Melemenidis S, Montay-Gruel P, Ollivier J, Viswanathan V, Jorge PG, Soto LA, Lau BC, Sadeghi C, Edlabadkar A, Zhang R, Ru N, Baulch JE, Manjappa R, Wang J, Le Bouteiller M, Surucu M, Yu A, Bush K, Skinner L, Maxim PG, Loo BW, Limoli CL, Vozenin MC, Frock RL. FLASH-RT does not affect chromosome translocations and junction structures beyond that of CONV-RT dose-rates. Radiother Oncol 2023; 188:109906. [PMID: 37690668 PMCID: PMC10591966 DOI: 10.1016/j.radonc.2023.109906] [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: 03/29/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND AND PURPOSE The impact of radiotherapy (RT) at ultra high vs conventional dose rate (FLASH vs CONV) on the generation and repair of DNA double strand breaks (DSBs) is an important question that remains to be investigated. Here, we tested the hypothesis as to whether FLASH-RT generates decreased chromosomal translocations compared to CONV-RT. MATERIALS AND METHODS We used two FLASH validated electron beams and high-throughput rejoin and genome-wide translocation sequencing (HTGTS-JoinT-seq), employing S. aureus and S. pyogenes Cas9 "bait" DNA double strand breaks (DSBs) in HEK239T cells, to measure differences in bait-proximal repair and their genome-wide translocations to "prey" DSBs generated after various irradiation doses, dose rates and oxygen tensions (normoxic, 21% O2; physiological, 4% O2; hypoxic, 2% and 0.5% O2). Electron irradiation was delivered using a FLASH capable Varian Trilogy and the eRT6/Oriatron at CONV (0.08-0.13 Gy/s) and FLASH (1x102-5x106 Gy/s) dose rates. Related experiments using clonogenic survival and γH2AX foci in the 293T and the U87 glioblastoma lines were also performed to discern FLASH-RT vs CONV-RT DSB effects. RESULTS Normoxic and physioxic irradiation of HEK293T cells increased translocations at the cost of decreasing bait-proximal repair but were indistinguishable between CONV-RT and FLASH-RT. Although no apparent increase in chromosome translocations was observed with hypoxia-induced apoptosis, the combined decrease in oxygen tension with IR dose-rate modulation did not reveal significant differences in the level of translocations nor in their junction structures. Furthermore, RT dose rate modality on U87 cells did not change γH2AX foci numbers at 1- and 24-hours post-irradiation nor did this affect 293T clonogenic survival. CONCLUSION Irrespective of oxygen tension, FLASH-RT produces translocations and junction structures at levels and proportions that are indistinguishable from CONV-RT.
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Affiliation(s)
- Paul G Barghouth
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stavros Melemenidis
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pierre Montay-Gruel
- Laboratory of Radiation Oncology, Department of Radiation Oncology, Lausanne University Hospital and University of Lausanne, Switzerland; Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Jonathan Ollivier
- Laboratory of Radiation Oncology, Department of Radiation Oncology, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Vignesh Viswanathan
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Patrik G Jorge
- Institute of Radiation Physics/CHUV, Lausanne University Hospital, Switzerland
| | - Luis A Soto
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brianna C Lau
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cheyenne Sadeghi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anushka Edlabadkar
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Richard Zhang
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Ning Ru
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Janet E Baulch
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Rakesh Manjappa
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jinghui Wang
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marie Le Bouteiller
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Murat Surucu
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amy Yu
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karl Bush
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lawrie Skinner
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter G Maxim
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Billy W Loo
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles L Limoli
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Marie-Catherine Vozenin
- Laboratory of Radiation Oncology, Department of Radiation Oncology, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Richard L Frock
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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6
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Nguyen MT, Kim SA, Cheng YY, Hong SH, Jin YS, Han NS. A qPCR Method to Assay Endonuclease Activity of Cas9-sgRNA Ribonucleoprotein Complexes. J Microbiol Biotechnol 2023; 33:1228-1237. [PMID: 37415091 PMCID: PMC10580886 DOI: 10.4014/jmb.2305.05010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
The CRISPR-Cas system has emerged as the most efficient genome editing technique for a wide range of cells. Delivery of the Cas9-sgRNA ribonucleoprotein complex (Cas9 RNP) has gained popularity. The objective of this study was to develop a quantitative polymerase chain reaction (qPCR)-based assay to quantify the double-strand break reaction mediated by Cas9 RNP. To accomplish this, the dextransucrase gene (dsr) from Leuconostoc citreum was selected as the target DNA. The Cas9 protein was produced using recombinant Escherichia coli BL21, and two sgRNAs were synthesized through in vitro transcription to facilitate binding with the dsr gene. Under optimized in vitro conditions, the 2.6 kb dsr DNA was specifically cleaved into 1.1 and 1.5 kb fragments by both Cas9-sgRNA365 and Cas9-sgRNA433. By monitoring changes in dsr concentration using qPCR, the endonuclease activities of the two Cas9 RNPs were measured, and their efficiencies were compared. Specifically, the specific activities of dsr365RNP and dsr433RNP were 28.74 and 34.48 (unit/μg RNP), respectively. The versatility of this method was also verified using different target genes, uracil phosphoribosyl transferase (upp) gene, of Bifidobacterium bifidum and specific sgRNAs. The assay method was also utilized to determine the impact of high electrical field on Cas9 RNP activity during an efficient electroporation process. Overall, the results demonstrated that the qPCR-based method is an effective tool for measuring the endonuclease activity of Cas9 RNP.
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Affiliation(s)
- Minh Tri Nguyen
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
- Faculty of Biology, Dalat University, 01- Phu Dong Thien Vuong, Dalat, Vietnam
| | - Seul-Ah Kim
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ya-Yun Cheng
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sung Hoon Hong
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nam Soo Han
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
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7
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Deng B, Xue J. HIV infection detection using CRISPR/Cas systems: Present and future prospects. Comput Struct Biotechnol J 2023; 21:4409-4423. [PMID: 37711183 PMCID: PMC10498128 DOI: 10.1016/j.csbj.2023.09.005] [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: 06/03/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection poses substantial medical risks to global public health. An essential strategy to combat the HIV epidemic is timely and effective virus testing. CRISPR-based assays combine the highly compatible CRISPR system with different elements, yielding portability, digitization capabilities, low economic burden and low operational thresholds. The application of CRISPR-based assays has demonstrated rapid, accurate, and accessible means of pathogen testing, suggesting great potential as point-of-care (POC) assays. This review outlines the different types of CRISPR/Cas systems based on Cas proteins and their applications for the detection of HIV. Additionally, we also offer an overview of future perspectives on CRISPR-based methods for HIV detection, including advances in nucleic acid amplification-free testing, improved personal testing, and refined testing for HIV genotypes and drug-resistant strains.
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Affiliation(s)
- Bingpeng Deng
- Beijing Key Laboratory for Animal Models of Emerging and Re-Emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China
- NHC Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
| | - Jing Xue
- Beijing Key Laboratory for Animal Models of Emerging and Re-Emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China
- NHC Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
- Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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8
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Bestas B, Wimberger S, Degtev D, Madsen A, Rottner AK, Karlsson F, Naumenko S, Callahan M, Touza JL, Francescatto M, Möller CI, Badertscher L, Li S, Cerboni S, Selfjord N, Ericson E, Gordon E, Firth M, Chylinski K, Taheri-Ghahfarokhi A, Bohlooly-Y M, Snowden M, Pangalos M, Nuttall B, Akcakaya P, Sienski G, Maresca M. A Type II-B Cas9 nuclease with minimized off-targets and reduced chromosomal translocations in vivo. Nat Commun 2023; 14:5474. [PMID: 37673883 PMCID: PMC10482872 DOI: 10.1038/s41467-023-41240-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 08/25/2023] [Indexed: 09/08/2023] Open
Abstract
Streptococcus pyogenes Cas9 (SpCas9) and derived enzymes are widely used as genome editors, but their promiscuous nuclease activity often induces undesired mutations and chromosomal rearrangements. Several strategies for mapping off-target effects have emerged, but they suffer from limited sensitivity. To increase the detection sensitivity, we develop an off-target assessment workflow that uses Duplex Sequencing. The strategy increases sensitivity by one order of magnitude, identifying previously unknown SpCas9's off-target mutations in the humanized PCSK9 mouse model. To reduce off-target risks, we perform a bioinformatic search and identify a high-fidelity Cas9 variant of the II-B subfamily from Parasutterella secunda (PsCas9). PsCas9 shows improved specificity as compared to SpCas9 across multiple tested sites, both in vitro and in vivo, including the PCSK9 site. In the future, while PsCas9 will offer an alternative to SpCas9 for research and clinical use, the Duplex Sequencing workflow will enable a more sensitive assessment of Cas9 editing outcomes.
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Affiliation(s)
- Burcu Bestas
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Sandra Wimberger
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Dmitrii Degtev
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Alexandra Madsen
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Antje K Rottner
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Karlsson
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | - Sergey Naumenko
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
| | - Megan Callahan
- Translational Genomics, Translational Medicine, R&D Oncology, AstraZeneca, Waltham, MA, USA
| | - Julia Liz Touza
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Margherita Francescatto
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | - Carl Ivar Möller
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Lukas Badertscher
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Songyuan Li
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Silvia Cerboni
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Niklas Selfjord
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Elke Ericson
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Euan Gordon
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | | | - Amir Taheri-Ghahfarokhi
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike Snowden
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Barrett Nuttall
- Translational Genomics, Translational Medicine, R&D Oncology, AstraZeneca, Waltham, MA, USA
| | - Pinar Akcakaya
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Grzegorz Sienski
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
| | - Marcello Maresca
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
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9
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Tsuboyama K, Dauparas J, Chen J, Laine E, Mohseni Behbahani Y, Weinstein JJ, Mangan NM, Ovchinnikov S, Rocklin GJ. Mega-scale experimental analysis of protein folding stability in biology and design. Nature 2023; 620:434-444. [PMID: 37468638 PMCID: PMC10412457 DOI: 10.1038/s41586-023-06328-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/14/2023] [Indexed: 07/21/2023]
Abstract
Advances in DNA sequencing and machine learning are providing insights into protein sequences and structures on an enormous scale1. However, the energetics driving folding are invisible in these structures and remain largely unknown2. The hidden thermodynamics of folding can drive disease3,4, shape protein evolution5-7 and guide protein engineering8-10, and new approaches are needed to reveal these thermodynamics for every sequence and structure. Here we present cDNA display proteolysis, a method for measuring thermodynamic folding stability for up to 900,000 protein domains in a one-week experiment. From 1.8 million measurements in total, we curated a set of around 776,000 high-quality folding stabilities covering all single amino acid variants and selected double mutants of 331 natural and 148 de novo designed protein domains 40-72 amino acids in length. Using this extensive dataset, we quantified (1) environmental factors influencing amino acid fitness, (2) thermodynamic couplings (including unexpected interactions) between protein sites, and (3) the global divergence between evolutionary amino acid usage and protein folding stability. We also examined how our approach could identify stability determinants in designed proteins and evaluate design methods. The cDNA display proteolysis method is fast, accurate and uniquely scalable, and promises to reveal the quantitative rules for how amino acid sequences encode folding stability.
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Affiliation(s)
- Kotaro Tsuboyama
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- PRESTO, Japan Science and Technology Agency, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jonathan Chen
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- McCormick School of Engineering, Northwestern University, Evanston, IL, USA
| | - Elodie Laine
- Sorbonne Université, CNRS, IBPS, Laboratory of Computational and Quantitative Biology (LCQB), UMR 7238, Paris, France
| | - Yasser Mohseni Behbahani
- Sorbonne Université, CNRS, IBPS, Laboratory of Computational and Quantitative Biology (LCQB), UMR 7238, Paris, France
| | - Jonathan J Weinstein
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Niall M Mangan
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA
| | - Gabriel J Rocklin
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
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10
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Esquerra-Ruvira B, Baquedano I, Ruiz R, Fernandez A, Montoliu L, Mojica FJM. Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering. Microb Biotechnol 2023. [PMID: 37097160 DOI: 10.1111/1751-7915.14266] [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: 02/06/2023] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Non-coding RNAs (crRNAs) produced from clustered regularly interspaced short palindromic repeats (CRISPR) loci and CRISPR-associated (Cas) proteins of the prokaryotic CRISPR-Cas systems form complexes that interfere with the spread of transmissible genetic elements through Cas-catalysed cleavage of foreign genetic material matching the guide crRNA sequences. The easily programmable targeting of nucleic acids enabled by these ribonucleoproteins has facilitated the implementation of CRISPR-based molecular biology tools for in vivo and in vitro modification of DNA and RNA targets. Despite the diversity of DNA-targeting Cas nucleases so far identified, native and engineered derivatives of the Streptococcus pyogenes SpCas9 are the most widely used for genome engineering, at least in part due to their catalytic robustness and the requirement of an exceptionally short motif (5'-NGG-3' PAM) flanking the target sequence. However, the large size of the SpCas9 variants impairs the delivery of the tool to eukaryotic cells and smaller alternatives are desirable. Here, we identify in a metagenome a new CRISPR-Cas9 system associated with a smaller Cas9 protein (EHCas9) that targets DNA sequences flanked by 5'-NGG-3' PAMs. We develop a simplified EHCas9 tool that specifically cleaves DNA targets and is functional for genome editing applications in prokaryotes and eukaryotic cells.
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Affiliation(s)
- Belen Esquerra-Ruvira
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Ignacio Baquedano
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Raul Ruiz
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Almudena Fernandez
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
| | - Francisco J M Mojica
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef", University of Alicante, Alicante, Spain
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11
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Advancement in CRISPR/Cas9 Technology to Better Understand and Treat Neurological Disorders. Cell Mol Neurobiol 2023; 43:1019-1035. [PMID: 35751791 DOI: 10.1007/s10571-022-01242-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/09/2022] [Indexed: 11/26/2022]
Abstract
Neurological disorders have complicated pathophysiology that may involve several genetic mutations. Conventional treatment has limitations as they only treat apparent symptoms. Although, personalized medicine is emerging as a promising neuro-intervention, lack of precision is the major pitfall. Clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system is evolving as a technological platform that may overcome the therapeutic limitations towards precision medicine. In the future, targeting genes in neurological disorders may be the mainstay of modern therapy. The present review on CRISPR/Cas9 and its application in various neurological disorders may provide a platform for its future clinical relevance towards developing precise and personalized medicine.
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12
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Barghouth PG, Melemenidis S, Montay-Gruel P, Ollivier J, Viswanathan V, Jorge PG, Soto LA, Lau BC, Sadeghi C, Edlabadkar A, Manjappa R, Wang J, Le Bouteiller M, Surucu M, Yu A, Bush K, Skinner L, Maxim PG, Loo BW, Limoli CL, Vozenin MC, Frock RL. FLASH-RT does not affect chromosome translocations and junction structures beyond that of CONV-RT dose-rates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534408. [PMID: 37034651 PMCID: PMC10081175 DOI: 10.1101/2023.03.27.534408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The molecular and cellular mechanisms driving the enhanced therapeutic ratio of ultra-high dose-rate radiotherapy (FLASH-RT) over slower conventional (CONV-RT) radiotherapy dose-rate remain to be elucidated. However, attenuated DNA damage and transient oxygen depletion are among several proposed models. Here, we tested whether FLASH-RT under physioxic (4% O 2 ) and hypoxic conditions (≤2% O 2 ) reduces genome-wide translocations relative to CONV-RT and whether any differences identified revert under normoxic (21% O 2 ) conditions. We employed high-throughput rejoin and genome-wide translocation sequencing ( HTGTS-JoinT-seq ), using S. aureus and S. pyogenes Cas9 "bait" DNA double strand breaks (DSBs), to measure differences in bait-proximal repair and their genome-wide translocations to "prey" DSBs generated by electron beam CONV-RT (0.08-0.13Gy/s) and FLASH-RT (1×10 2 -5×10 6 Gy/s), under varying ionizing radiation (IR) doses and oxygen tensions. Normoxic and physioxic irradiation of HEK293T cells increased translocations at the cost of decreasing bait-proximal repair but were indistinguishable between CONV-RT and FLASH-RT. Although no apparent increase in chromosome translocations was observed with hypoxia-induced apoptosis, the combined decrease in oxygen tension with IR dose-rate modulation did not reveal significant differences in the level of translocations nor in their junction structures. Thus, Irrespective of oxygen tension, FLASH-RT produces translocations and junction structures at levels and proportions that are indistinguishable from CONV-RT.
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Affiliation(s)
- Paul G. Barghouth
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stavros Melemenidis
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pierre Montay-Gruel
- Laboratory of Radiation Oncology, Department of Radiation Oncology. Lausanne University Hospital and University of Lausanne, Switzerland
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Jonathan Ollivier
- Laboratory of Radiation Oncology, Department of Radiation Oncology. Lausanne University Hospital and University of Lausanne, Switzerland
| | - Vignesh Viswanathan
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Patrik G. Jorge
- Institute of Radiation Physics/CHUV, Lausanne University Hospital, Switzerland
| | - Luis A. Soto
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brianna C. Lau
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cheyenne Sadeghi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anushka Edlabadkar
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rakesh Manjappa
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jinghui Wang
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marie Le Bouteiller
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Murat Surucu
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amy Yu
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karl Bush
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lawrie Skinner
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter G. Maxim
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Billy W. Loo
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles L. Limoli
- Department of Radiation Oncology, University of California, Irvine, CA 92697-2695, USA
| | - Marie-Catherine Vozenin
- Laboratory of Radiation Oncology, Department of Radiation Oncology. Lausanne University Hospital and University of Lausanne, Switzerland
| | - Richard L. Frock
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
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13
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Puppulin L, Ishikawa J, Sumino A, Marchesi A, Flechsig H, Umeda K, Kodera N, Nishimasu H, Shibata M. Dynamics of Target DNA Binding and Cleavage by Staphylococcus aureus Cas9 as Revealed by High-Speed Atomic Force Microscopy. ACS NANO 2023; 17:4629-4641. [PMID: 36848598 DOI: 10.1021/acsnano.2c10709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Programmable DNA binding and cleavage by CRISPR-Cas9 has revolutionized the life sciences. However, the off-target cleavage observed in DNA sequences with some homology to the target still represents a major limitation for a more widespread use of Cas9 in biology and medicine. For this reason, complete understanding of the dynamics of DNA binding, interrogation and cleavage by Cas9 is crucial to improve the efficiency of genome editing. Here, we use high-speed atomic force microscopy (HS-AFM) to investigate Staphylococcus aureus Cas9 (SaCas9) and its dynamics of DNA binding and cleavage. Upon binding to single-guide RNA (sgRNA), SaCas9 forms a close bilobed structure that transiently and flexibly adopts also an open configuration. The SaCas9-mediated DNA cleavage is characterized by release of cleaved DNA and immediate dissociation, confirming that SaCas9 operates as a multiple turnover endonuclease. According to present knowledge, the process of searching for target DNA is mainly governed by three-dimensional diffusion. Independent HS-AFM experiments show a potential long-range attractive interaction between SaCas9-sgRNA and its target DNA. The interaction precedes the formation of the stable ternary complex and is observed exclusively in the vicinity of the protospacer-adjacent motif (PAM), up to distances of several nanometers. The direct visualization of the process by sequential topographic images suggests that SaCas9-sgRNA binds to the target sequence first, while the following binding of the PAM is accompanied by local DNA bending and formation of the stable complex. Collectively, our HS-AFM data reveal a potential and unexpected behavior of SaCas9 during the search for DNA targets.
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Affiliation(s)
- Leonardo Puppulin
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Junichiro Ishikawa
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Ayumi Sumino
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Arin Marchesi
- Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, Via Tronto, 10/A Torrette di Ancona, 60126, Ancona, Italy
| | - Holger Flechsig
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kenichi Umeda
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Hiroshi Nishimasu
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Inamori Research Institute for Science, Shimogyo-ku, Kyoto 600-8411, Japan
| | - Mikihiro Shibata
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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14
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Adeyinka OS, Tabassum B, Koloko BL, Ogungbe IV. Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis. PLANTA 2023; 257:78. [PMID: 36913066 DOI: 10.1007/s00425-023-04110-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The enhancement of CRISPR-Cas gene editing with robust nuclease activity promotes genetic modification of desirable agronomic traits, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits in crops. The genetic diversity of food crops has reduced tremendously over the past twelve millennia due to plant domestication. This reduction presents significant challenges for the future especially considering the risks posed by global climate change to food production. While crops with improved phenotypes have been generated through crossbreeding, mutation breeding, and transgenic breeding over the years, improving phenotypic traits through precise genetic diversification has been challenging. The challenges are broadly associated with the randomness of genetic recombination and conventional mutagenesis. This review highlights how emerging gene-editing technologies reduce the burden and time necessary for developing desired traits in plants. Our focus is to provide readers with an overview of the advances in CRISPR-Cas-based genome editing for crop improvement. The use of CRISPR-Cas systems in generating genetic diversity to enhance the quality and nutritional value of staple food crops is discussed. We also outlined recent applications of CRISPR-Cas in developing pest-resistant crops and removing unwanted traits, such as allergenicity from crops. Genome editing tools continue to evolve and present unprecedented opportunities to enhance crop germplasm via precise mutations at the desired loci of the plant genome.
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Affiliation(s)
- Olawale Samuel Adeyinka
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA.
| | - Bushra Tabassum
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Ifedayo Victor Ogungbe
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA
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15
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Lopez FB, McKeown PC, Fort A, Brychkova G, Spillane C. The boys are back in town: Rethinking the function of ribosomal DNA repeats in the genomic era. MOLECULAR PLANT 2023; 16:514-516. [PMID: 36680344 DOI: 10.1016/j.molp.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/06/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Affiliation(s)
- Francesca B Lopez
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, H91 REW4 Galway, Ireland.
| | - Peter C McKeown
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, H91 REW4 Galway, Ireland
| | - Antoine Fort
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, H91 REW4 Galway, Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, H91 REW4 Galway, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, H91 REW4 Galway, Ireland.
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16
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Vos PD, Filipovska A, Rackham O. Frankenstein Cas9: engineering improved gene editing systems. Biochem Soc Trans 2022; 50:1505-1516. [PMID: 36305591 DOI: 10.1042/bst20220873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 01/05/2024]
Abstract
The discovery of CRISPR-Cas9 and its widespread use has revolutionised and propelled research in biological sciences. Although the ability to target Cas9's nuclease activity to specific sites via an easily designed guide RNA (gRNA) has made it an adaptable gene editing system, it has many characteristics that could be improved for use in biotechnology. Cas9 exhibits significant off-target activity and low on-target nuclease activity in certain contexts. Scientists have undertaken ambitious protein engineering campaigns to bypass these limitations, producing several promising variants of Cas9. Cas9 variants with improved and alternative activities provide exciting new tools to expand the scope and fidelity of future CRISPR applications.
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Affiliation(s)
- Pascal D Vos
- Curtin Medical School, Curtin University, Bentley, Western Australia 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia 6009, Australia
| | - Oliver Rackham
- Curtin Medical School, Curtin University, Bentley, Western Australia 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia 6009, Australia
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17
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Pelea O, Fulga TA, Sauka-Spengler T. RNA-Responsive gRNAs for Controlling CRISPR Activity: Current Advances, Future Directions, and Potential Applications. CRISPR J 2022; 5:642-659. [PMID: 36206027 PMCID: PMC9618385 DOI: 10.1089/crispr.2022.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
CRISPR-Cas9 has emerged as a major genome manipulation tool. As Cas9 can cause off-target effects, several methods for controlling the expression of CRISPR systems were developed. Recent studies have shown that CRISPR activity could be controlled by sensing expression levels of endogenous transcripts. This is particularly interesting, as endogenous RNAs could harbor important information about the cell type, disease state, and environmental challenges cells are facing. Single-guide RNA (sgRNA) engineering played a major role in the development of RNA-responsive CRISPR systems. Following further optimizations, RNA-responsive sgRNAs could enable the development of novel therapeutic and research applications. This review introduces engineering strategies that could be employed to modify Streptococcus pyogenes sgRNAs with a focus on recent advances made toward the development of RNA-responsive sgRNAs. Future directions and potential applications of these technologies are also discussed.
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Affiliation(s)
- Oana Pelea
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA.,Address correspondence to: Oana Pelea, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom,
| | - Tudor A. Fulga
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA.,Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Address correspondence to: Tatjana Sauka-Spengler, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom,
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18
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Major L, McClements ME, MacLaren RE. New CRISPR Tools to Correct Pathogenic Mutations in Usher Syndrome. Int J Mol Sci 2022; 23:ijms231911669. [PMID: 36232969 PMCID: PMC9569511 DOI: 10.3390/ijms231911669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
Inherited retinal degenerations are a leading cause of blindness in the UK. Significant advances have been made to tackle this issue in recent years, with a pioneering FDA approved gene therapy treatment (Luxturna®), which targets a loss of function mutation in the RPE65 gene. However, there remain notable shortcomings to this form of gene replacement therapy. In particular, the lack of viability for gene sequences exceeding the 4.7 kb adeno-associated virus (AAV) packaging limit or for toxic gain of function mutations. The USH2A gene at ~15.7 kb for instance is too large for AAV delivery: a safe and effective vehicle capable of transducing photoreceptor cells for gene replacement therapy. Usher Syndrome is a clinically and genetically heterogenous deaf-blindness syndrome with autosomal recessive inheritance. The USH2A gene encodes the protein usherin, which localises to the photoreceptor cilium and cochlear hair cells. Mutations in the USH2A gene cause Usher Syndrome type II (USH2), which is the most common subtype of Usher Syndrome and the focus of this review. To date, researchers have been unable to create an efficient, safe editing tool that is small enough to fit inside a single AAV vector for delivery into human cells. This article reviews the potential of CRISPR technology, derived from bacterial defence mechanisms, to overcome these challenges; delivering tools to precisely edit and correct small insertions, deletions and base transitions in USH2A without the need to deliver the full-length gene. Such an ultra-compact therapy could make strides in combating a significant cause of blindness in young people.
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Affiliation(s)
- Lauren Major
- Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Correspondence:
| | - Michelle E. McClements
- Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Robert E. MacLaren
- Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences & NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
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19
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Nye DB, Tanner NA. Chimeric DNA byproducts in strand displacement amplification using the T7 replisome. PLoS One 2022; 17:e0273979. [PMID: 36121810 PMCID: PMC9484634 DOI: 10.1371/journal.pone.0273979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
Recent advances in next generation sequencing technologies enable reading DNA molecules hundreds of kilobases in length and motivate development of DNA amplification methods capable of producing long amplicons. In vivo, DNA replication is performed not by a single polymerase enzyme, but multiprotein complexes called replisomes. Here, we investigate strand-displacement amplification reactions using the T7 replisome, a macromolecular complex of a helicase, a single-stranded DNA binding protein, and a DNA polymerase. The T7 replisome may initiate processive DNA synthesis from DNA nicks, and the reaction of a 48 kilobase linear double stranded DNA substrate with the T7 replisome and nicking endonucleases is shown to produce discrete DNA amplicons. To gain a mechanistic understanding of this reaction, we utilized Oxford Nanopore long-read sequencing technology. Sequence analysis of the amplicons revealed chimeric DNA reads and uncovered a connection between template switching and polymerase exonuclease activity. Nanopore sequencing provides insight to guide the further development of isothermal amplification methods for long DNA, and our results highlight the need for high-specificity, high-turnover nicking endonucleases to initiate DNA amplification without thermal denaturation.
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Affiliation(s)
- Dillon B. Nye
- Nucleic Acid Replication Division, New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Nathan A. Tanner
- Nucleic Acid Replication Division, New England Biolabs Inc., Ipswich, Massachusetts, United States of America
- * E-mail:
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20
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Chen P, Wang L, Qin P, Yin BC, Ye BC. An RNA-based catalytic hairpin assembly circuit coupled with CRISPR-Cas12a for one-step detection of microRNAs. Biosens Bioelectron 2022; 207:114152. [DOI: 10.1016/j.bios.2022.114152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/12/2022] [Accepted: 03/01/2022] [Indexed: 12/26/2022]
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21
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Schiermeyer A, Cerda-Bennasser P, Schmelter T, Huang X, Christou P, Schillberg S. Rapid production of SaCas9 in plant-based cell-free lysate for activity testing. Biotechnol J 2022; 17:e2100564. [PMID: 35316566 DOI: 10.1002/biot.202100564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/11/2022] [Accepted: 03/17/2022] [Indexed: 11/11/2022]
Abstract
Cas9 nucleases have become the most versatile tool for genome editing projects in a broad range of organisms. The recombinant production of Cas9 nuclease is desirable for in vitro activity assays or the preparation of ribonucleoproteins (RNPs) for DNA-free genome editing approaches. For the rapid production of Cas9, we explored the use of a recently established cell-free lysate from tobacco (Nicotiana tabacum L.) BY-2 cells. Using this system, the 130-kDa Cas9 nuclease from Staphylococcus aureus (SaCas9) was produced and subsequently purified via affinity chromatography. The purified apoenzyme was supplemented with 10 different sgRNAs, and the nuclease activity was confirmed by the linearization of plasmid DNA containing cloned DNA target sequences.
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Affiliation(s)
- Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Pedro Cerda-Bennasser
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Thomas Schmelter
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
| | - Xin Huang
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute for Phytopathology, Justus-Liebig-University Giessen, Giessen, Germany
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22
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Mattiello L, Rütgers M, Sua-Rojas MF, Tavares R, Soares JS, Begcy K, Menossi M. Molecular and Computational Strategies to Increase the Efficiency of CRISPR-Based Techniques. FRONTIERS IN PLANT SCIENCE 2022; 13:868027. [PMID: 35712599 PMCID: PMC9194676 DOI: 10.3389/fpls.2022.868027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The prokaryote-derived Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas mediated gene editing tools have revolutionized our ability to precisely manipulate specific genome sequences in plants and animals. The simplicity, precision, affordability, and robustness of this technology have allowed a myriad of genomes from a diverse group of plant species to be successfully edited. Even though CRISPR/Cas, base editing, and prime editing technologies have been rapidly adopted and implemented in plants, their editing efficiency rate and specificity varies greatly. In this review, we provide a critical overview of the recent advances in CRISPR/Cas9-derived technologies and their implications on enhancing editing efficiency. We highlight the major efforts of engineering Cas9, Cas12a, Cas12b, and Cas12f proteins aiming to improve their efficiencies. We also provide a perspective on the global future of agriculturally based products using DNA-free CRISPR/Cas techniques. The improvement of CRISPR-based technologies efficiency will enable the implementation of genome editing tools in a variety of crop plants, as well as accelerate progress in basic research and molecular breeding.
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Affiliation(s)
- Lucia Mattiello
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Mark Rütgers
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Maria Fernanda Sua-Rojas
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Rafael Tavares
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - José Sérgio Soares
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Kevin Begcy
- Environmental Horticulture Department, University of Florida, Gainesville, FL, United States
| | - Marcelo Menossi
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
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23
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Vos PD, Rossetti G, Mantegna JL, Siira SJ, Gandadireja AP, Bruce M, Raven SA, Khersonsky O, Fleishman SJ, Filipovska A, Rackham O. Computationally designed hyperactive Cas9 enzymes. Nat Commun 2022; 13:3023. [PMID: 35641498 PMCID: PMC9156780 DOI: 10.1038/s41467-022-30598-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/10/2022] [Indexed: 12/01/2022] Open
Abstract
The ability to alter the genomes of living cells is key to understanding how genes influence the functions of organisms and will be critical to modify living systems for useful purposes. However, this promise has long been limited by the technical challenges involved in genetic engineering. Recent advances in gene editing have bypassed some of these challenges but they are still far from ideal. Here we use FuncLib to computationally design Cas9 enzymes with substantially higher donor-independent editing activities. We use genetic circuits linked to cell survival in yeast to quantify Cas9 activity and discover synergistic interactions between engineered regions. These hyperactive Cas9 variants function efficiently in mammalian cells and introduce larger and more diverse pools of insertions and deletions into targeted genomic regions, providing tools to enhance and expand the possible applications of CRISPR-based gene editing. The ability to alter the genomes of living cells is key to understanding how genes influence the functions of organisms and will be critical to modify living systems for useful purposes. Here, the authors use computational design to discover Cas9 enzymes with increased activity.
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Affiliation(s)
- Pascal D Vos
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Giulia Rossetti
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Jessica L Mantegna
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
| | - Andrianto P Gandadireja
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
| | - Mitchell Bruce
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Samuel A Raven
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia
| | - Olga Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Oliver Rackham
- Curtin Medical School, Curtin University, Bentley, WA, Australia. .,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia. .,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia. .,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia.
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24
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Jacobs R, Singh P, Smith T, Arbuthnot P, Maepa MB. Prospects of viral vector-mediated delivery of sequences encoding anti-HBV designer endonucleases. Gene Ther 2022:10.1038/s41434-022-00342-5. [PMID: 35606493 DOI: 10.1038/s41434-022-00342-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/09/2022]
Abstract
Available treatment for chronic hepatitis B virus (HBV) infection offers modest functional curative efficacy. The viral replicative intermediate comprising covalently closed circular DNA (cccDNA) is responsible for persistent chronic HBV infection. Hence, current efforts have focused on developing therapies that disable cccDNA. Employing gene editing tools has emerged as an attractive strategy, with the end goal of establishing permanently inactivated cccDNA. Although anti-HBV designer nucleases are effective in vivo, none has yet progressed to clinical trial. Lack of safe and efficient delivery systems remains the limiting factor. Several vectors may be used to deliver anti-HBV gene editor-encoding sequences, with viral vectors being at the forefront. Despite the challenges associated with packaging large gene editor-encoding sequences into viral vectors, advancement in the field is overcoming such limitations. Translation of viral vector-mediated gene editing against HBV to clinical application is within reach. This review discusses the prospects of delivering HBV targeted designer nucleases using viral vectors.
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Affiliation(s)
- Ridhwaanah Jacobs
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Prashika Singh
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tiffany Smith
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mohube Betty Maepa
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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25
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Bonillo M, Pfromm J, Fischer MD. Challenges to Gene Editing Approaches in the Retina. Klin Monbl Augenheilkd 2022; 239:275-283. [PMID: 35316854 DOI: 10.1055/a-1757-9810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Retinal gene therapy has recently been at the cutting edge of clinical development in the diverse field of genetic therapies. The retina is an attractive target for genetic therapies such as gene editing due to the distinctive anatomical and immunological features of the eye, known as immune privilege, so that inherited retinal diseases (IRDs) have been studied in several clinical studies. Thus, rapid strides are being made toward developing targeted treatments for IRDs. Gene editing in the retina faces a group of heterogenous challenges, including editing efficiencies, off-target effects, the anatomy of the target organ, immune responses, inactivation, and identifying optimal application methods. As clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas) based technologies are at the forefront of current gene editing advances, their specific editing efficiency challenges and potential off-target effects were assessed. The immune privilege of the eye reduces the likelihood of systemic immune responses following retinal gene therapy, but possible immune responses must not be discounted. Immune responses to gene editing in the retina may be humoral or cell mediated, with immunologically active cells, including microglia, implicated in facilitating possible immune responses to gene editing. Immunogenicity of gene therapeutics may also lead to the inactivation of edited cells, reducing potential therapeutic benefits. This review outlines the broad spectrum of potential challenges currently facing retinal gene editing, with the goal of facilitating further advances in the safety and efficacy of gene editing therapies.
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Affiliation(s)
- Mario Bonillo
- Clinic of Ophthalmology, University Eye Hospital, University Hospital Tübingen, Tübingen, Germany.,Clinic of Ophthalmology, Institute for Ophthalmic Research, University Hospital Tübingen, Tübingen, Germany
| | - Julia Pfromm
- Clinic of Ophthalmology, University Eye Hospital, University Hospital Tübingen, Tübingen, Germany.,Clinic of Ophthalmology, Institute for Ophthalmic Research, University Hospital Tübingen, Tübingen, Germany
| | - M Dominik Fischer
- Clinic of Ophthalmology, University Eye Hospital, University Hospital Tübingen, Tübingen, Germany.,Clinic of Ophthalmology, Institute for Ophthalmic Research, University Hospital Tübingen, Tübingen, Germany.,Oxford University NHS Foundation Trust, Oxford Eye Hospital, Oxford, United Kingdom of Great Britain and Northern Ireland.,Department of Clinical Neurosciences, University of Oxford Nuffield Laboratory of Ophthalmology, Oxford, United Kingdom of Great Britain and Northern Ireland
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26
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Hacker L, Capdeville N, Feller L, Enderle-Kukla J, Dorn A, Puchta H. The DNA-dependent protease AtWSS1A suppresses persistent double strand break formation during replication. THE NEW PHYTOLOGIST 2022; 233:1172-1187. [PMID: 34761387 DOI: 10.1111/nph.17848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
The protease WSS1A is an important factor in the repair of DNA-protein crosslinks in plants. Here we show that the loss of WSS1A leads to a reduction of 45S rDNA repeats and chromosomal fragmentation in Arabidopsis. Moreover, in the absence of any factor of the RTR (RECQ4A/TOP3α/RMI1/2) complex, which is involved in the dissolution of DNA replication intermediates, WSS1A becomes essential for viability. If WSS1A loss is combined with loss of the classical (c) or alternative (a) nonhomologous end joining (NHEJ) pathways of double-strand break (DSB) repair, the resulting mutants show proliferation defects and enhanced chromosome fragmentation, which is especially aggravated in the absence of aNHEJ. This indicates that WSS1A is involved either in the suppression of DSB formation or in DSB repair itself. To test the latter we induced DSB by CRISPR/Cas9 at different loci in wild-type and mutant cells and analyzed their repair by deep sequencing. However, no change in the quality of the repair events and only a slight increase in their quantity was found. Thus, by removing complex DNA-protein structures, WSS1A seems to be required for the repair of replication intermediates which would otherwise be resolved into persistent DSB leading to genome instability.
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Affiliation(s)
- Leonie Hacker
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Niklas Capdeville
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Laura Feller
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Janina Enderle-Kukla
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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27
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Díaz-Galicia E, Grünberg R, Arold ST. How to Find the Right RNA-Sensing CRISPR-Cas System for an In Vitro Application. BIOSENSORS 2022; 12:bios12020053. [PMID: 35200314 PMCID: PMC8869480 DOI: 10.3390/bios12020053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems have a great and still largely untapped potential for in vitro applications, in particular, for RNA biosensing. However, there is currently no systematic guide on selecting the most appropriate RNA-targeting CRISPR-Cas system for a given application among thousands of potential candidates. We provide an overview of the currently described Cas effector systems and review existing Cas-based RNA detection methods. We then propose a set of systematic selection criteria for selecting CRISPR-Cas candidates for new applications. Using this approach, we identify four candidates for in vitro RNA.
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Affiliation(s)
- Escarlet Díaz-Galicia
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Raik Grünberg
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
- Correspondence: (R.G.); (S.T.A.)
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, F-34090 Montpellier, France
- Correspondence: (R.G.); (S.T.A.)
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28
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Aldag P, Welzel F, Jakob L, Schmidbauer A, Rutkauskas M, Fettes F, Grohmann D, Seidel R. Probing the stability of the SpCas9-DNA complex after cleavage. Nucleic Acids Res 2021; 49:12411-12421. [PMID: 34792162 PMCID: PMC8643700 DOI: 10.1093/nar/gkab1072] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 is a ribonucleoprotein complex that sequence-specifically binds and cleaves double-stranded DNA. Wildtype Cas9 and its nickase and cleavage-incompetent mutants have been used in various biological techniques due to their versatility and programmable specificity. Cas9 has been shown to bind very stably to DNA even after cleavage of the individual DNA strands, inhibiting further turnovers and considerably slowing down in-vivo repair processes. This poses an obstacle in genome editing applications. Here, we employed single-molecule magnetic tweezers to investigate the binding stability of different Streptococcus pyogenes Cas9 variants after cleavage by challenging them with supercoiling. We find that different release mechanisms occur depending on which DNA strand is cleaved. After initial target strand cleavage, supercoils are only removed after the collapse of the R-loop. We identified several states with different stabilities of the R-loop. Most importantly, we find that the post-cleavage state of Cas9 exhibits a higher stability than the pre-cleavage state. After non-target strand cleavage, supercoils are immediately but slowly released by swiveling of the non-target strand around Cas9 bound to the target strand. Consequently, Cas9 and its non-target strand nicking mutant stay stably bound to the DNA for many hours even at elevated torsional stress.
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Affiliation(s)
- Pierre Aldag
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Fabian Welzel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Leonhard Jakob
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
| | - Andreas Schmidbauer
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
| | - Marius Rutkauskas
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Fergus Fettes
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
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29
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Hirschenberger M, Stadler N, Fellermann M, Sparrer KMJ, Kirchhoff F, Barth H, Papatheodorou P. CRISPA: A Non-viral, Transient Cas9 Delivery System Based on Reengineered Anthrax Toxin. Front Pharmacol 2021; 12:770283. [PMID: 34733166 PMCID: PMC8558532 DOI: 10.3389/fphar.2021.770283] [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: 09/03/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
Translating the CRISPR/Cas9 genome editing technology into clinics is still hampered by rather unspecific, unsafe and/or inconvenient approaches for the delivery of its main components - the Cas9 endonuclease and a guide RNA - into cells. Here, we describe the development of a novel transient and non-viral Cas9 delivery strategy based on the translocation machinery of the Bacillus anthracis anthrax toxin, PA (protective antigen). We show that Cas9 variants fused to the N-terminus of the lethal factor or to a hexahistidine tag are shuttled through channels formed by PA into the cytosol of human cells. As proof-of-principle, we applied our new approach, denoted as CRISPA, to knock out lipolysis-stimulated lipoprotein receptor (LSR) in the human colon cancer cell line HCT116 and green-fluorescent protein (GFP) in human embryonic kidney 293T cells stably expressing GFP. Notably, we confirmed that the transporter PA can be adapted to recognize specific host cell-surface receptor proteins and may be optimized for cell type-selective delivery of Cas9. Altogether, CRISPA provides a novel, transient and non-viral way to deliver Cas9 into specific cells. Thus, this system is an additional step towards safe translation of the CRISPR/Cas9 technology into clinics.
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Affiliation(s)
- Maximilian Hirschenberger
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany.,Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Nicole Stadler
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | - Maximilian Fellermann
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Holger Barth
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
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30
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Aquino-Jarquin G. Current advances in overcoming obstacles of CRISPR/Cas9 off-target genome editing. Mol Genet Metab 2021; 134:77-86. [PMID: 34391646 DOI: 10.1016/j.ymgme.2021.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022]
Abstract
CRISPR/Cas9-based technology has revolutionized biomedical research by providing a high-fidelity gene-editing method, foreshadowing a significant impact on the therapeutics of many human genetic disorders previously considered untreatable. However, off-target events represent a critical hurdle before genome editing can be fully established in clinical practice. This mini-review recapitulates some recent advances for detecting and overcoming off-target effects mediated by the CRISPR/Cas9 system that could increase the likelihood of clinical success of the CRISPR-based approaches.
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Affiliation(s)
- Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico; Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, Mexico.
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31
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Schmidt MJ, Gupta A, Bednarski C, Gehrig-Giannini S, Richter F, Pitzler C, Gamalinda M, Galonska C, Takeuchi R, Wang K, Reiss C, Dehne K, Lukason MJ, Noma A, Park-Windhol C, Allocca M, Kantardzhieva A, Sane S, Kosakowska K, Cafferty B, Tebbe J, Spencer SJ, Munzer S, Cheng CJ, Scaria A, Scharenberg AM, Cohnen A, Coco WM. Improved CRISPR genome editing using small highly active and specific engineered RNA-guided nucleases. Nat Commun 2021; 12:4219. [PMID: 34244505 PMCID: PMC8271026 DOI: 10.1038/s41467-021-24454-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
Streptococcus pyogenes (Spy) Cas9 has potential as a component of gene therapeutics for incurable diseases. One of its limitations is its large size, which impedes its formulation and delivery in therapeutic applications. Smaller Cas9s are an alternative, but lack robust activity or specificity and frequently recognize longer PAMs. Here, we investigated four uncharacterized, smaller Cas9s and found three employing a "GG" dinucleotide PAM similar to SpyCas9. Protein engineering generated synthetic RNA-guided nucleases (sRGNs) with editing efficiencies and specificities exceeding even SpyCas9 in vitro and in human cell lines on disease-relevant targets. sRGN mRNA lipid nanoparticles displayed manufacturing advantages and high in vivo editing efficiency in the mouse liver. Finally, sRGNs, but not SpyCas9, could be packaged into all-in-one AAV particles with a gRNA and effected robust in vivo editing of non-human primate (NHP) retina photoreceptors. Human gene therapy efforts are expected to benefit from these improved alternatives to existing CRISPR nucleases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Kui Wang
- Casebia Therapeutics LLC, Cambridge, MA, USA
| | | | | | | | - Akiko Noma
- Casebia Therapeutics LLC, Cambridge, MA, USA
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Čermák T. Sequence modification on demand: search and replace tools for precise gene editing in plants. Transgenic Res 2021; 30:353-379. [PMID: 34086167 DOI: 10.1007/s11248-021-00253-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/05/2021] [Indexed: 12/26/2022]
Abstract
Until recently, our ability to generate allelic diversity in plants was limited to introduction of variants from domesticated and wild species by breeding via uncontrolled recombination or the use of chemical and physical mutagens-processes that are lengthy and costly or lack specificity, respectively. Gene editing provides a faster and more precise way to create new variation, although its application in plants has been dominated by the creation of short insertion and deletion mutations leading to loss of gene function, mostly due to the dependence of editing outcomes on DNA repair pathway choices intrinsic to higher eukaryotes. Other types of edits such as point mutations and precise and pre-designed targeted sequence insertions have rarely been implemented, despite providing means to modulate the expression of target genes or to engineer the function and stability of their protein products. Several advancements have been developed in recent years to facilitate custom editing by regulation of repair pathway choices or by taking advantage of alternative types of DNA repair. We have seen the advent of novel gene editing tools that are independent of DNA double-strand break repair, and methods completely independent of host DNA repair processes are being increasingly explored. With the aim to provide a comprehensive review of the state-of-the-art methodology for allele replacement in plants, I discuss the adoption of these improvements for plant genome engineering.
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Park J, Lim JM, Jung I, Heo SJ, Park J, Chang Y, Kim HK, Jung D, Yu JH, Min S, Yoon S, Cho SR, Park T, Kim HH. Recording of elapsed time and temporal information about biological events using Cas9. Cell 2021; 184:1047-1063.e23. [PMID: 33539780 DOI: 10.1016/j.cell.2021.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/08/2020] [Accepted: 01/12/2021] [Indexed: 01/14/2023]
Abstract
DNA has not been utilized to record temporal information, although DNA has been used to record biological information and to compute mathematical problems. Here, we found that indel generation by Cas9 and guide RNA can occur at steady rates, in contrast to typical dynamic biological reactions, and the accumulated indel frequency can be a function of time. By measuring indel frequencies, we developed a method for recording and measuring absolute time periods over hours to weeks in mammalian cells. These time-recordings were conducted in several cell types, with different promoters and delivery vectors for Cas9, and in both cultured cells and cells of living mice. As applications, we recorded the duration of chemical exposure and the lengths of elapsed time since the onset of biological events (e.g., heat exposure and inflammation). We propose that our systems could serve as synthetic "DNA clocks."
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Affiliation(s)
- Jihye Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung Min Lim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Inkyung Jung
- Division of Biostatistics, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Department of Biostatistics and Computing, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Seok-Jae Heo
- Division of Biostatistics, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Department of Biostatistics and Computing, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Jinman Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Yoojin Chang
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hui Kwon Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Dongmin Jung
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ji Hea Yu
- Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Seonwoo Min
- Electrical and Computer Engineering, Seoul National University, Seoul 00826, Republic of Korea
| | - Sungroh Yoon
- Electrical and Computer Engineering, Seoul National University, Seoul 00826, Republic of Korea; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 00826, Republic of Korea; Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul 00826, Republic of Korea
| | - Sung-Rae Cho
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Department and Research Institute of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Taeyoung Park
- Department of Applied Statistics, Yonsei University, Seoul 03722, Republic of Korea; Department of Statistics and Data Science, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyongbum Henry Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea; Graduate Program of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul, Republic of Korea; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.
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Sgro A, Blancafort P. Epigenome engineering: new technologies for precision medicine. Nucleic Acids Res 2021; 48:12453-12482. [PMID: 33196851 PMCID: PMC7736826 DOI: 10.1093/nar/gkaa1000] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/10/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Chromatin adopts different configurations that are regulated by reversible covalent modifications, referred to as epigenetic marks. Epigenetic inhibitors have been approved for clinical use to restore epigenetic aberrations that result in silencing of tumor-suppressor genes, oncogene addictions, and enhancement of immune responses. However, these drugs suffer from major limitations, such as a lack of locus selectivity and potential toxicities. Technological advances have opened a new era of precision molecular medicine to reprogram cellular physiology. The locus-specificity of CRISPR/dCas9/12a to manipulate the epigenome is rapidly becoming a highly promising strategy for personalized medicine. This review focuses on new state-of-the-art epigenome editing approaches to modify the epigenome of neoplasms and other disease models towards a more 'normal-like state', having characteristics of normal tissue counterparts. We highlight biomolecular engineering methodologies to assemble, regulate, and deliver multiple epigenetic effectors that maximize the longevity of the therapeutic effect, and we discuss limitations of the platforms such as targeting efficiency and intracellular delivery for future clinical applications.
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Affiliation(s)
- Agustin Sgro
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
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Wong PK, Cheah FC, Syafruddin SE, Mohtar MA, Azmi N, Ng PY, Chua EW. CRISPR Gene-Editing Models Geared Toward Therapy for Hereditary and Developmental Neurological Disorders. Front Pediatr 2021; 9:592571. [PMID: 33791256 PMCID: PMC8006930 DOI: 10.3389/fped.2021.592571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/19/2021] [Indexed: 12/26/2022] Open
Abstract
Hereditary or developmental neurological disorders (HNDs or DNDs) affect the quality of life and contribute to the high mortality rates among neonates. Most HNDs are incurable, and the search for new and effective treatments is hampered by challenges peculiar to the human brain, which is guarded by the near-impervious blood-brain barrier. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR), a gene-editing tool repurposed from bacterial defense systems against viruses, has been touted by some as a panacea for genetic diseases. CRISPR has expedited the research into HNDs, enabling the generation of in vitro and in vivo models to simulate the changes in human physiology caused by genetic variation. In this review, we describe the basic principles and workings of CRISPR and the modifications that have been made to broaden its applications. Then, we review important CRISPR-based studies that have opened new doors to the treatment of HNDs such as fragile X syndrome and Down syndrome. We also discuss how CRISPR can be used to generate research models to examine the effects of genetic variation and caffeine therapy on the developing brain. Several drawbacks of CRISPR may preclude its use at the clinics, particularly the vulnerability of neuronal cells to the adverse effect of gene editing, and the inefficiency of CRISPR delivery into the brain. In concluding the review, we offer some suggestions for enhancing the gene-editing efficacy of CRISPR and how it may be morphed into safe and effective therapy for HNDs and other brain disorders.
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Affiliation(s)
- Poh Kuan Wong
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Fook Choe Cheah
- Department of Paediatrics, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | | | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Norazrina Azmi
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Pei Yuen Ng
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Eng Wee Chua
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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36
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Janik E, Niemcewicz M, Ceremuga M, Krzowski L, Saluk-Bijak J, Bijak M. Various Aspects of a Gene Editing System-CRISPR-Cas9. Int J Mol Sci 2020; 21:E9604. [PMID: 33339441 PMCID: PMC7767219 DOI: 10.3390/ijms21249604] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
The discovery of clustered, regularly interspaced short palindromic repeats (CRISPR) and their cooperation with CRISPR-associated (Cas) genes is one of the greatest advances of the century and has marked their application as a powerful genome engineering tool. The CRISPR-Cas system was discovered as a part of the adaptive immune system in bacteria and archaea to defend from plasmids and phages. CRISPR has been found to be an advanced alternative to zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN) for gene editing and regulation, as the CRISPR-Cas9 protein remains the same for various gene targets and just a short guide RNA sequence needs to be altered to redirect the site-specific cleavage. Due to its high efficiency and precision, the Cas9 protein derived from the type II CRISPR system has been found to have applications in many fields of science. Although CRISPR-Cas9 allows easy genome editing and has a number of benefits, we should not ignore the important ethical and biosafety issues. Moreover, any tool that has great potential and offers significant capabilities carries a level of risk of being used for non-legal purposes. In this review, we present a brief history and mechanism of the CRISPR-Cas9 system. We also describe on the applications of this technology in gene regulation and genome editing; the treatment of cancer and other diseases; and limitations and concerns of the use of CRISPR-Cas9.
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Affiliation(s)
- Edyta Janik
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.)
| | - Marcin Niemcewicz
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.)
| | - Michal Ceremuga
- Military Institute of Armament Technology, Prymasa Stefana Wyszyńskiego 7, 05-220 Zielonka, Poland;
| | - Lukasz Krzowski
- Biodefense Laboratory, Biomedical Engineering Centre, Institute of Optoelectronics, Military University of Technology, gen. Sylwestra Kaliskiego 2, 00-908 Warsaw, Poland;
| | - Joanna Saluk-Bijak
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland;
| | - Michal Bijak
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.)
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37
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Kotliar D, Lin AE, Logue J, Hughes TK, Khoury NM, Raju SS, Wadsworth MH, Chen H, Kurtz JR, Dighero-Kemp B, Bjornson ZB, Mukherjee N, Sellers BA, Tran N, Bauer MR, Adams GC, Adams R, Rinn JL, Melé M, Schaffner SF, Nolan GP, Barnes KG, Hensley LE, McIlwain DR, Shalek AK, Sabeti PC, Bennett RS. Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics. Cell 2020; 183:1383-1401.e19. [PMID: 33159858 PMCID: PMC7707107 DOI: 10.1016/j.cell.2020.10.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/10/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022]
Abstract
Ebola virus (EBOV) causes epidemics with high mortality yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cells during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, finding that immature, proliferative monocyte-lineage cells with reduced antigen-presentation capacity replace conventional monocyte subsets, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying intracellular viral RNA, we identify molecular determinants of tropism among circulating immune cells and examine temporal dynamics in viral and host gene expression. Within infected cells, EBOV downregulates STAT1 mRNA and interferon signaling, and it upregulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating pathways the virus manipulates for its replication. This study sheds light on EBOV tropism, replication dynamics, and elicited immune response and provides a framework for characterizing host-virus interactions under maximum containment.
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Affiliation(s)
- Dylan Kotliar
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Aaron E Lin
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA.
| | - James Logue
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Travis K Hughes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Nadine M Khoury
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Siddharth S Raju
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marc H Wadsworth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Han Chen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Jonathan R Kurtz
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Bonnie Dighero-Kemp
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Zach B Bjornson
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Brian A Sellers
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD 20814, USA
| | - Nancy Tran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Matthew R Bauer
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gordon C Adams
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ricky Adams
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - John L Rinn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Marta Melé
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia 08034, Spain
| | - Stephen F Schaffner
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kayla G Barnes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - David R McIlwain
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Richard S Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
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Gasiunas G, Young JK, Karvelis T, Kazlauskas D, Urbaitis T, Jasnauskaite M, Grusyte MM, Paulraj S, Wang PH, Hou Z, Dooley SK, Cigan M, Alarcon C, Chilcoat ND, Bigelyte G, Curcuru JL, Mabuchi M, Sun Z, Fuchs RT, Schildkraut E, Weigele PR, Jack WE, Robb GB, Venclovas Č, Siksnys V. A catalogue of biochemically diverse CRISPR-Cas9 orthologs. Nat Commun 2020; 11:5512. [PMID: 33139742 PMCID: PMC7606464 DOI: 10.1038/s41467-020-19344-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/02/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial Cas9 nucleases from type II CRISPR-Cas antiviral defence systems have been repurposed as genome editing tools. Although these proteins are found in many microbes, only a handful of variants are used for these applications. Here, we use bioinformatic and biochemical analyses to explore this largely uncharacterized diversity. We apply cell-free biochemical screens to assess the protospacer adjacent motif (PAM) and guide RNA (gRNA) requirements of 79 Cas9 proteins, thus identifying at least 7 distinct gRNA classes and 50 different PAM sequence requirements. PAM recognition spans the entire spectrum of T-, A-, C-, and G-rich nucleotides, from single nucleotide recognition to sequence strings longer than 4 nucleotides. Characterization of a subset of Cas9 orthologs using purified components reveals additional biochemical diversity, including both narrow and broad ranges of temperature dependence, staggered-end DNA target cleavage, and a requirement for long stretches of homology between gRNA and DNA target. Our results expand the available toolset of RNA-programmable CRISPR-associated nucleases.
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Affiliation(s)
| | - Joshua K Young
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA.
| | - Tautvydas Karvelis
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania
| | - Darius Kazlauskas
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania
| | - Tomas Urbaitis
- CasZyme, Vilnius, LT-10257, Lithuania
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania
| | | | | | - Sushmitha Paulraj
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Po-Hao Wang
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
- Inari Agriculture, West Lafayette, IN, 47906, USA
| | - Zhenglin Hou
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Shane K Dooley
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Mark Cigan
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
- Genus plc, Deforest, WI, 53532, USA
| | - Clara Alarcon
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - N Doane Chilcoat
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Greta Bigelyte
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania
| | | | | | - Zhiyi Sun
- New England Biolabs, Ipswich, MA, 01938, USA
| | | | | | | | | | | | - Česlovas Venclovas
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania
| | - Virginijus Siksnys
- CasZyme, Vilnius, LT-10257, Lithuania.
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania.
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Hua K, Jiang Y, Tao X, Zhu J. Precision genome engineering in rice using prime editing system. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2167-2169. [PMID: 32372479 PMCID: PMC7589318 DOI: 10.1111/pbi.13395] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 05/04/2023]
Affiliation(s)
- Kai Hua
- Shanghai Center for Plant Stress BiologyCAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Yuwei Jiang
- Shanghai Center for Plant Stress BiologyCAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoping Tao
- Shanghai Center for Plant Stress BiologyCAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Jian‐Kang Zhu
- Shanghai Center for Plant Stress BiologyCAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteINUSA
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40
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Zhang S, Zhang Q, Hou X, Guo L, Wang F, Bi L, Zhang X, Li H, Wen F, Xi X, Huang X, Shen B, Sun B. Dynamics of Staphylococcus aureus Cas9 in DNA target Association and Dissociation. EMBO Rep 2020; 21:e50184. [PMID: 32790142 PMCID: PMC7534634 DOI: 10.15252/embr.202050184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 07/11/2020] [Accepted: 07/21/2020] [Indexed: 12/29/2022] Open
Abstract
Staphylococcus aureus Cas9 (SaCas9) is an RNA-guided endonuclease that targets complementary DNA adjacent to a protospacer adjacent motif (PAM) for cleavage. Its small size facilitates in vivo delivery for genome editing in various organisms. Herein, using single-molecule and ensemble approaches, we systemically study the mechanism of SaCas9 underlying its interplay with DNA. We find that the DNA binding and cleavage of SaCas9 require complementarities of 6- and 18-bp of PAM-proximal DNA with guide RNA, respectively. These activities are mediated by two steady interactions among the ternary complex, one of which is located approximately 6 bp from the PAM and beyond the apparent footprint of SaCas9 on DNA. Notably, the other interaction within the protospacer is significantly strong and thus poses DNA-bound SaCas9 a persistent block to DNA-tracking motors. Intriguingly, after cleavage, SaCas9 autonomously releases the PAM-distal DNA while retaining binding to the PAM. This partial DNA release immediately abolishes its strong interaction with the protospacer DNA and consequently promotes its subsequent dissociation from the PAM. Overall, these data provide a dynamic understanding of SaCas9 and instruct its effective applications.
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Affiliation(s)
- Siqi Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qian Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xi‐Miao Hou
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Lijuan Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Fangzhu Wang
- State Key Laboratory of Reproductive MedicineCenter for Global HealthNanjing Medical UniversityNanjingChina
| | - Lulu Bi
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Xia Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Hai‐Hong Li
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Fengcai Wen
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xu‐Guang Xi
- The LBPAEcole Normale Supérieure Paris‐SaclayCNRSUniversité Paris SaclayGif‐sur-YvetteFrance
| | - Xingxu Huang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Bin Shen
- State Key Laboratory of Reproductive MedicineCenter for Global HealthNanjing Medical UniversityNanjingChina
| | - Bo Sun
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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41
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Ates I, Rathbone T, Stuart C, Bridges PH, Cottle RN. Delivery Approaches for Therapeutic Genome Editing and Challenges. Genes (Basel) 2020; 11:E1113. [PMID: 32977396 PMCID: PMC7597956 DOI: 10.3390/genes11101113] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023] Open
Abstract
Impressive therapeutic advances have been possible through the advent of zinc-finger nucleases and transcription activator-like effector nucleases. However, discovery of the more efficient and highly tailorable clustered regularly interspaced short palindromic repeats (CRISPR) and associated proteins (Cas9) has provided unprecedented gene-editing capabilities for treatment of various inherited and acquired diseases. Despite recent clinical trials, a major barrier for therapeutic gene editing is the absence of safe and effective methods for local and systemic delivery of gene-editing reagents. In this review, we elaborate on the challenges and provide practical considerations for improving gene editing. Specifically, we highlight issues associated with delivery of gene-editing tools into clinically relevant cells.
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Affiliation(s)
- Ilayda Ates
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA; (I.A.); (T.R.); (C.S.)
| | - Tanner Rathbone
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA; (I.A.); (T.R.); (C.S.)
| | - Callie Stuart
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA; (I.A.); (T.R.); (C.S.)
| | - P. Hudson Bridges
- College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Renee N. Cottle
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA; (I.A.); (T.R.); (C.S.)
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42
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Eitzinger S, Asif A, Watters KE, Iavarone AT, Knott GJ, Doudna JA, Minhas FUAA. Machine learning predicts new anti-CRISPR proteins. Nucleic Acids Res 2020; 48:4698-4708. [PMID: 32286628 PMCID: PMC7229843 DOI: 10.1093/nar/gkaa219] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 01/30/2023] Open
Abstract
The increasing use of CRISPR–Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR–Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that inhibit the CRISPR–Cas adaptive immune system. However, comparing all currently known anti-CRISPRs does not reveal a shared set of properties for facile bioinformatic identification of new anti-CRISPR families. Here, we describe AcRanker, a machine learning based method to aid direct identification of new potential anti-CRISPRs using only protein sequence information. Using a training set of known anti-CRISPRs, we built a model based on XGBoost ranking. We then applied AcRanker to predict candidate anti-CRISPRs from predicted prophage regions within self-targeting bacterial genomes and discovered two previously unknown anti-CRISPRs: AcrllA20 (ML1) and AcrIIA21 (ML8). We show that AcrIIA20 strongly inhibits Streptococcus iniae Cas9 (SinCas9) and weakly inhibits Streptococcus pyogenes Cas9 (SpyCas9). We also show that AcrIIA21 inhibits SpyCas9, Streptococcus aureus Cas9 (SauCas9) and SinCas9 with low potency. The addition of AcRanker to the anti-CRISPR discovery toolkit allows researchers to directly rank potential anti-CRISPR candidate genes for increased speed in testing and validation of new anti-CRISPRs. A web server implementation for AcRanker is available online at http://acranker.pythonanywhere.com/.
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Affiliation(s)
- Simon Eitzinger
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Amina Asif
- Department of Computer and Information Sciences, Pakistan Institute of Engineering and Applied Sciences (PIEAS), PO Nilore, Islamabad, Pakistan.,FAST School of Computing, National University of Computer and Emerging Sciences (NUCES), Islamabad, Pakistan
| | - Kyle E Watters
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA.,Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158.,Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Fayyaz Ul Amir Afsar Minhas
- Department of Computer and Information Sciences, Pakistan Institute of Engineering and Applied Sciences (PIEAS), PO Nilore, Islamabad, Pakistan.,Department of Computer Science, University of Warwick, Coventry, CV4 7AL, UK
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43
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Richter MF, Zhao KT, Eton E, Lapinaite A, Newby GA, Thuronyi BW, Wilson C, Koblan LW, Zeng J, Bauer DE, Doudna JA, Liu DR. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat Biotechnol 2020; 38:883-891. [PMID: 32433547 PMCID: PMC7357821 DOI: 10.1038/s41587-020-0453-z] [Citation(s) in RCA: 443] [Impact Index Per Article: 110.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/02/2020] [Accepted: 02/07/2020] [Indexed: 12/19/2022]
Abstract
Applications of adenine base editors (ABEs) have been constrained by the limited compatibility of the deoxyadenosine deaminase component with Cas homologs other than SpCas9. We evolved the deaminase component of ABE7.10 using phage-assisted non-continuous and continuous evolution (PANCE and PACE), which resulted in ABE8e. ABE8e contains eight additional mutations that increase activity (kapp) 590-fold compared with that of ABE7.10. ABE8e offers substantially improved editing efficiencies when paired with a variety of Cas9 or Cas12 homologs. ABE8e is more processive than ABE7.10, which could benefit screening, disruption of regulatory regions and multiplex base editing applications. A modest increase in Cas9-dependent and -independent DNA off-target editing, and in transcriptome-wide RNA off-target editing can be ameliorated by the introduction of an additional mutation in the TadA-8e domain. Finally, we show that ABE8e can efficiently install natural mutations that upregulate fetal hemoglobin expression in the BCL11A enhancer or in the the HBG promoter in human cells, targets that were poorly edited with ABE7.10. ABE8e augments the effectiveness and applicability of adenine base editing.
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Affiliation(s)
- Michelle F Richter
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Kevin T Zhao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Elliot Eton
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Audrone Lapinaite
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - B W Thuronyi
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry, Williams College, Williamstown, MA, USA
| | - Christopher Wilson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Luke W Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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44
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Wang AS, Chen LC, Wu RA, Hao Y, McSwiggen DT, Heckert AB, Richardson CD, Gowen BG, Kazane KR, Vu JT, Wyman SK, Shin JJ, Darzacq X, Walter JC, Corn JE. The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells. Mol Cell 2020; 79:221-233.e5. [PMID: 32603710 PMCID: PMC7398558 DOI: 10.1016/j.molcel.2020.06.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 02/26/2020] [Accepted: 06/05/2020] [Indexed: 12/23/2022]
Abstract
Cas9 is a prokaryotic RNA-guided DNA endonuclease that binds substrates tightly in vitro but turns over rapidly when used to manipulate genomes in eukaryotic cells. Little is known about the factors responsible for dislodging Cas9 or how they influence genome engineering. Unbiased detection through proximity labeling of transient protein interactions in cell-free Xenopus laevis egg extract identified the dimeric histone chaperone facilitates chromatin transcription (FACT) as an interactor of substrate-bound Cas9. FACT is both necessary and sufficient to displace dCas9, and FACT immunodepletion converts Cas9's activity from multi-turnover to single turnover. In human cells, FACT depletion extends dCas9 residence times, delays genome editing, and alters the balance between indel formation and homology-directed repair. FACT knockdown also increases epigenetic marking by dCas9-based transcriptional effectors with a concomitant enhancement of transcriptional modulation. FACT thus shapes the intrinsic cellular response to Cas9-based genome manipulation most likely by determining Cas9 residence times.
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Affiliation(s)
- Alan S Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Leo C Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - R Alex Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yvonne Hao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David T McSwiggen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute of Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alec B Heckert
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute of Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher D Richardson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Benjamin G Gowen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katelynn R Kazane
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathan T Vu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stacia K Wyman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jiyung J Shin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute of Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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45
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Li A, Tanner MR, Lee CM, Hurley AE, De Giorgi M, Jarrett KE, Davis TH, Doerfler AM, Bao G, Beeton C, Lagor WR. AAV-CRISPR Gene Editing Is Negated by Pre-existing Immunity to Cas9. Mol Ther 2020; 28:1432-1441. [PMID: 32348718 PMCID: PMC7264438 DOI: 10.1016/j.ymthe.2020.04.017] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/03/2020] [Accepted: 04/15/2020] [Indexed: 02/07/2023] Open
Abstract
Adeno-associated viral (AAV) vectors are a leading candidate for the delivery of CRISPR-Cas9 for therapeutic genome editing in vivo. However, AAV-based delivery involves persistent expression of the Cas9 nuclease, a bacterial protein. Recent studies indicate a high prevalence of neutralizing antibodies and T cells specific to the commonly used Cas9 orthologs from Streptococcus pyogenes (SpCas9) and Staphylococcus aureus (SaCas9) in humans. We tested in a mouse model whether pre-existing immunity to SaCas9 would pose a barrier to liver genome editing with AAV packaging CRISPR-Cas9. Although efficient genome editing occurred in mouse liver with pre-existing SaCas9 immunity, this was accompanied by an increased proportion of CD8+ T cells in the liver. This cytotoxic T cell response was characterized by hepatocyte apoptosis, loss of recombinant AAV genomes, and complete elimination of genome-edited cells, and was followed by compensatory liver regeneration. Our results raise important efficacy and safety concerns for CRISPR-Cas9-based in vivo genome editing in the liver.
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Affiliation(s)
- Ang Li
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Mark R Tanner
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ayrea E Hurley
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marco De Giorgi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kelsey E Jarrett
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy H Davis
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Alexandria M Doerfler
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA.
| | - Christine Beeton
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - William R Lagor
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
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46
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Mekler V, Kuznedelov K, Severinov K. Quantification of the affinities of CRISPR-Cas9 nucleases for cognate protospacer adjacent motif (PAM) sequences. J Biol Chem 2020; 295:6509-6517. [PMID: 32241913 PMCID: PMC7212624 DOI: 10.1074/jbc.ra119.012239] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/31/2020] [Indexed: 11/06/2022] Open
Abstract
The CRISPR/Cas9 nucleases have been widely applied for genome editing in various organisms. Cas9 nucleases complexed with a guide RNA (Cas9-gRNA) find their targets by scanning and interrogating the genomic DNA for sequences complementary to the gRNA. Recognition of the DNA target sequence requires a short protospacer adjacent motif (PAM) located outside this sequence. Given that the efficiency of target location may depend on the strength of interactions that promote target recognition, here we sought to compare affinities of different Cas9 nucleases for their cognate PAM sequences. To this end, we measured affinities of Cas9 nucleases from Streptococcus pyogenes, Staphylococcus aureus, and Francisella novicida complexed with guide RNAs (gRNAs) (SpCas9-gRNA, SaCas9-gRNA, and FnCas9-gRNA, respectively) and of three engineered SpCas9-gRNA variants with altered PAM specificities for short, PAM-containing DNA probes. We used a "beacon" assay that measures the relative affinities of DNA probes by determining their ability to competitively affect the rate of Cas9-gRNA binding to fluorescently labeled target DNA derivatives called "Cas9 beacons." We observed significant differences in the affinities for cognate PAM sequences among the studied Cas9 enzymes. The relative affinities of SpCas9-gRNA and its engineered variants for canonical and suboptimal PAMs correlated with previous findings on the efficiency of these PAM sequences in genome editing. These findings suggest that high affinity of a Cas9 nuclease for its cognate PAM promotes higher genome-editing efficiency.
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Affiliation(s)
- Vladimir Mekler
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, New Jersey 08854
| | - Konstantin Kuznedelov
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, New Jersey 08854
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, New Jersey 08854
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 119334, Russia
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47
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Becskei A. Tuning up Transcription Factors for Therapy. Molecules 2020; 25:E1902. [PMID: 32326099 PMCID: PMC7221782 DOI: 10.3390/molecules25081902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/19/2022] Open
Abstract
The recent developments in the delivery and design of transcription factors put their therapeutic applications within reach, exemplified by cell replacement, cancer differentiation and T-cell based cancer therapies. The success of such applications depends on the efficacy and precision in the action of transcription factors. The biophysical and genetic characterization of the paradigmatic prokaryotic repressors, LacI and TetR and the designer transcription factors, transcription activator-like effector (TALE) and CRISPR-dCas9 revealed common principles behind their efficacy, which can aid the optimization of transcriptional activators and repressors. Further studies will be required to analyze the linkage between dissociation constants and enzymatic activity, the role of phase separation and squelching in activation and repression and the long-range interaction of transcription factors with epigenetic regulators in the context of the chromosomes. Understanding these mechanisms will help to tailor natural and synthetic transcription factors to the needs of specific applications.
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Affiliation(s)
- Attila Becskei
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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48
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Whinn KS, van Oijen AM, Ghodke H. Spy-ing on Cas9: Single-molecule tools reveal the enzymology of Cas9. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019. [DOI: 10.1016/j.cobme.2019.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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49
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Soubeyrand S, Lau P, Peters V, McPherson R. Off-target effects of CRISPRa on interleukin-6 expression. PLoS One 2019; 14:e0224113. [PMID: 31658298 PMCID: PMC6816553 DOI: 10.1371/journal.pone.0224113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/04/2019] [Indexed: 12/29/2022] Open
Abstract
Inactive fusion variants of the CRISPR-Cas9 system are increasingly being used as standard methodology to study transcription regulation. Their ability to readily manipulate the native genomic loci is particularly advantageous. In this work, we serendipitously uncover the key cytokine IL6 as an off-target of the activating derivative of CRISPR (CRISPRa) while studying RP11-326A19.4, a novel long-non coding RNA (lncRNA). Increasing RP11-326A19.4 expression in HEK293T cells via CRISPRa-mediated activation of its promoter region induced genome-wide transcriptional changes, including upregulation of IL6, an important cytokine. IL6 was increased in response to distinct sgRNA targeting the RP11-326A19.4 promoter region, suggesting specificity. Loss of the cognate sgRNA recognition sites failed to abolish CRISPRa mediated activation of IL6 however, pointing to off-target effects. Bioinformatic approaches did not reveal predicted off-target binding sites. Off-target activation of IL6 was sustained and involved low level activation of known IL6 regulators. Increased IL6 remained sensitive to further activation by TNFα, consistent with the existence of independent mechanisms. This study provides experimental evidence that CRISPRa has discrete, unpredictable off-targeting limitations that must be considered when using this emerging technology.
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Affiliation(s)
- Sébastien Soubeyrand
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Paulina Lau
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Victoria Peters
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Ruth McPherson
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
- Department of Medicine, Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
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50
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Schindele A, Dorn A, Puchta H. CRISPR/Cas brings plant biology and breeding into the fast lane. Curr Opin Biotechnol 2019; 61:7-14. [PMID: 31557657 DOI: 10.1016/j.copbio.2019.08.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022]
Abstract
CRISPR/Cas is in the process of inducing the biggest transformation of plant breeding since the green revolution. Whereas initial efforts focused mainly on changing single traits by error prone non-homologous end joining, the last two years saw a tremendous technical progress achieving more complex genetic, epigenetic and transcriptional changes. The efficiencies of inducing directed changes by homologous recombination have been improved significantly and strategies to break genetic linkages by inducing chromosomal rearrangements have been developed. Cas13 systems have been applied to degrade viral and mRNA in plants. Most importantly, a historical breakthrough was accomplished: By introducing multiple genomic changes simultaneously, domestication of wild species in a single generation has been demonstrated, speeding up breeding dramatically.
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Affiliation(s)
- Angelina Schindele
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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