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Molteni C, Forni D, Cagliani R, Bravo IG, Sironi M. Evolution and diversity of nucleotide and dinucleotide composition in poxviruses. J Gen Virol 2023; 104. [PMID: 37792576 DOI: 10.1099/jgv.0.001897] [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] [Indexed: 10/06/2023] Open
Abstract
Poxviruses (family Poxviridae) have long dsDNA genomes and infect a wide range of hosts, including insects, birds, reptiles and mammals. These viruses have substantial incidence, prevalence and disease burden in humans and in other animals. Nucleotide and dinucleotide composition, mostly CpG and TpA, have been largely studied in viral genomes because of their evolutionary and functional implications. We analysed here the nucleotide and dinucleotide composition, as well as codon usage bias, of a set of representative poxvirus genomes, with a very diverse host spectrum. After correcting for overall nucleotide composition, entomopoxviruses displayed low overall GC content, no enrichment in TpA and large variation in CpG enrichment, while chordopoxviruses showed large variation in nucleotide composition, no obvious depletion in CpG and a weak trend for TpA depletion in GC-rich genomes. Overall, intergenome variation in dinucleotide composition in poxviruses is largely accounted for by variation in overall genomic GC levels. Nonetheless, using vaccinia virus as a model, we found that genes expressed at the earliest times in infection are more CpG-depleted than genes expressed at later stages. This observation has parallels in betahepesviruses (also large dsDNA viruses) and suggests an antiviral role for the innate immune system (e.g. via the zinc-finger antiviral protein ZAP) in the early phases of poxvirus infection. We also analysed codon usage bias in poxviruses and we observed that it is mostly determined by genomic GC content, and that stratification after host taxonomy does not contribute to explaining codon usage bias diversity. By analysis of within-species diversity, we show that genomic GC content is the result of mutational biases. Poxvirus genomes that encode a DNA ligase are significantly AT-richer than those that do not, suggesting that DNA repair systems shape mutation biases. Our data shed light on the evolution of poxviruses and inform strategies for their genetic manipulation for therapeutic purposes.
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Affiliation(s)
- Cristian Molteni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Ignacio G Bravo
- Laboratoire MIVEGEC (Univ Montpellier CNRS, IRD), Centre National de la Recherche Scientifique, Montpellier, France
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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2
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Whelan JT, Singaravelu R, Wang F, Pelin A, Tamming LA, Pugliese G, Martin NT, Crupi MJF, Petryk J, Austin B, He X, Marius R, Duong J, Jones C, Fekete EEF, Alluqmani N, Chen A, Boulton S, Huh MS, Tang MY, Taha Z, Scut E, Diallo JS, Azad T, Lichty BD, Ilkow CS, Bell JC. CRISPR-mediated rapid arming of poxvirus vectors enables facile generation of the novel immunotherapeutic STINGPOX. Front Immunol 2023; 13:1050250. [PMID: 36713447 PMCID: PMC9880309 DOI: 10.3389/fimmu.2022.1050250] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/05/2022] [Indexed: 01/15/2023] Open
Abstract
Poxvirus vectors represent versatile modalities for engineering novel vaccines and cancer immunotherapies. In addition to their oncolytic capacity and immunogenic influence, they can be readily engineered to express multiple large transgenes. However, the integration of multiple payloads into poxvirus genomes by traditional recombination-based approaches can be highly inefficient, time-consuming and cumbersome. Herein, we describe a simple, cost-effective approach to rapidly generate and purify a poxvirus vector with multiple transgenes. By utilizing a simple, modular CRISPR/Cas9 assisted-recombinant vaccinia virus engineering (CARVE) system, we demonstrate generation of a recombinant vaccinia virus expressing three distinct transgenes at three different loci in less than 1 week. We apply CARVE to rapidly generate a novel immunogenic vaccinia virus vector, which expresses a bacterial diadenylate cyclase. This novel vector, STINGPOX, produces cyclic di-AMP, a STING agonist, which drives IFN signaling critical to the anti-tumor immune response. We demonstrate that STINGPOX can drive IFN signaling in primary human cancer tissue explants. Using an immunocompetent murine colon cancer model, we demonstrate that intratumoral administration of STINGPOX in combination with checkpoint inhibitor, anti-PD1, promotes survival post-tumour challenge. These data demonstrate the utility of CRISPR/Cas9 in the rapid arming of poxvirus vectors with therapeutic payloads to create novel immunotherapies.
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Affiliation(s)
- Jack T. Whelan
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Ragunath Singaravelu
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada,Public Health Agency of Canada, Ottawa, ON, Canada
| | - Fuan Wang
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON, Canada,MG DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Adrian Pelin
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Levi A. Tamming
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Giuseppe Pugliese
- Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Nikolas T. Martin
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Mathieu J. F. Crupi
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Julia Petryk
- Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Bradley Austin
- Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Xiaohong He
- Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Ricardo Marius
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Jessie Duong
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Carter Jones
- Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Emily E. F. Fekete
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Nouf Alluqmani
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Andrew Chen
- Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Stephen Boulton
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Michael S. Huh
- Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Matt Y. Tang
- Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Zaid Taha
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Elena Scut
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Jean-Simon Diallo
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Taha Azad
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Brian D. Lichty
- McMaster Immunology Research Centre, Department of Medicine, McMaster University, Hamilton, ON, Canada,MG DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada,*Correspondence: John C. Bell, ; Carolina S. Ilkow, ; Brian D. Lichty,
| | - Carolina S. Ilkow
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada,*Correspondence: John C. Bell, ; Carolina S. Ilkow, ; Brian D. Lichty,
| | - John C. Bell
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Centre for Innovation Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, ON, Canada,*Correspondence: John C. Bell, ; Carolina S. Ilkow, ; Brian D. Lichty,
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3
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El Nachef L, Berthel E, Ferlazzo ML, Le Reun E, Al-Choboq J, Restier-Verlet J, Granzotto A, Sonzogni L, Bourguignon M, Foray N. Cancer and Radiosensitivity Syndromes: Is Impaired Nuclear ATM Kinase Activity the Primum Movens? Cancers (Basel) 2022; 14:cancers14246141. [PMID: 36551628 PMCID: PMC9776478 DOI: 10.3390/cancers14246141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/01/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
There are a number of genetic syndromes associated with both high cancer risk and clinical radiosensitivity. However, the link between these two notions remains unknown. Particularly, some cancer syndromes are caused by mutations in genes involved in DNA damage signaling and repair. How are the DNA sequence errors propagated and amplified to cause cell transformation? Conversely, some cancer syndromes are caused by mutations in genes involved in cell cycle checkpoint control. How is misrepaired DNA damage produced? Lastly, certain genes, considered as tumor suppressors, are not involved in DNA damage signaling and repair or in cell cycle checkpoint control. The mechanistic model based on radiation-induced nucleoshuttling of the ATM kinase (RIANS), a major actor of the response to ionizing radiation, may help in providing a unified explanation of the link between cancer proneness and radiosensitivity. In the frame of this model, a given protein may ensure its own specific function but may also play additional biological role(s) as an ATM phosphorylation substrate in cytoplasm. It appears that the mutated proteins that cause the major cancer and radiosensitivity syndromes are all ATM phosphorylation substrates, and they generally localize in the cytoplasm when mutated. The relevance of the RIANS model is discussed by considering different categories of the cancer syndromes.
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Affiliation(s)
- Laura El Nachef
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Elise Berthel
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Mélanie L. Ferlazzo
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Eymeric Le Reun
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Joelle Al-Choboq
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Juliette Restier-Verlet
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Adeline Granzotto
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Laurène Sonzogni
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
| | - Michel Bourguignon
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
- Department of Biophysics and Nuclear Medicine, Université Paris Saclay (UVSQ), 78035 Versailles, France
| | - Nicolas Foray
- Inserm, U1296 Unit, Radiation: Defense, Health and Environment, Centre Léon-Bérard, 69008 Lyon, France
- Correspondence: ; Tel.: +33-04-7878-2828
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Ciszewski WM, Sobierajska K, Stasiak A, Wagner W. Lactate drives cellular DNA repair capacity: Role of lactate and related short-chain fatty acids in cervical cancer chemoresistance and viral infection. Front Cell Dev Biol 2022; 10:1012254. [PMID: 36340042 PMCID: PMC9627168 DOI: 10.3389/fcell.2022.1012254] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2023] Open
Abstract
The characteristic feature of a cancer microenvironment is the presence of a highly elevated concentration of L-lactate in the tumor niche. The lactate-rich environment is also maintained by commensal mucosal microbiota, which has immense potential for affecting cancer cells through its receptoric and epigenetic modes of action. Some of these lactate activities might be associated with the failure of anticancer therapy as a consequence of the drug resistance acquired by cancer cells. Upregulation of cellular DNA repair capacity and enhanced drug efflux are the most important cellular mechanisms that account for ineffective radiotherapy and drug-based therapies. Here, we present the recent scientific knowledge on the role of the HCA1 receptor for lactate and lactate intrinsic activity as an HDAC inhibitor in the development of an anticancer therapy-resistant tumor phenotype, with special focus on cervical cancer cells. In addition, a recent study highlighted the viable role of interactions between mammalian cells and microorganisms in the female reproductive tract and demonstrated an interesting mechanism regulating the efficacy of retroviral transduction through lactate-driven modulation of DNA-PKcs cellular localization. To date, very few studies have focused on the mechanisms of lactate-driven enhancement of DNA repair and upregulation of particular multidrug-resistance proteins in cancer cells with respect to their intracellular regulatory mechanisms triggered by lactate. This review presents the main achievements in the field of lactate impact on cell biology that may promote undesirable alterations in cancer physiology and mitigate retroviral infections.
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Affiliation(s)
| | | | - Anna Stasiak
- Department of Hormone Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Waldemar Wagner
- Laboratory of Cellular Immunology, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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5
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López-Muñoz AD, Rastrojo A, Martín R, Alcami A. High-throughput engineering of cytoplasmic- and nuclear-replicating large dsDNA viruses by CRISPR/Cas9. J Gen Virol 2022; 103:001797. [PMID: 36260063 PMCID: PMC10019086 DOI: 10.1099/jgv.0.001797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The application of CRISPR/Cas9 to improve genome engineering efficiency for large dsDNA viruses has been extensively described, but a robust and versatile method for high-throughput generation of marker-free recombinants for a desired locus has not yet been reported. Cytoplasmic-replicating viruses use their own repair enzymes for homologous recombination, while nuclear-replicating viruses use the host repair machinery. This is translated into a wide range of Cas9-induced homologous recombination efficiencies, depending on the virus replication compartment and viral/host repair machinery characteristics and accessibility. However, the use of Cas9 as a selection agent to target parental virus genomes robustly improves the selection of desired recombinants across large dsDNA viruses. We used ectromelia virus (ECTV) and herpes simplex virus (HSV) type 1 and 2 to optimize a CRISPR/Cas9 method that can be used versatilely for efficient genome editing and selection of both cytoplasmic- and nuclear-replicating viruses. We performed a genome-wide genetic variant analysis of mutations located at predicted off-target sequences for 20 different recombinants, showing off-target-free accuracy by deep sequencing. Our results support this optimized method as an efficient, accurate and versatile approach to enhance the two critical factors of high-throughput viral genome engineering: generation and colour-based selection of recombinants. This application of CRISPR/Cas9 reduces the time and labour for screening of desired recombinants, allowing for high-throughput generation of large collections of mutant dsDNA viruses for a desired locus, optimally in less than 2 weeks.
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Affiliation(s)
- Alberto Domingo López-Muñoz
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain.,Present address: Cellular Biology Section, Laboratory of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain.,Present address: Genetic Unit, Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Rocío Martín
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
| | - Antonio Alcami
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
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Abstract
Genetic recombination is used as a tool for modifying the composition of poxvirus genomes in both discovery and applied research. This review documents the history behind the development of these tools as well as what has been learned about the processes that catalyze virus recombination and the links between it and DNA replication and repair. The study of poxvirus recombination extends back to the 1930s with the discovery that one virus can reactivate another by a process later shown to generate recombinants. In the years that followed it was shown that recombinants can be produced in virus-by-virus crosses within a genus (e.g., variola-by-rabbitpox) and efforts were made to produce recombination-based genetic maps with modest success. The marker rescue mapping method proved more useful and led to methods for making genetically engineered viruses. Many further insights into the mechanism of recombination have been provided by transfection studies which have shown that this is a high-frequency process associated with hybrid DNA formation and inextricably linked to replication. The links reflect the fact that poxvirus DNA polymerases, specifically the vaccinia virus E9 enzyme, can catalyze strand transfer in in vivo and in vitro reactions dependent on the 3'-to-5' proofreading exonuclease and enhanced by the I3 replicative single-strand DNA binding protein. These reactions have shaped the composition of virus genomes and are modulated by constraints imposed on virus-virus interactions by viral replication in cytoplasmic factories. As recombination reactions are used for replication fork assembly and repair in many biological systems, further study of these reactions may provide new insights into still poorly understood features of poxvirus DNA replication.
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Affiliation(s)
- David Hugh Evans
- Department of Medical Microbiology & Immunology and Li Ka Shing Institute of Virology, The University of Alberta, Edmonton, AB T6G 2J7, Canada
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7
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Tang N, Zhang Y, Shen Z, Yao Y, Nair V. Application of CRISPR-Cas9 Editing for Virus Engineering and the Development of Recombinant Viral Vaccines. CRISPR J 2021; 4:477-490. [PMID: 34406035 DOI: 10.1089/crispr.2021.0017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas technology, discovered originally as a bacterial defense system, has been extensively repurposed as a powerful tool for genome editing for multiple applications in biology. In the field of virology, CRISPR-Cas9 technology has been widely applied on genetic recombination and engineering of genomes of various viruses to ask some fundamental questions about virus-host interactions. Its high efficiency, specificity, versatility, and low cost have also provided great inspiration and hope in the field of vaccinology to solve a series of bottleneck problems in the development of recombinant viral vaccines. This review highlights the applications of CRISPR editing in the technological advances compared to the traditional approaches used for the construction of recombinant viral vaccines and vectors, the main factors affecting their application, and the challenges that need to be overcome for further streamlining their effective usage in the prevention and control of diseases. Factors affecting efficiency, target specificity, and fidelity of CRISPR-Cas editing in the context of viral genome editing and development of recombinant vaccines are also discussed.
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Affiliation(s)
- Na Tang
- Shandong Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, P.R. China; University of Oxford, Oxford, United Kingdom
| | - Yaoyao Zhang
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash road, Guildford, Surrey, United Kingdom; University of Oxford, Oxford, United Kingdom
| | - Zhiqiang Shen
- Shandong Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, P.R. China; University of Oxford, Oxford, United Kingdom
| | - Yongxiu Yao
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash road, Guildford, Surrey, United Kingdom; University of Oxford, Oxford, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash road, Guildford, Surrey, United Kingdom; University of Oxford, Oxford, United Kingdom.,The Jenner Institute Laboratories, University of Oxford, Oxford, United Kingdom; and University of Oxford, Oxford, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
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8
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Vallée G, Norris P, Paszkowski P, Noyce RS, Evans DH. Vaccinia Virus Gene Acquisition through Nonhomologous Recombination. J Virol 2021; 95:e0031821. [PMID: 33910949 PMCID: PMC8223923 DOI: 10.1128/jvi.00318-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/19/2021] [Indexed: 01/04/2023] Open
Abstract
Many of the genes encoded by poxviruses are orthologs of cellular genes. These virus genes serve different purposes, but perhaps of most interest is the way some have been repurposed to inhibit the antiviral pathways that their cellular homologs still regulate. What is unclear is how these virus genes were acquired, although it is presumed to have been catalyzed by some form(s) of nonhomologous recombination (NHR). We used transfection assays and substrates encoding a fluorescent and drug-selectable marker to examine the NHR frequency in vaccinia virus (VAC)-infected cells. These studies showed that when cells were transfected with linear duplex DNAs bearing VAC N2L gene homology, it yielded a recombinant frequency (RF) of 6.7 × 10-4. In contrast, DNA lacking any VAC homology reduced the yield of recombinants ∼400-fold (RF = 1.6 × 10-6). DNA-RNA hybrids were also substrates, although homologous molecules yielded fewer recombinants (RF = 2.1 × 10-5), and nonhomologous substrates yielded only rare recombinants (RF ≤ 3 × 10-8). NHR was associated with genome rearrangements ranging from simple insertions with flanking sequence duplications to large-scale indels that produced helper-dependent viruses. The insert was often also partially duplicated and would rapidly rearrange through homologous recombination. Most of the virus-insert junctions exhibited little or no preexiting microhomology, although a few encoded VAC topoisomerase recognition sites (C/T·CCTT). These studies show that VAC can catalyze NHR through a process that may reflect a form of aberrant replication fork repair. Although it is less efficient than classical homologous recombination, the rates of NHR may still be high enough to drive virus evolution. IMPORTANCE Large DNA viruses sometimes interfere in antiviral defenses using repurposed and mutant forms of the cellular proteins that mediate these same reactions. Such virus orthologs of cellular genes were presumably captured through nonhomologous recombination, perhaps in the distant past, but nothing is known about the processes that might promote "gene capture" or even how often these events occur over the course of an infectious cycle. This study shows that nonhomologous recombination in vaccinia virus-infected cells is frequent enough to seed a small but still significant portion of novel recombinants into large populations of newly replicated virus particles. This offers a route by which a pool of virus might survey the host genome for sequences that offer a selective growth advantage and potentially drive discontinuous virus evolution (saltation) through the acquisition of adventitious traits.
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Affiliation(s)
- Greg Vallée
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Peter Norris
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Patrick Paszkowski
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Ryan S. Noyce
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - David H. Evans
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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9
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Laudermilch E, Chandran K. MAVERICC: Marker-free Vaccinia Virus Engineering of Recombinants through in vitro CRISPR/Cas9 Cleavage. J Mol Biol 2021; 433:166896. [PMID: 33639215 DOI: 10.1016/j.jmb.2021.166896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/23/2022]
Abstract
Vaccinia virus (VACV)-based vectors are in extensive use as vaccines and cancer immunotherapies. VACV engineering has traditionally relied on homologous recombination between a parental viral genome and a transgene-bearing transfer plasmid, an inefficient process that necessitates the use of a selection or screening marker to isolate recombinants. Recent extensions of this approach have sought to enhance the recovery of transgene-bearing viruses through the use of CRISPR-Cas9 engineering to cleave the viral genome in infected cells. However, these methods do not completely eliminate the generation of WT viral progeny and thus continue to require multiple rounds of viral propagation and plaque purification. Here, we describe MAVERICC (marker-free vaccinia virus engineering of recombinants through in vitroCRISPR/Cas9 cleavage), a new strategy to engineer recombinant VACVs in a manner that overcomes current limitations. MAVERICC also leverages the CRISPR/Cas9 system but requires no markers and yields essentially pure preparations of the desired recombinants in a single step. We used this approach to introduce point mutations, insertions, and deletions at multiple locations in the VACV genome, both singly and in combination. The efficiency and versatility of MAVERICC make it an ideal choice for generating mutants and mutant libraries at arbitrarily selected locations in the viral genome to build complex VACV vectors, effect vector improvements, and facilitate the study of poxvirus biology.
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Affiliation(s)
- Ethan Laudermilch
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States.
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10
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Matía A, Lorenzo MM, Blasco R. Tools for the targeted genetic modification of poxvirus genomes. Curr Opin Virol 2020; 44:183-190. [PMID: 33242829 DOI: 10.1016/j.coviro.2020.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022]
Abstract
The potential of viruses as biotechnology platforms is becoming more appealing due to technological advances in synthetic biology techniques and to the increasing accessibility of means to manipulate virus genomes. Among viral systems, poxviruses, and their prototype member Vaccinia Virus, are one of the outstanding choices for different biotechnological and medical applications based on heterologous gene expression, recombinant vaccines or oncolytic viruses. The refinement of genetic engineering methods on Vaccinia Virus over the last decades have contributed to facilitate the manipulation of the genomes of poxviruses, and may aid in the improvement of virus variants designed for different goals through reverse genetic approaches. Targeted genetic changes are usually performed by homologous recombination with the viral genome. In addition to the classic approach, recent methodological advances that may assist new strategies for the mutation or edition of poxvirus genomes are reviewed.
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Affiliation(s)
- Alejandro Matía
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (I.N.I.A.), Ctra. La Coruña km 7.5, E-28040 Madrid, Spain
| | - María M Lorenzo
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (I.N.I.A.), Ctra. La Coruña km 7.5, E-28040 Madrid, Spain
| | - Rafael Blasco
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (I.N.I.A.), Ctra. La Coruña km 7.5, E-28040 Madrid, Spain.
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Rapid poxvirus engineering using CRISPR/Cas9 as a selection tool. Commun Biol 2020; 3:643. [PMID: 33144673 PMCID: PMC7641209 DOI: 10.1038/s42003-020-01374-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/01/2020] [Indexed: 02/08/2023] Open
Abstract
In standard uses of CRISPR/Cas9 technology, the cutting of genomes and their efficient repair are considered to go hand-in-hand to achieve desired genetic changes. This includes the current approach for engineering genomes of large dsDNA viruses. However, for poxviruses we show that Cas9-guide RNA complexes cut viral genomes soon after their entry into cells, but repair of these breaks is inefficient. As a result, Cas9 targeting makes only modest, if any, improvements to basal rates of homologous recombination between repair constructs and poxvirus genomes. Instead, Cas9 cleavage leads to inhibition of poxvirus DNA replication thereby suppressing virus spread in culture. This unexpected outcome allows Cas9 to be used as a powerful tool for selecting conventionally generated poxvirus recombinants, which are otherwise impossible to separate from a large background of parental virus without the use of marker genes. This application of CRISPR/Cas9 greatly speeds up the generation of poxvirus-based vaccines, making this platform considerably more attractive in the context of personalised cancer vaccines and emerging disease outbreaks. Gowripalan, Smith et al. use CRISPR/Cas9 technology to rapidly select recombinant poxviruses without using selectable marker genes. They find that Cas9 cleavage inhibits poxvirus DNA replication, suppressing virus spread in culture. This application makes poxviruses more attractive vector platforms for fighting cancer and emerging disease outbreaks.
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Hristova DB, Lauer KB, Ferguson BJ. Viral interactions with non-homologous end-joining: a game of hide-and-seek. J Gen Virol 2020; 101:1133-1144. [PMID: 32735206 PMCID: PMC7879558 DOI: 10.1099/jgv.0.001478] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023] Open
Abstract
There are extensive interactions between viruses and the host DNA damage response (DDR) machinery. The outcome of these interactions includes not only direct effects on viral nucleic acids and genome replication, but also the activation of host stress response signalling pathways that can have further, indirect effects on viral life cycles. The non-homologous end-joining (NHEJ) pathway is responsible for the rapid and imprecise repair of DNA double-stranded breaks in the nucleus that would otherwise be highly toxic. Whilst directly repairing DNA, components of the NHEJ machinery, in particular the DNA-dependent protein kinase (DNA-PK), can activate a raft of downstream signalling events that activate antiviral, cell cycle checkpoint and apoptosis pathways. This combination of possible outcomes results in NHEJ being pro- or antiviral depending on the infection. In this review we will describe the broad range of interactions between NHEJ components and viruses and their consequences for both host and pathogen.
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Affiliation(s)
- Dayana B. Hristova
- Department of Pathology, Division of Immunology, University of Cambridge, Cambridge, UK
| | - Katharina B. Lauer
- Department of Pathology, Division of Immunology, University of Cambridge, Cambridge, UK
- Present address: ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Brian J. Ferguson
- Department of Pathology, Division of Immunology, University of Cambridge, Cambridge, UK
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