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Alvaro-Aranda L, Petitalot A, Djeghmoum Y, Panigada D, Singh J, Ehlén Å, Vugic D, Martin C, Miron S, Contreras-Perez A, Nhiri N, Boucherit V, Lafitte P, Dumoulin I, Quiles F, Rouleau E, Jacquet E, Feliubadaló L, del Valle J, Sharan SK, Stoppa-Lyonnet D, Zinn-Justin S, Lázaro C, Caputo S, Carreira A. The BRCA2 R2645G variant increases DNA binding and induces hyper-recombination. Nucleic Acids Res 2024; 52:6964-6976. [PMID: 38142462 PMCID: PMC11229362 DOI: 10.1093/nar/gkad1222] [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: 08/08/2023] [Revised: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 12/26/2023] Open
Abstract
BRCA2 tumor suppressor protein ensures genome integrity by mediating DNA repair via homologous recombination (HR). This function is executed in part by its canonical DNA binding domain located at the C-terminus (BRCA2CTD), the only folded domain of the protein. Most germline pathogenic missense variants are located in this highly conserved region which binds to single-stranded DNA (ssDNA) and to the acidic protein DSS1. These interactions are essential for the HR function of BRCA2. Here, we report that the variant R2645G, identified in breast cancer and located at the DSS1 interface, unexpectedly increases the ssDNA binding activity of BRCA2CTDin vitro. Human cells expressing this variant display a hyper-recombination phenotype, chromosomal instability in the form of chromatid gaps when exposed to DNA damage, and increased PARP inhibitor sensitivity. In mouse embryonic stem cells (mES), this variant alters viability and confers sensitivity to cisplatin and Mitomycin C. These results suggest that BRCA2 interaction with ssDNA needs to be tightly regulated to limit HR and prevent chromosomal instability and we propose that this control mechanism involves DSS1. Given that several missense variants located within this region have been identified in breast cancer patients, these findings might have clinical implications for carriers.
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Affiliation(s)
- Lucia Alvaro-Aranda
- Genome Instability and Cancer Predisposition Laboratory, Centro de Biologia Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid 28049, Spain
| | - Ambre Petitalot
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Yasmina Djeghmoum
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Davide Panigada
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Jenny Kaur Singh
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Åsa Ehlén
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Domagoj Vugic
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Charlotte Martin
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Simona Miron
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, 91190 Gif-sur-Yvette, France
| | - Aida Contreras-Perez
- Genome Instability and Cancer Predisposition Laboratory, Centro de Biologia Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid 28049, Spain
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, Paris-Saclay University, CNRS, 91190 Gif-sur-Yvette, France
| | - Virginie Boucherit
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Philippe Lafitte
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Isaac Dumoulin
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Francisco Quiles
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, Spain
- Ciber Oncología (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Etienne Rouleau
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, Paris-Saclay University, CNRS, 91190 Gif-sur-Yvette, France
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, Spain
- Ciber Oncología (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Jesús del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, Spain
- Ciber Oncología (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris 75005, France
- Paris-Cité University, Paris, France
- INSERM U830, Institut Curie, Paris 75005, France
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, 91190 Gif-sur-Yvette, France
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, Spain
- Ciber Oncología (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris 75005, France
- PSL Research University, Paris 75005, France
| | - Aura Carreira
- Genome Instability and Cancer Predisposition Laboratory, Centro de Biologia Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid 28049, Spain
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France
- Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
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2
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Liu Z, Liu H, Huang C, Zhou Q, Luo Y. Hybrid Cas12a Variants with Relaxed PAM Requirements Expand Genome Editing Compatibility. ACS Synth Biol 2024; 13:1809-1819. [PMID: 38819403 DOI: 10.1021/acssynbio.4c00103] [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: 06/01/2024]
Abstract
Cas12a is a widely used programmable nuclease for genome editing across a variety of organisms, but its application is limited by its PAM recognition restriction. To alleviate these PAM constraints, protein engineering efforts have been applied to expand the PAM recognition range. In this study, we designed and constructed 990 synthetic hybrid Cas12a chimeras through domain shuffling and screened an efficient hybrid Cas12a (ehCas12a) that could recognize a broad range PAM of 5'-TYYN-3' (Y is T or C and N is A, T, C, or G). Furthermore, we constructed an ehCas12a variant, ehCas12a RRVR (T167R/N572R/K578V/N582R), with expanded PAM preference to 5'-TNYN, TWRV-3' (W is A or T, R is A or G, and V is A, C, or G), which can efficiently recognize -2* A/G PAMs that are barely recognized by Cas12a-type proteins and their mutants. Finally, we demonstrated that the DNase-inactivated ehCas12a RRVR base editor (dehCas12a RRVR-BE) was capable of targeting noncanonical PAMs in vivo and disease-related loci for potential therapeutic applications. Overall, our findings highlight the modular design and reconfiguration of Cas proteins for enhanced functionality.
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Affiliation(s)
- Zhenyu Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huayi Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chaoqun Huang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Qun Zhou
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yunzi Luo
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Tangxing Road 133, Nanshan District, Shenzhen 518071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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3
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Eden T, Schaffrath AZ, Wesolowski J, Stähler T, Tode N, Richter N, Schäfer W, Hambach J, Hermans-Borgmeyer I, Woens J, Le Gall CM, Wendler S, Linke-Winnebeck C, Stobbe M, Budnicki I, Wanney A, Heitz Y, Schimmelpfennig L, Schweitzer L, Zimmer D, Stahl E, Seyfried F, Gebhardt AJ, Dieckow L, Riecken K, Fehse B, Bannas P, Magnus T, Verdoes M, Figdor CG, Hartlepp KF, Schleer H, Füner J, Tomas NM, Haag F, Rissiek B, Mann AM, Menzel S, Koch-Nolte F. Generation of nanobodies from transgenic 'LamaMice' lacking an endogenous immunoglobulin repertoire. Nat Commun 2024; 15:4728. [PMID: 38830864 PMCID: PMC11148044 DOI: 10.1038/s41467-024-48735-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/02/2024] [Indexed: 06/05/2024] Open
Abstract
Due to their exceptional solubility and stability, nanobodies have emerged as powerful building blocks for research tools and therapeutics. However, their generation in llamas is cumbersome and costly. Here, by inserting an engineered llama immunoglobulin heavy chain (IgH) locus into IgH-deficient mice, we generate a transgenic mouse line, which we refer to as 'LamaMouse'. We demonstrate that LamaMice solely express llama IgH molecules without association to Igκ or λ light chains. Immunization of LamaMice with AAV8, the receptor-binding domain of the SARS-CoV-2 spike protein, IgE, IgG2c, and CLEC9A enabled us to readily select respective target-specific nanobodies using classical hybridoma and phage display technologies, single B cell screening, and direct cloning of the nanobody-repertoire into a mammalian expression vector. Our work shows that the LamaMouse represents a flexible and broadly applicable platform for a facilitated selection of target-specific nanobodies.
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Affiliation(s)
- Thomas Eden
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alessa Z Schaffrath
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Janusz Wesolowski
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias Stähler
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Natalie Tode
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nathalie Richter
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Waldemar Schäfer
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Hambach
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Irm Hermans-Borgmeyer
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jannis Woens
- Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Camille M Le Gall
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sabrina Wendler
- ChromoTek GmbH, Martinsried, Germany - A part of Proteintech Group, Martinsried, Germany
| | | | - Martina Stobbe
- ChromoTek GmbH, Martinsried, Germany - A part of Proteintech Group, Martinsried, Germany
| | | | | | | | | | | | | | | | - Fabienne Seyfried
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna J Gebhardt
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lynn Dieckow
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Bannas
- Department of Radiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Magnus
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martijn Verdoes
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carl G Figdor
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Klaus F Hartlepp
- ChromoTek GmbH, Martinsried, Germany - A part of Proteintech Group, Martinsried, Germany
| | | | | | - Nicola M Tomas
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Björn Rissiek
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna M Mann
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Menzel
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Core Facility Nanobodies, University of Bonn, Bonn, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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4
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Zhao C, Porter JM, Burke PC, Arnberg N, Smith JG. Alpha-defensin binding expands human adenovirus tropism. PLoS Pathog 2024; 20:e1012317. [PMID: 38900833 PMCID: PMC11230588 DOI: 10.1371/journal.ppat.1012317] [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: 02/21/2024] [Revised: 07/08/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024] Open
Abstract
Mammalian α-defensins are a family of abundant effector peptides of the mucosal innate immune system. Although primarily considered to be antimicrobial, α-defensins can increase rather than block infection by certain prominent bacterial and viral pathogens in cell culture and in vivo. We have shown previously that exposure of mouse and human adenoviruses (HAdVs) to α-defensins is able to overcome competitive inhibitors that block cell binding, leading us to hypothesize a defensin-mediated binding mechanism that is independent of known viral receptors. To test this hypothesis, we used genetic approaches to demonstrate that none of several primary receptors nor integrin co-receptors are needed for human α-defensin-mediated binding of HAdV to cells; however, infection remains integrin dependent. Thus, our studies have revealed a novel pathway for HAdV binding to cells that bypasses viral primary receptors. We speculate that this pathway functions in parallel with receptor-mediated entry and contributes to α-defensin-enhanced infection of susceptible cells. Remarkably, we also found that in the presence of α-defensins, HAdV tropism is expanded to non-susceptible cells, even when viruses are exposed to a mixture of both susceptible and non-susceptible cells. Therefore, we propose that in the presence of sufficient concentrations of α-defensins, such as in the lung or gut, integrin expression rather than primary receptor expression will dictate HAdV tropism in vivo. In summary, α-defensins may contribute to tissue tropism not only through the neutralization of susceptible viruses but also by allowing certain defensin-resistant viruses to bind to cells independently of previously described mechanisms.
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Affiliation(s)
- Cheng Zhao
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jessica M. Porter
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Phillip C. Burke
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Niklas Arnberg
- Department of Clinical Microbiology, Division of Virology and Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Jason G. Smith
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, United States of America
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5
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Zhao C, Porter JM, Burke PC, Arnberg N, Smith JG. Alpha-defensin binding expands human adenovirus tropism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596681. [PMID: 38854108 PMCID: PMC11160700 DOI: 10.1101/2024.05.30.596681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Mammalian α-defensins are a family of abundant effector peptides of the mucosal innate immune system. Although primarily considered to be antimicrobial, α-defensins can increase rather than block infection by certain prominent bacterial and viral pathogens in cell culture and in vivo . We have shown previously that exposure of mouse and human adenoviruses (HAdVs) to α-defensins is able to overcome competitive inhibitors that block cell binding, leading us to hypothesize a defensin-mediated binding mechanism that is independent of known viral receptors. To test this hypothesis, we used genetic approaches to demonstrate that none of several primary receptors nor integrin co-receptors are needed for human α-defensin-mediated binding of HAdV to cells; however, infection remains integrin dependent. Thus, our studies have revealed a novel pathway for HAdV binding to cells that bypasses viral primary receptors. We speculate that this pathway functions in parallel with receptor-mediated entry and contributes to α-defensin-enhanced infection of susceptible cells. Remarkably, we also found that in the presence of α-defensins, HAdV tropism is expanded to non-susceptible cells, even when viruses are exposed to a mixture of both susceptible and non-susceptible cells. Therefore, we propose that in the presence of sufficient concentrations of α-defensins, such as in the lung or gut, integrin expression rather than primary receptor expression will dictate HAdV tropism in vivo . In summary, α-defensins may contribute to tissue tropism not only through the neutralization of susceptible viruses but also by allowing certain defensin-resistant viruses to bind to cells independently of previously described mechanisms. Author Summary In this study, we demonstrate a novel mechanism for binding of human adenoviruses (HAdVs) to cells that is dependent upon interactions with α-defensin host defense peptides but is independent of known viral receptors and co-receptors. To block normal receptor-mediated HAdV infection, we made genetic changes to both host cells and HAdVs. Under these conditions, α-defensins restored cell binding; however, infection still required the function of HAdV integrin co-receptors. This was true for multiple types of HAdVs that use different primary receptors and for cells that are either naturally devoid of HAdV receptors or were engineered to be receptor deficient. These observations suggest that in the presence of concentrations of α-defensins that would be found naturally in the lung or intestine, there are two parallel pathways for HAdV binding to cells that converge on integrins for productive infection. Moreover, these binding pathways function independently, and both operate in mixed culture. Thus, we have found that viruses can co-opt host defense molecules to expand their tropism.
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6
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Lei R, Qing E, Odle A, Yuan M, Gunawardene CD, Tan TJC, So N, Ouyang WO, Wilson IA, Gallagher T, Perlman S, Wu NC, Wong LYR. Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning. Nat Commun 2024; 15:4056. [PMID: 38744813 PMCID: PMC11094058 DOI: 10.1038/s41467-024-48104-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we perform a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identify mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we show that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chaminda D Gunawardene
- Center for Virus-Host Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Natalie So
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wenhao O Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA.
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA.
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, 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.
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA.
- Center for Virus-Host Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
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7
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Iyer RF, Verweij MC, Nair SS, Morrow D, Mansouri M, Chakravarty D, Beechwood T, Meyer C, Uebelhoer L, Lauron EJ, Selseth A, John N, Thin TH, Dzedzik S, Havenar-Daughton C, Axthelm MK, Douglas J, Korman A, Bhardwaj N, Tewari AK, Hansen S, Malouli D, Picker LJ, Früh K. CD8 + T cell targeting of tumor antigens presented by HLA-E. SCIENCE ADVANCES 2024; 10:eadm7515. [PMID: 38728394 PMCID: PMC11086602 DOI: 10.1126/sciadv.adm7515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024]
Abstract
The nonpolymorphic major histocompatibility complex E (MHC-E) molecule is up-regulated on many cancer cells, thus contributing to immune evasion by engaging inhibitory NKG2A/CD94 receptors on NK cells and tumor-infiltrating T cells. To investigate whether MHC-E expression by cancer cells can be targeted for MHC-E-restricted T cell control, we immunized rhesus macaques (RM) with rhesus cytomegalovirus (RhCMV) vectors genetically programmed to elicit MHC-E-restricted CD8+ T cells and to express established tumor-associated antigens (TAAs) including prostatic acidic phosphatase (PAP), Wilms tumor-1 protein, or Mesothelin. T cell responses to all three tumor antigens were comparable to viral antigen-specific responses with respect to frequency, duration, phenotype, epitope density, and MHC restriction. Thus, CMV-vectored cancer vaccines can bypass central tolerance by eliciting T cells to noncanonical epitopes. We further demonstrate that PAP-specific, MHC-E-restricted CD8+ T cells from RhCMV/PAP-immunized RM respond to PAP-expressing HLA-E+ prostate cancer cells, suggesting that the HLA-E/NKG2A immune checkpoint can be exploited for CD8+ T cell-based immunotherapies.
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Affiliation(s)
- Ravi F. Iyer
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Marieke C. Verweij
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Sujit S. Nair
- Department of Urology and Tisch Cancer Institute, Icahn School of Medicine at Mt Sinai, New York, NY 10029, USA
| | - David Morrow
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Mandana Mansouri
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Dimple Chakravarty
- Department of Urology and Tisch Cancer Institute, Icahn School of Medicine at Mt Sinai, New York, NY 10029, USA
| | - Teresa Beechwood
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | | | - Luke Uebelhoer
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | | | - Andrea Selseth
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Nessy John
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Tin Htwe Thin
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Siarhei Dzedzik
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Michael K. Axthelm
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | | | - Alan Korman
- Vir Biotechnology, San Francisco, CA 14158, USA
| | - Nina Bhardwaj
- Department of Urology and Tisch Cancer Institute, Icahn School of Medicine at Mt Sinai, New York, NY 10029, USA
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ashutosh K. Tewari
- Department of Urology and Tisch Cancer Institute, Icahn School of Medicine at Mt Sinai, New York, NY 10029, USA
| | - Scott Hansen
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Daniel Malouli
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Louis J. Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | - Klaus Früh
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
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8
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Contreras E, Liang C, Mahoney HL, Javier JL, Luce ML, Labastida Medina K, Bozza T, Schmidt TM. Flp-recombinase mouse line for genetic manipulation of ipRGCs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592761. [PMID: 38766000 PMCID: PMC11100754 DOI: 10.1101/2024.05.06.592761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Light has myriad impacts on behavior, health, and physiology. These signals originate in the retina and are relayed to the brain by more than 40 types of retinal ganglion cells (RGCs). Despite a growing appreciation for the diversity of RGCs, how these diverse channels of light information are ultimately integrated by the ~50 retinorecipient brain targets to drive these light-evoked effects is a major open question. This gap in understanding primarily stems from a lack of genetic tools that specifically label, manipulate, or ablate specific RGC types. Here, we report the generation and characterization of a new mouse line (Opn4FlpO), in which FlpO is expressed from the Opn4 locus, to manipulate the melanopsin-expressing, intrinsically photosensitive retinal ganglion cells. We find that the Opn4FlpO line, when crossed to multiple reporters, drives expression that is confined to ipRGCs and primarily labels the M1-M3 subtypes. Labeled cells in this mouse line show the expected intrinsic, melanopsin-based light response and morphological features consistent with the M1-M3 subtypes. In alignment with the morphological and physiological findings, we see strong innervation of non-image forming brain targets by ipRGC axons, and weaker innervation of image forming targets in Opn4FlpO mice labeled using AAV-based and FlpO-reporter lines. Consistent with the FlpO insertion disrupting the endogenous Opn4 transcript, we find that Opn4FlpO/FlpO mice show deficits in the pupillary light reflex, demonstrating their utility for behavioral research in future experiments. Overall, the Opn4FlpO mouse line drives Flp-recombinase expression that is confined to ipRGCs and most effectively drives recombination in M1-M3 ipRGCs. This mouse line will be of broad use to those interested in manipulating ipRGCs through a Flp-based recombinase for intersectional studies or in combination with other, non-Opn4 Cre driver lines.
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Affiliation(s)
- E Contreras
- Department of Neurobiology, Northwestern University, Evanston, IL
- Northwestern University Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - C Liang
- Department of Neurobiology, Northwestern University, Evanston, IL
| | - H L Mahoney
- Department of Neurobiology, Northwestern University, Evanston, IL
| | - J L Javier
- Department of Neurobiology, Northwestern University, Evanston, IL
| | - M L Luce
- Department of Neurobiology, Northwestern University, Evanston, IL
| | | | - T Bozza
- Department of Neurobiology, Northwestern University, Evanston, IL
| | - T M Schmidt
- Department of Neurobiology, Northwestern University, Evanston, IL
- Department of Ophthalmology, Feinberg School of Medicine, Chicago, IL
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9
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Poulos MG, Ramalingam P, Winiarski A, Gutkin MC, Katsnelson L, Carter C, Pibouin-Fragner L, Eichmann A, Thomas JL, Miquerol L, Butler JM. Complementary and Inducible creER T2 Mouse Models for Functional Evaluation of Endothelial Cell Subtypes in the Bone Marrow. Stem Cell Rev Rep 2024; 20:1135-1149. [PMID: 38438768 PMCID: PMC11087254 DOI: 10.1007/s12015-024-10703-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2024] [Indexed: 03/06/2024]
Abstract
In the adult bone marrow (BM), endothelial cells (ECs) are an integral component of the hematopoietic stem cell (HSC)-supportive niche, which modulates HSC activity by producing secreted and membrane-bound paracrine signals. Within the BM, distinct vascular arteriole, transitional, and sinusoidal EC subtypes display unique paracrine expression profiles and create anatomically-discrete microenvironments. However, the relative contributions of vascular endothelial subtypes in supporting hematopoiesis is unclear. Moreover, constitutive expression and off-target activity of currently available endothelial-specific and endothelial-subtype-specific murine cre lines potentially confound data analysis and interpretation. To address this, we describe two tamoxifen-inducible cre-expressing lines, Vegfr3-creERT2 and Cx40-creERT2, that efficiently label sinusoidal/transitional and arteriole endothelium respectively in adult marrow, without off-target activity in hematopoietic or perivascular cells. Utilizing an established mouse model in which cre-dependent recombination constitutively-activates MAPK signaling within adult endothelium, we identify arteriole ECs as the driver of MAPK-mediated hematopoietic dysfunction. These results define complementary tamoxifen-inducible creERT2-expressing mouse lines that label functionally-discrete and non-overlapping sinusoidal/transitional and arteriole EC populations in the adult BM, providing a robust toolset to investigate the differential contributions of vascular subtypes in maintaining hematopoietic homeostasis.
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Affiliation(s)
- Michael G Poulos
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, 32610, USA
- Division of Hematology/Oncology, University of Florida, 1333 Center Drive, BH-022D, Gainesville, FL, 32610, USA
| | - Pradeep Ramalingam
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, 32610, USA
- Division of Hematology/Oncology, University of Florida, 1333 Center Drive, BH-022D, Gainesville, FL, 32610, USA
| | - Agatha Winiarski
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, 32610, USA
| | - Michael C Gutkin
- Ansary Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Lizabeth Katsnelson
- Ansary Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Cody Carter
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, 32610, USA
| | | | - Anne Eichmann
- Université de Paris Cité, Inserm, PARCC, 75015, Paris, France
- Department of Molecular and Cellular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Jean-Leon Thomas
- Department of Neurology, Yale University School of Medicine, New Haven, CT, 06511, USA
- Paris Brain Institute, Université Pierre et Marie Curie Paris, 06 UMRS1127, Sorbonne Université, Paris Brain Institute, Paris, France
| | - Lucile Miquerol
- Aix-Marseille Université, CNRS UMR 7288, IBDM, 13288, Marseille, France
| | - Jason M Butler
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, 32610, USA.
- Ansary Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
- Division of Hematology/Oncology, University of Florida, 1333 Center Drive, BH-022D, Gainesville, FL, 32610, USA.
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10
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Visalli MA, Nale Lovett DJ, Kornfeind EM, Herrington H, Xiao YT, Lee D, Plair P, Wilder SG, Garza BK, Young A, Visalli RJ. Mutagenesis and functional analysis of the varicella-zoster virus portal protein. J Virol 2024; 98:e0060323. [PMID: 38517165 PMCID: PMC11019927 DOI: 10.1128/jvi.00603-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024] Open
Abstract
Herpesviruses replicate by cleaving concatemeric dsDNA into single genomic units that are packaged through an oligomeric portal present in preformed procapsids. In contrast to what is known about phage portal proteins, details concerning herpesvirus portal structure and function are not as well understood. A panel of 65 Varicella-Zoster virus (VZV) recombinant portal proteins with five amino acid in-frame insertions were generated by random transposon mutagenesis of the VZV portal gene, ORF54. Subsequently, 65 VZVLUC recombinant viruses (TNs) were generated via recombineering. Insertions were mapped to predicted portal domains (clip, wing, stem, wall, crown, and β-hairpin tunnel-loop) and recombinant viruses were characterized for plaque morphology, replication kinetics, pORF54 expression, and classified based on replication in non-complementing (ARPE19) or complementing (ARPE54C50) cell lines. The N- and C-termini were tolerant to insertion mutagenesis, as were certain clip sub-domains. The majority of mutants mapping to the wing, wall, β-hairpin tunnel loop, and stem domains were lethal. Elimination of the predicted ORF54 start codon revealed that the first 40 amino acids of the N-terminus were not required for viral replication. Stop codon insertions in the C-terminus showed that the last 100 amino acids were not required for viral replication. Lastly, a putative protease cleavage site was identified in the C-terminus of pORF54. Cleavage was likely orchestrated by a viral protease; however, processing was not required for DNA encapsidation and viral replication. The panel of recombinants should prove valuable in future studies to dissect mammalian portal structure and function.IMPORTANCEThough nucleoside analogs and a live-attenuated vaccine are currently available to treat some human herpesvirus family members, alternate methods of combating herpesvirus infection could include blocking viral replication at the DNA encapsidation stage. The approval of Letermovir provided proof of concept regarding the use of encapsidation inhibitors to treat herpesvirus infections in the clinic. We propose that small-molecule compounds could be employed to interrupt portal oligomerization, assembly into the capsid vertex, or affect portal function/dynamics. Targeting portal at any of these steps would result in disruption of viral DNA packaging and a decrease or absence of mature infectious herpesvirus particles. The oligomeric portals of herpesviruses are structurally conserved, and therefore, it may be possible to find a single compound capable of targeting portals from one or more of the herpesvirus subfamilies. Drug candidates from such a series would be effective against viruses resistant to the currently available antivirals.
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Affiliation(s)
- Melissa A. Visalli
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Dakota J. Nale Lovett
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Ellyn M. Kornfeind
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Haley Herrington
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Yi Tian Xiao
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Daniel Lee
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Patience Plair
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - S. Garrett Wilder
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Bret K. Garza
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Ashton Young
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
| | - Robert J. Visalli
- Department of Biomedical Sciences, Mercer University School of Medicine, Savannah, Georgia, USA
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11
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Jiang H, Nace R, Carrasco TF, Zhang L, Whye Peng K, Russell SJ. Oncolytic varicella-zoster virus engineered with ORF8 deletion and armed with drug-controllable interleukin-12. J Immunother Cancer 2024; 12:e008307. [PMID: 38527762 DOI: 10.1136/jitc-2023-008307] [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] [Accepted: 01/30/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND The varicella-zoster virus (VZV), belonging to the group of human α-herpesviruses, has yet to be developed as a platform for oncolytic virotherapy, despite indications from clinical case reports suggesting a potential association between VZV infection and cancer remission. METHODS Here, we constructed oncolytic VZV candidates based on the vaccine strain vOka and the laboratory strain Ellen. These newly engineered viruses were subsequently assessed for their oncolytic properties in the human MeWo melanoma xenograft model and the mouse B16-F10-nectin1 melanoma syngeneic model. RESULTS In the MeWo xenograft model, both vOka and Ellen exhibited potent antitumor efficacy. However, it was observed that introducing a hyperfusogenic mutation into glycoprotein B led to a reduction in VZV's effectiveness. Notably, the deletion of ORF8 (encodes viral deoxyuridine triphosphatase) attenuated the replication of VZV both in vitro and in vivo, but it did not compromise VZV's oncolytic potency. We further armed the VZV Ellen-ΔORF8 vector with a tet-off controlled mouse single-chain IL12 (scIL12) gene cassette. This augmented virus was validated for its oncolytic activity and triggered systemic antitumor immune responses in the immunocompetent B16-F10-nectin1 model. CONCLUSIONS These findings highlight the potential of using Ellen-ΔORF8-tet-off-scIL12 as a novel VZV-based oncolytic virotherapy.
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Affiliation(s)
- Haifei Jiang
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Rebecca Nace
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Lianwen Zhang
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Kah Whye Peng
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
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12
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Finci LI, Chakrabarti M, Gulten G, Finney J, Grose C, Fox T, Yang R, Nissley DV, McCormick F, Esposito D, Balius TE, Simanshu DK. Structural dynamics of RAF1-HSP90-CDC37 and HSP90 complexes reveal asymmetric client interactions and key structural elements. Commun Biol 2024; 7:260. [PMID: 38431713 PMCID: PMC10908828 DOI: 10.1038/s42003-024-05959-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/22/2024] [Indexed: 03/05/2024] Open
Abstract
RAF kinases are integral to the RAS-MAPK signaling pathway, and proper RAF1 folding relies on its interaction with the chaperone HSP90 and the cochaperone CDC37. Understanding the intricate molecular interactions governing RAF1 folding is crucial for comprehending this process. Here, we present a cryo-EM structure of the closed-state RAF1-HSP90-CDC37 complex, where the C-lobe of the RAF1 kinase domain binds to one side of the HSP90 dimer, and an unfolded N-lobe segment of the RAF1 kinase domain threads through the center of the HSP90 dimer. CDC37 binds to the kinase C-lobe, mimicking the N-lobe with its HxNI motif. We also describe structures of HSP90 dimers without RAF1 and CDC37, displaying only N-terminal and middle domains, which we term the semi-open state. Employing 1 μs atomistic simulations, energetic decomposition, and comparative structural analysis, we elucidate the dynamics and interactions within these complexes. Our quantitative analysis reveals that CDC37 bridges the HSP90-RAF1 interaction, RAF1 binds HSP90 asymmetrically, and that HSP90 structural elements engage RAF1's unfolded region. Additionally, N- and C-terminal interactions stabilize HSP90 dimers, and molecular interactions in HSP90 dimers rearrange between the closed and semi-open states. Our findings provide valuable insight into the contributions of HSP90 and CDC37 in mediating client folding.
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Affiliation(s)
- Lorenzo I Finci
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mayukh Chakrabarti
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gulcin Gulten
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph Finney
- National Cryo-EM Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Carissa Grose
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tara Fox
- National Cryo-EM Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Renbin Yang
- Center for Molecular Microscopy, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Trent E Balius
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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13
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Park SC, Steffan BN, Yun Lim F, Gupta R, Ayaloglu Butun F, Chen H, Ye R, Decker T, Wu CC, Kelleher NL, Woo Bok J, Keller NP. Terpenoid balance in Aspergillus nidulans unveiled by heterologous squalene synthase expression. SCIENCE ADVANCES 2024; 10:eadk7416. [PMID: 38381828 PMCID: PMC10881027 DOI: 10.1126/sciadv.adk7416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
Filamentous fungi produce numerous uncharacterized natural products (NPs) that are often challenging to characterize because of cryptic expression in laboratory conditions. Previously, we have successfully isolated novel NPs by expressing fungal artificial chromosomes (FACs) from a variety of fungal species into Aspergillus nidulans. Here, we demonstrate a twist to FAC utility wherein heterologous expression of a Pseudogymnoascus destructans FAC in A. nidulans altered endogenous terpene biosynthetic pathways. In contrast to wild type, the FAC transformant produced increased levels of squalene and aspernidine type compounds, including three new nidulenes (1- 2, and 5), and lost nearly all ability to synthesize the major A. nidulans characteristic terpene, austinol. Deletion of a squalene synthase gene in the FAC restored wild-type chemical profiles. The altered squalene to farnesyl pyrophosphate ratio leading to synthesis of nidulenes and aspernidines at the expense of farnesyl pyrophosphate-derived austinols provides unexpected insight into routes of terpene synthesis in fungi.
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Affiliation(s)
- Sung Chul Park
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, USA
| | - Breanne N. Steffan
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, USA
| | - Fang Yun Lim
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Raveena Gupta
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | | | | | - Rosa Ye
- Intact Genomics Inc., St. Louis, MO, USA
| | | | | | - Neil L. Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, USA
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, USA
- Department of Plant Pathology, University of Wisconsin–Madison, Madison, WI, USA
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14
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Leavitt JC, Woodbury BM, Gilcrease EB, Bridges CM, Teschke CM, Casjens SR. Bacteriophage P22 SieA-mediated superinfection exclusion. mBio 2024; 15:e0216923. [PMID: 38236051 PMCID: PMC10883804 DOI: 10.1128/mbio.02169-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/10/2023] [Indexed: 01/19/2024] Open
Abstract
Many temperate phages encode prophage-expressed functions that interfere with superinfection of the host bacterium by external phages. Salmonella phage P22 has four such systems that are expressed from the prophage in a lysogen that are encoded by the c2 (repressor), gtrABC, sieA, and sieB genes. Here we report that the P22-encoded SieA protein is necessary and sufficient for exclusion by the SieA system and that it is an inner membrane protein that blocks DNA injection by P22 and its relatives, but has no effect on infection by other tailed phage types. The P22 virion injects its DNA through the host cell membranes and periplasm via a conduit assembled from three "ejection proteins" after their release from the virion. Phage P22 mutants that overcome the SieA block were isolated, and they have amino acid changes in the C-terminal regions of the gene 16 and 20 encoded ejection proteins. Three different single-amino acid changes in these proteins are required to obtain nearly full resistance to SieA. Hybrid P22 phages that have phage HK620 ejection protein genes are also partially resistant to SieA. There are three sequence types of extant phage-encoded SieA proteins that are less than 30% identical to one another, yet comparison of two of these types found no differences in phage target specificity. Our data strongly suggest a model in which the inner membrane protein SieA interferes with the assembly or function of the periplasmic gp20 and membrane-bound gp16 DNA delivery conduit.IMPORTANCEThe ongoing evolutionary battle between bacteria and the viruses that infect them is a critical feature of bacterial ecology on Earth. Viruses can kill bacteria by infecting them. However, when their chromosomes are integrated into a bacterial genome as a prophage, viruses can also protect the host bacterium by expressing genes whose products defend against infection by other viruses. This defense property is called "superinfection exclusion." A significant fraction of bacteria harbor prophages that encode such protective systems, and there are many different molecular strategies by which superinfection exclusion is mediated. This report is the first to describe the mechanism by which bacteriophage P22 SieA superinfection exclusion protein protects its host bacterium from infection by other P22-like phages. The P22 prophage-encoded inner membrane SieA protein prevents infection by blocking transport of superinfecting phage DNA across the inner membrane during injection.
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Affiliation(s)
- Justin C Leavitt
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Brianna M Woodbury
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Charles M Bridges
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Sherwood R Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, USA
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15
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Chou S, Watanabe J. Ganciclovir and maribavir cross-resistance revisited: Relative drug susceptibilities of canonical cytomegalovirus mutants. Antiviral Res 2024; 222:105792. [PMID: 38163624 PMCID: PMC10922325 DOI: 10.1016/j.antiviral.2023.105792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Therapeutic use of maribavir for human cytomegalovirus infection has renewed attention to the extent of cross-resistance with ganciclovir as the existing standard therapy. Each drug selects in vivo for a characteristic set of resistance mutations in the viral UL97 kinase gene. To improve the calibration of relative susceptibilities to each drug, genetic variants at relevant UL97 codons were extensively phenotyped using the same baseline viral clone, cell culture conditions and growth readout. Ganciclovir-selected mutations at codons 460, 520, 592, 594, 595 and 603 conferred 2.8-fold (C603Y) to 12-fold (M460I) increases in ganciclovir 50% inhibitory concentrations (EC50) over wild type baseline, while conferring maribavir EC50 fold changes ranging from 0.21-fold (M460I) to 1.9-fold (A594V). Maribavir-selected mutations at codons 409, 411 and 480 conferred maribavir EC50 fold changes ranging from 17 (H411Y) to 210 (C480F), while conferring ganciclovir EC50 fold changes ranging from 0.7 (H411Y) to 2.3 (C480F). The P-loop substitution F342Y, selected by either drug, is confirmed to confer 4.7-fold and 6-fold increases in maribavir and ganciclovir EC50s respectively, and suggests this part of the ATP-binding domain of UL97 to be involved in moderate resistance to both drugs. The maribavir hypersensitivity of M460I and M460V may be advantageous.
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Affiliation(s)
- Sunwen Chou
- Department of Veterans Affairs Medical Center, Portland, OR, USA; Division of Infectious Diseases, Oregon Health and Science University, USA.
| | - Justin Watanabe
- Department of Veterans Affairs Medical Center, Portland, OR, USA
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16
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Qian W, Yamaguchi N, Lis P, Cammer M, Knaut H. Pulses of RhoA signaling stimulate actin polymerization and flow in protrusions to drive collective cell migration. Curr Biol 2024; 34:245-259.e8. [PMID: 38096821 PMCID: PMC10872453 DOI: 10.1016/j.cub.2023.11.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/03/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023]
Abstract
In animals, cells often move as collectives to shape organs, close wounds, or-in the case of disease-metastasize. To accomplish this, cells need to generate force to propel themselves forward. The motility of singly migrating cells is driven largely by an interplay between Rho GTPase signaling and the actin network. Whether cells migrating as collectives use the same machinery for motility is unclear. Using the zebrafish posterior lateral line primordium as a model for collective cell migration, we find that active RhoA and myosin II cluster on the basal sides of the primordium cells and are required for primordium motility. Positive and negative feedbacks cause RhoA and myosin II activities to pulse. These pulses of RhoA signaling stimulate actin polymerization at the tip of the protrusions and myosin-II-dependent actin flow and protrusion retraction at the base of the protrusions and deform the basement membrane underneath the migrating primordium. This suggests that RhoA-induced actin flow on the basal sides of the cells constitutes the motor that pulls the primordium forward, a scenario that likely underlies collective migration in other contexts.
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Affiliation(s)
- Weiyi Qian
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - Naoya Yamaguchi
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Patrycja Lis
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Michael Cammer
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Holger Knaut
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA.
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17
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Duan J, Yuan B, Jia F, Li X, Chen C, Li G. Development of an Efficient and Seamless Genetic Manipulation Method for Xenorhabdus and Its Application for Enhancing the Production of Fabclavines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:274-283. [PMID: 38109418 DOI: 10.1021/acs.jafc.3c04136] [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: 12/20/2023]
Abstract
Xenorhabdus can produce numerous natural products, but their development has been hampered by the lack of a seamless genetic manipulation method. In this study, we compared several lethal genes and determined the sacB gene as the most effective counter-selection marker and then established a dual selection/counter-selection system by integrating neo and sacB genes into one cassette. This provides an efficient and seamless genetic manipulation method for Xenorhabdus. Using this method, DNA fragments ranging from 205 to 47,788 bp in length were seamlessly knocked out or replaced with impressively high positive rates of 80 to 100% in Xenorhabdus budapestensis XBD8. In addition, the method was successfully applied with good efficiency (45-100%) in Xenorhabdus nematophila CB6. To further validate the method, different constitutive promoters were used to replace the native fclC promoter in a batch experiment. The positivity rate remained consistently high, at 46.3%. In comparison to WT XBD8, the recombinant strain MX14 demonstrated a significant increase in the production of fabclavine 7 and fabclavine 8 by 4.97-fold and 3.22-fold, respectively, while the overall production of fabclavines was enhanced by 3.52-fold.
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Affiliation(s)
- Jiaqi Duan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Baoming Yuan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fenglian Jia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaohui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chang Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Beijing Green Agricultural Science and Technology Group Co., Ltd, Beijing 100193, China
| | - Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-Product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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18
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Asakawa K, Handa H, Kawakami K. In Vivo Optogenetic Phase Transition of an Intrinsically Disordered Protein. Methods Mol Biol 2024; 2707:257-264. [PMID: 37668918 DOI: 10.1007/978-1-0716-3401-1_17] [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: 09/06/2023]
Abstract
Proteins containing intrinsically disordered regions (IDRs) control a wide variety of cellular processes by assembly of membrane-less organelles via IDR-mediated liquid-liquid phase separation. Dysregulated IDR-mediated phase transition has been implicated in the pathogenesis of diseases characterized by deposition of abnormal protein aggregates. Here, we describe a method to enhance interactions between the IDRs of the RNA/DNA-binding protein and TAR DNA-binding protein 43 (TDP-43) by light to drive its phase transition in the motor neurons of zebrafish. The optically controlled TDP-43 phase transition in motor neurons, in vivo, provides a unique opportunity to evaluate the impact of dysregulated TDP-43 phase transition on the physiology of motor neurons. This will help to address the etiology of neurodegenerative diseases associated with abnormal TDP-43 phase transition and aggregation, including amyotrophic lateral sclerosis (ALS).
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Affiliation(s)
- Kazuhide Asakawa
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
| | - Hiroshi Handa
- Department of Molecular Pharmacology, Center for Future Medical Research, Tokyo Medical University, Tokyo, Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
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19
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de Jong LA, van Oosten L, Pijlman GP. Scarless Baculovirus Genome Editing Using Lambda-Red Recombineering in E. coli. Methods Mol Biol 2024; 2829:109-126. [PMID: 38951330 DOI: 10.1007/978-1-0716-3961-0_8] [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: 07/03/2024]
Abstract
Baculoviruses are widely used for their potential as biological pesticide and as platform for the production of recombinant proteins and gene therapy vectors. The Baculovirus Expression Vector System (BEVS) is used for high level of expression of (multiple) proteins in insect cells. Baculovirus recombinants can be quickly constructed by transposition of the gene(s) of interest into a so-called bacmid, which is a baculovirus infectious clone maintained as single-copy, bacterial artificial chromosome in Escherichia coli. A two-step homologous recombineering technique using the lambda-red system in E. coli allows for scarless editing of the bacmid with PCR products based on sequence homology. In the first step, a selection cassette with 50 bp homology arms, typically generated by PCR, is inserted into the designated locus. In the second step, the selection cassette is removed based on a negative selection marker, such as SacB or rpsL. This lambda-red recombineering technique can be used for multiple gene editing purposes, including (large) deletions, insertions, and even single point mutations. Moreover, since there are no remnants of the editing process, successive modifications of the same bacmid are possible. This chapter provides detailed instructions to design and perform two-step homologous recombineering of baculovirus bacmid DNA in E. coli. We present two case studies demonstrating the utility of this technique for creating a deletion mutant of the chitinase and cathepsin genes and for introducing a single point mutation in the baculovirus gene gp41. This scarless genome editing approach can facilitate functional studies of baculovirus genes and improve the production of recombinant proteins using the BEVS.
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Affiliation(s)
- Linda A de Jong
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Linda van Oosten
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands.
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20
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Liu J, Jaijyan DK, Chen Y, Feng C, Yang S, Xu Z, Zhan N, Hong C, Li S, Cheng T, Zhu H. Cytomegalovirus-vectored COVID-19 vaccines elicit neutralizing antibodies against the SARS-CoV-2 Omicron variant (BA.2) in mice. Microbiol Spectr 2023; 11:e0246323. [PMID: 37971259 PMCID: PMC10883801 DOI: 10.1128/spectrum.02463-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Cytomegalovirus (CMV) has been used as a novel viral vector for vaccine development and gene therapy. Coronavirus disease 2019 is an infectious disease caused by the SARS-CoV-2 virus, which is highly mutable and is still circulating globally. The study showed that the CMV viral vector caused transient systemic infection and induced robust transgene expression in vivo. CMV vectors expressing different SARS-CoV-2 proteins were immunogenic and could elicit neutralizing antibodies against a highly mutated Omicron variant (BA.2). The expression level of receptor-binding domain (RBD) protein was higher than that of full-length S protein using CMV as a vaccine vector, and CMV vector expression RBD protein elicited higher RBD-binding and neutralizing antibodies. Moreover, the study showed that CMV-vectored vaccines would not cause unexpected viral transmission, and pre-existing immunity might impair the immunogenicity of subsequent CMV-vectored vaccines. These works provide meaningful insights for the development of a CMV-based vector vaccine platform and the prevention and control strategies for SARS-CoV-2 infection.
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Affiliation(s)
- Jian Liu
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Dabbu Kumar Jaijyan
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School , Newark, New Jersey, USA
| | - Yanling Chen
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Changcan Feng
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Shaomin Yang
- Shenzhen Municipal Key Laboratory for Pain Medicine, Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital , Shenzhen, Guangdong, China
| | - Zhenglong Xu
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Nichun Zhan
- School of Biological Sciences and Biotechnology, Minnan Normal University , Zhangzhou, Fujian, China
| | - Congming Hong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University , Xiamen, Fujian, China
| | - Shuxuan Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University , Xiamen, Fujian, China
| | - Tong Cheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Sciences, Xiamen University , Xiamen, Fujian, China
| | - Hua Zhu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School , Newark, New Jersey, USA
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21
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Lei R, Qing E, Odle A, Yuan M, Tan TJ, So N, Ouyang WO, Wilson IA, Gallagher T, Perlman S, Wu NC, Wong LYR. Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569051. [PMID: 38076875 PMCID: PMC10705381 DOI: 10.1101/2023.11.28.569051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we performed a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identified mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we showed that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Natalie So
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wenhao O. Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, 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
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Center for Virus-Host-Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
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22
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Mishra AP, Hartford S, Chittela RK, Sahu S, Kharat SS, Alvaro-Aranda L, Contreras-Perez A, Sullivan T, Martin BK, Albaugh M, Southon E, Burkett S, Karim B, Carreira A, Tessarollo L, Sharan SK. Characterization of BRCA2 R3052Q variant in mice supports its functional impact as a low-risk variant. Cell Death Dis 2023; 14:753. [PMID: 37980415 PMCID: PMC10657400 DOI: 10.1038/s41419-023-06289-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/29/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Pathogenic variants in BRCA2 are known to significantly increase the lifetime risk of developing breast and ovarian cancers. Sequencing-based genetic testing has resulted in the identification of thousands of BRCA2 variants that are considered to be variants of uncertain significance (VUS) because the disease risk associated with them is unknown. One such variant is p.Arg3052Gln, which has conflicting interpretations of pathogenicity in the ClinVar variant database. Arginine at position 3052 in BRCA2 plays an important role in stabilizing its C-terminal DNA binding domain. We have generated a knock-in mouse model expressing this variant to examine its role on growth and survival in vivo. Homozygous as well as hemizygous mutant mice are viable, fertile and exhibit no overt phenotype. While we did not observe any hematopoietic defects in adults, we did observe a marked reduction in the in vitro proliferative ability of fetal liver cells that were also hypersensitive to PARP inhibitor, olaparib. In vitro studies performed on embryonic and adult fibroblasts derived from the mutant mice showed significant reduction in radiation induced RAD51 foci formation as well as increased genomic instability after mitomycin C treatment. We observed mis-localization of a fraction of R3052Q BRCA2 protein to the cytoplasm which may explain the observed in vitro phenotypes. Our findings suggest that BRCA2 R3052Q should be considered as a hypomorphic variant.
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Affiliation(s)
- Arun Prakash Mishra
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Suzanne Hartford
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Rajani Kant Chittela
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Applied Genomics Section, Bhabha Atomic Research Center, Trombay, Mumbai, 400085, India
| | - Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Suhas S Kharat
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Lucia Alvaro-Aranda
- Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
| | - Aida Contreras-Perez
- Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Betty K Martin
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mary Albaugh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sandra Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Baktiar Karim
- Molecular Histotechnology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Aura Carreira
- Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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23
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Dirck A, Diggins NL, Crawford LB, Perez WD, Parkins CJ, Struthers HH, Turner R, Pham AH, Mitchell J, Papen CR, Malouli D, Hancock MH, Caposio P. HCMV UL8 interaction with β-catenin and DVL2 regulates viral reactivation in CD34 + hematopoietic progenitor cells. J Virol 2023; 97:e0124123. [PMID: 37772824 PMCID: PMC10617580 DOI: 10.1128/jvi.01241-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE CD34+ hematopoietic progenitor cells (HPCs) are an important cellular reservoir for latent human cytomegalovirus (HCMV). Several HCMV genes are expressed during latency that are involved with the maintenance of the viral genome in CD34+ HPC. However, little is known about the process of viral reactivation in these cells. Here, we describe a viral protein, pUL8, and its interaction and stabilization with members of the Wnt/β-catenin pathway as an important component of viral reactivation. We further define that pUL8 and β-catenin interact with DVL2 via a PDZ-binding domain, and loss of UL8 interaction with β-catenin-DVL2 restricts viral reactivation. Our findings will be instrumental in understanding the molecular processes involved in HCMV reactivation in order to design new antiviral therapeutics.
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Affiliation(s)
- Aaron Dirck
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Nicole L. Diggins
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Lindsey B. Crawford
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Wilma D. Perez
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Christopher J. Parkins
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Hillary H. Struthers
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Rebekah Turner
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Andrew H. Pham
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Jennifer Mitchell
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Courtney R. Papen
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Daniel Malouli
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Meaghan H. Hancock
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Patrizia Caposio
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
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24
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Wong LYR, Odle A, Luhmann E, Wu DC, Wang Y, Teo QW, Ptak C, Sariol A, Lowery S, Mack M, Meyerholz DK, Wu NC, Radoshevich L, Perlman S. Contrasting roles of MERS-CoV and SARS-CoV-2 internal proteins in pathogenesis in mice. mBio 2023; 14:e0247623. [PMID: 37882568 PMCID: PMC10746224 DOI: 10.1128/mbio.02476-23] [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: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
Betacoronaviruses encode an internal (I) gene via an alternative reading frame within the nucleocapsid gene, called ORF8b for Middle-East respiratory syndrome coronavirus (MERS-CoV) and ORF9b for severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. Previous reports suggested that proteins 8b and 9b are involved in evading multiple innate immune signaling pathways. However, their roles in mediating pathogenesis in infected animals have not been determined. In this study, we abrogated the expression of protein 8b in MERS-CoV and protein 9b in SARS-CoV-2. Using mouse models of MERS-CoV and SARS-CoV-2 infection, we found that MERS-CoV lacking protein 8b expression was more virulent, while SARS-CoV-2 lacking protein 9b expression was attenuated compared with the respective wild-type viruses. Upon further analysis, we detected increased levels of type I interferon and enhanced infiltration of immune cells to the lungs of mice infected with MERS-CoV lacking protein 8b expression. These data suggest that the I protein of MERS-CoV plays a role in limiting pathogenesis while that of SARS-CoV-2 enhances disease severity. IMPORTANCE The function of betacoronavirus internal protein has been relatively understudied. The earliest report on the internal protein of mouse hepatitis virus suggested that the internal protein is a structural protein without significant functions in virus replication and virulence. However, the internal proteins of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle-East respiratory syndrome coronavirus, and SARS-CoV-2 have been shown to evade immune responses. Despite the reported functions of the internal protein in these highly pathogenic human coronaviruses, its role in mediating pathogenesis in experimentally infected animals has not been characterized. Our data indicated that despite the similar genomic location and expression strategy of these internal proteins, their effects on virulence are vastly different and virus specific, highlighting the complexity between host-virus interaction and disease outcome.
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Affiliation(s)
- Lok-Yin Roy Wong
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Abby Odle
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Emma Luhmann
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Douglas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Qi Wen Teo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Celeste Ptak
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Alan Sariol
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Shea Lowery
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Matthias Mack
- Department of Internal Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Lilliana Radoshevich
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
- Department of Immunology, University of Iowa, Iowa City, Iowa, USA
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
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25
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Park SC, Steffan BN, Lim FY, Gupta R, Butun FA, Chen H, Ye R, Decker T, Wu CC, Kelleher NL, Bok JW, Keller NP. Terpenoid balance in Aspergillus nidulans unveiled by heterologous squalene synthase expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563295. [PMID: 37905136 PMCID: PMC10614972 DOI: 10.1101/2023.10.20.563295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Filamentous fungi produce numerous uncharacterized natural products (NPs) that are often challenging to characterize due to cryptic expression in laboratory conditions. Previously, we have successfully isolated novel NPs by expressing fungal artificial chromosomes (FACs) from a variety of fungal species into Aspergillus nidulans. Here, we demonstrate a new twist to FAC utility wherein heterologous expression of a Pseudogymnoascus destructans FAC in A. nidulans altered endogenous terpene biosynthetic pathways. In contrast to wildtype, the FAC transformant produced increased levels of squalene and aspernidine type compounds, including three new nidulenes (1-2, 5), and lost nearly all ability to synthesize the major A. nidulans characteristic terpene, austinol. Deletion of a squalene synthase gene in the FAC restored wildtype chemical profiles. The altered squalene to farnesyl pyrophosphate ratio leading to synthesis of nidulenes and aspernidines at the expense of farnesyl pyrophosphate derived austinols provides unexpected insight into routes of terpene synthesis in fungi.
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Affiliation(s)
- Sung Chul Park
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI
| | - Breanne N. Steffan
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI
| | - Fang Yun Lim
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle WA
| | - Raveena Gupta
- Department of Chemistry, Northwestern University, IL
| | | | | | | | | | | | | | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI
- Department of Plant Pathology, University of Wisconsin–Madison, Madison, WI
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26
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Rudolph A, Nyerges A, Chiappino-Pepe A, Landon M, Baas-Thomas M, Church G. Strategies to identify and edit improvements in synthetic genome segments episomally. Nucleic Acids Res 2023; 51:10094-10106. [PMID: 37615546 PMCID: PMC10570025 DOI: 10.1093/nar/gkad692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/30/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
Genome engineering projects often utilize bacterial artificial chromosomes (BACs) to carry multi-kilobase DNA segments at low copy number. However, all stages of whole-genome engineering have the potential to impose mutations on the synthetic genome that can reduce or eliminate the fitness of the final strain. Here, we describe improvements to a multiplex automated genome engineering (MAGE) protocol to improve recombineering frequency and multiplexability. This protocol was applied to recoding an Escherichia coli strain to replace seven codons with synonymous alternatives genome wide. Ten 44 402-47 179 bp de novo synthesized DNA segments contained in a BAC from the recoded strain were unable to complement deletion of the corresponding 33-61 wild-type genes using a single antibiotic resistance marker. Next-generation sequencing (NGS) was used to identify 1-7 non-recoding mutations in essential genes per segment, and MAGE in turn proved a useful strategy to repair these mutations on the recoded segment contained in the BAC when both the recoded and wild-type copies of the mutated genes had to exist by necessity during the repair process. Finally, two web-based tools were used to predict the impact of a subset of non-recoding missense mutations on strain fitness using protein structure and function calls.
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Affiliation(s)
- Alexandra Rudolph
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Akos Nyerges
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anush Chiappino-Pepe
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
| | - Matthieu Landon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
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27
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Qian W, Yamaguchi N, Lis P, Cammer M, Knaut H. Pulses of RhoA Signaling Stimulate Actin Polymerization and Flow in Protrusions to Drive Collective Cell Migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560679. [PMID: 37873192 PMCID: PMC10592895 DOI: 10.1101/2023.10.03.560679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
In animals, cells often move as collectives to shape organs, close wounds, or-in the case of disease-metastasize. To accomplish this, cells need to generate force to propel themselves forward. The motility of singly migrating cells is driven largely by an interplay between Rho GTPase signaling and the actin network (Yamada and Sixt, 2019). Whether cells migrating as collectives use the same machinery for motility is unclear. Using the zebrafish posterior lateral line primordium as a model for collective cell migration, we find that active RhoA and myosin II cluster on the basal sides of the primordium cells and are required for primordium motility. Positive and negative feedbacks cause RhoA and myosin II activities to pulse. These pulses of RhoA signaling stimulate actin polymerization at the tip of the protrusions and myosin II-dependent actin flow and protrusion retraction at the base of the protrusions, and deform the basement membrane underneath the migrating primordium. This suggests that RhoA-induced actin flow on the basal sides of the cells constitutes the motor that pulls the primordium forward, a scenario that likely underlies collective migration in other-but not all (Bastock and Strutt, 2007; Lebreton and Casanova, 2013; Matthews et al., 2008)-contexts.
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Affiliation(s)
- Weiyi Qian
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University Grossman School of Medicine, New York, United States
- These authors contributed equally to this work
| | - Naoya Yamaguchi
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University Grossman School of Medicine, New York, United States
- These authors contributed equally to this work
| | - Patrycja Lis
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University Grossman School of Medicine, New York, United States
| | - Michael Cammer
- Microscopy laboratory, New York University Grossman School of Medicine, New York, United States
| | - Holger Knaut
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University Grossman School of Medicine, New York, United States
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28
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Zeng J, Jaijyan DK, Yang S, Pei S, Tang Q, Zhu H. Exploring the Potential of Cytomegalovirus-Based Vectors: A Review. Viruses 2023; 15:2043. [PMID: 37896820 PMCID: PMC10612100 DOI: 10.3390/v15102043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/28/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Viral vectors have emerged as powerful tools for delivering and expressing foreign genes, playing a pivotal role in gene therapy. Among these vectors, cytomegalovirus (CMV) stands out as a promising viral vector due to its distinctive attributes including large packaging capacity, ability to achieve superinfection, broad host range, capacity to induce CD8+ T cell responses, lack of integration into the host genome, and other qualities that make it an appealing vector candidate. Engineered attenuated CMV strains such as Towne and AD169 that have a ~15 kb genomic DNA deletion caused by virus passage guarantee human safety. CMV's large genome enables the efficient incorporation of substantial foreign genes as demonstrated by CMV vector-based therapies for SIV, tuberculosis, cancer, malaria, aging, COVID-19, and more. CMV is capable of reinfecting hosts regardless of prior infection or immunity, making it highly suitable for multiple vector administrations. In addition to its broad cellular tropism and sustained high-level gene expression, CMV triggers robust, virus-specific CD8+ T cell responses, offering a significant advantage as a vaccine vector. To date, successful development and testing of murine CMV (MCMV) and rhesus CMV (RhCMV) vectors in animal models have demonstrated the efficacy of CMV-based vectors. These investigations have explored the potential of CMV vectors for vaccines against HIV, cancer, tuberculosis, malaria, and other infectious pathogens, as well as for other gene therapy applications. Moreover, the generation of single-cycle replication CMV vectors, produced by deleting essential genes, ensures robust safety in an immunocompromised population. The results of these studies emphasize CMV's effectiveness as a gene delivery vehicle and shed light on the future applications of a CMV vector. While challenges such as production complexities and storage limitations need to be addressed, ongoing efforts to bridge the gap between animal models and human translation continue to fuel the optimism surrounding CMV-based vectors. This review will outline the properties of CMV vectors and discuss their future applications as well as possible limitations.
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Affiliation(s)
- Janine Zeng
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Dabbu Kumar Jaijyan
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Shaomin Yang
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518060, China
| | - Shakai Pei
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, 520 W Street NW, Washington, DC 20059, USA
| | - Hua Zhu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
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29
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Asakawa K, Handa H, Kawakami K. Dysregulated TDP-43 proteostasis perturbs excitability of spinal motor neurons during brainstem-mediated fictive locomotion in zebrafish. Dev Growth Differ 2023; 65:446-452. [PMID: 37452624 DOI: 10.1111/dgd.12879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/24/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Spinal motor neurons (SMNs) are the primary target of degeneration in amyotrophic lateral sclerosis (ALS). Degenerating motor neurons accumulate cytoplasmic TAR DNA-binding protein 43 (TDP-43) aggregates in most ALS cases. This SMN pathology can occur without mutation in the coding sequence of the TDP-43-encoding gene, TARDBP. Whether and how wild-type TDP-43 drives pathological changes in SMNs in vivo remains largely unexplored. In this study, we develop a two-photon calcium imaging setup in which tactile-evoked neural responses of motor neurons in the brainstem and spinal cord can be monitored using the calcium indicator GCaMP. We devise a piezo-assisted tactile stimulator that reproducibly evokes a brainstem descending neuron upon tactile stimulation of the head. A direct comparison between caudal primary motor neurons (CaPs) with or without TDP-43 overexpression in contiguous spinal segments demonstrates that CaPs overexpressing TDP-43 display attenuated Ca2+ transients during fictive escape locomotion evoked by the tactile stimulation. These results show that excessive amounts of TDP-43 protein reduce the neuronal excitability of SMNs and potentially contribute to asymptomatic pathological lesions of SMNs and movement disorders in patients with ALS.
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Affiliation(s)
- Kazuhide Asakawa
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Japan
| | - Hiroshi Handa
- Department of Molecular Pharmacology, Center for Future Medical Research, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
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Arnold EA, Kaai RJ, Leung K, Brinkley MR, Kelnhofer-Millevolte LE, Guo MS, Avgousti DC. Adenovirus protein VII binds the A-box of HMGB1 to repress interferon responses. PLoS Pathog 2023; 19:e1011633. [PMID: 37703278 PMCID: PMC10519595 DOI: 10.1371/journal.ppat.1011633] [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: 04/18/2023] [Revised: 09/25/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023] Open
Abstract
Viruses hijack host proteins to promote infection and dampen host defenses. Adenovirus encodes the multifunctional protein VII that serves both to compact viral genomes inside the virion and disrupt host chromatin. Protein VII binds the abundant nuclear protein high mobility group box 1 (HMGB1) and sequesters HMGB1 in chromatin. HMGB1 is an abundant host nuclear protein that can also be released from infected cells as an alarmin to amplify inflammatory responses. By sequestering HMGB1, protein VII prevents its release, thus inhibiting downstream inflammatory signaling. However, the consequences of this chromatin sequestration on host transcription are unknown. Here, we employ bacterial two-hybrid interaction assays and human cell culture to interrogate the mechanism of the protein VII-HMGB1 interaction. HMGB1 contains two DNA binding domains, the A- and B-boxes, that bend DNA to promote transcription factor binding while the C-terminal tail regulates this interaction. We demonstrate that protein VII interacts directly with the A-box of HMGB1, an interaction that is inhibited by the HMGB1 C-terminal tail. By cellular fractionation, we show that protein VII renders A-box containing constructs insoluble, thereby acting to prevent their release from cells. This sequestration is not dependent on HMGB1's ability to bind DNA but does require post-translational modifications on protein VII. Importantly, we demonstrate that protein VII inhibits expression of interferon β, in an HMGB1-dependent manner, but does not affect transcription of downstream interferon-stimulated genes. Together, our results demonstrate that protein VII specifically harnesses HMGB1 through its A-box domain to depress the innate immune response and promote infection.
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Affiliation(s)
- Edward A. Arnold
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Robin J. Kaai
- Molecular & Cellular Biology, Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Katie Leung
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Mia R. Brinkley
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | | | - Monica S. Guo
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Daphne C. Avgousti
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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31
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Moy MA, Collins-McMillen D, Crawford L, Parkins C, Zeltzer S, Caviness K, Zaidi SSA, Caposio P, Goodrum F. Stabilization of the human cytomegalovirus UL136p33 reactivation determinant overcomes the requirement for UL135 for replication in hematopoietic cells. J Virol 2023; 97:e0014823. [PMID: 37565749 PMCID: PMC10506481 DOI: 10.1128/jvi.00148-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/20/2023] [Indexed: 08/12/2023] Open
Abstract
Human cytomegalovirus (HCMV) is a beta herpesvirus that persists indefinitely in the human host through a latent infection. The polycistronic UL133-UL138 gene locus of HCMV encodes genes regulating latency and reactivation. While UL138 is pro-latency, restricting virus replication in CD34+ hematopoietic progenitor cells (HPCs), UL135 overcomes this restriction and is required for reactivation. By contrast, UL136 is expressed with later kinetics and encodes multiple proteins with differential roles in latency and reactivation. Like UL135, the largest UL136 isoform, UL136p33, is required for reactivation from latency in HPCs; viruses failing to express either protein are unresponsive to reactivation stimuli. Furthermore, UL136p33 is unstable, and its instability is important for the establishment of latency, and sufficient accumulation of UL136p33 is a checkpoint for reactivation. We hypothesized that stabilizing UL136p33 might overcome the requirement of UL135 for replication. We generated recombinant viruses lacking UL135 that expressed a stabilized variant of UL136p33. Stabilizing UL136p33 did not impact the replication of the UL135 mutant virus in fibroblasts. However, in the context of infection in HPCs, stabilization of UL136p33 strikingly compensated for the loss of UL135, resulting in increased replication in CD34+ HPCs and in humanized NOD-scid IL2Rγcnull (huNSG) mice. This finding suggests that while UL135 is essential for replication in HPCs, it functions largely at steps preceding the accumulation of UL136p33, and that stabilized expression of UL136p33 largely overcomes the requirement for UL135. Taken together, our genetic evidence indicates an epistatic relationship between UL136p33 and UL135, whereby UL135 may initiate events early in reactivation that drive the accumulation of UL136p33 to a threshold required for productive reactivation. IMPORTANCE Human cytomegalovirus (HCMV) is one of nine human herpesviruses and a significant human pathogen. While HCMV establishes a lifelong latent infection that is typically asymptomatic in healthy individuals, its reactivation from latency can have devastating consequences in the immunocompromised. Defining viral genes important in the establishment of or reactivation from latency is important to defining the molecular basis of latent and replicative states and in controlling infection and CMV disease. Here we define a genetic relationship between two viral genes in controlling virus reactivation from latency using primary human hematopoietic progenitor cells and humanized mouse models.
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Affiliation(s)
- Melissa A. Moy
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona, USA
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Donna Collins-McMillen
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Lindsey Crawford
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, USA
| | - Christopher Parkins
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, USA
| | - Sebastian Zeltzer
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Katie Caviness
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Graduate Interdisciplinary Program in Genetics, University of Arizona, Tucson, Arizona, USA
| | | | - Patrizia Caposio
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, USA
| | - Felicia Goodrum
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona, USA
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Graduate Interdisciplinary Program in Genetics, University of Arizona, Tucson, Arizona, USA
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32
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Bebelman MP, Setiawan IM, Bergkamp ND, van Senten JR, Crudden C, Bebelman JPM, Verweij FJ, van Niel G, Siderius M, Pegtel DM, Smit MJ. Exosomal release of the virus-encoded chemokine receptor US28 contributes to chemokine scavenging. iScience 2023; 26:107412. [PMID: 37575190 PMCID: PMC10415803 DOI: 10.1016/j.isci.2023.107412] [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: 03/04/2023] [Revised: 06/22/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023] Open
Abstract
The human cytomegalovirus (HCMV)-encoded chemokine receptor US28 contributes to various aspects of the viral life cycle and promotes immune evasion by scavenging chemokines from the microenvironment of HCMV-infected cells. In contrast to the plasma membrane localization of most human chemokine receptors, US28 has a predominant intracellular localization. In this study, we used immunofluorescence and electron microscopy to determine the localization of US28 upon exogenous expression, as well as in HCMV-infected cells. We observed that US28 localizes to late endosomal compartments called multivesicular bodies (MVBs), where it is sorted in intraluminal vesicles. Live-cell total internal reflection fluorescence (TIRF) microscopy revealed that US28-containing MVBs can fuse with the plasma membrane, resulting in the secretion of US28 on exosomes. Exosomal US28 binds the chemokines CX3CL1 and CCL5, and US28-containing exosomes inhibited the CX3CL1-CX3CR1 signaling axis. These findings suggest that exosomal release of US28 contributes to chemokine scavenging and immune evasion by HCMV.
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Affiliation(s)
- Maarten P. Bebelman
- Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
- Department Pathology, Cancer Center Amsterdam, VU University Medical Center, de Boelelaan 1118, Amsterdam 1081 HZ, the Netherlands
| | - Irfan M. Setiawan
- Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Nick D. Bergkamp
- Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Jeffrey R. van Senten
- Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Caitrin Crudden
- Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
- Department Pathology, Cancer Center Amsterdam, VU University Medical Center, de Boelelaan 1118, Amsterdam 1081 HZ, the Netherlands
| | - Jan Paul M. Bebelman
- Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Frederik J. Verweij
- Division of Cell Biology, Neurobiology and Biophysics, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Guillaume van Niel
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266 Université de Paris, Paris, France
| | - Marco Siderius
- Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - D. Michiel Pegtel
- Department Pathology, Cancer Center Amsterdam, VU University Medical Center, de Boelelaan 1118, Amsterdam 1081 HZ, the Netherlands
| | - Martine J. Smit
- Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
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33
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Leavitt JC, Woodbury BM, Gilcrease EB, Bridges CM, Teschke CM, Casjens SR. Bacteriophage P22 SieA mediated superinfection exclusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553423. [PMID: 37645741 PMCID: PMC10461980 DOI: 10.1101/2023.08.15.553423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Many temperate phages encode prophage-expressed functions that interfere with superinfection of the host bacterium by external phages. Salmonella phage P22 has four such systems that are expressed from the prophage in a lysogen that are encoded by the c2 (repressor), gtrABC, sieA, and sieB genes. Here we report that the P22-encoded SieA protein is the only phage protein required for exclusion by the SieA system, and that it is an inner membrane protein that blocks DNA injection by P22 and its relatives, but has no effect on infection by other tailed phage types. The P22 virion injects its DNA through the host cell membranes and periplasm via a conduit assembled from three "ejection proteins" after their release from the virion. Phage P22 mutants were isolated that overcome the SieA block, and they have amino acid changes in the C-terminal regions of the gene 16 and 20 encoded ejection proteins. Three different single amino acid changes in these proteins are required to obtain nearly full resistance to SieA. Hybrid P22 phages that have phage HK620 ejection protein genes are also partially resistant to SieA. There are three sequence types of extant phage-encoded SieA proteins that are less than 30% identical to one another, yet comparison of two of these types found no differences in target specificity. Our data are consistent with a model in which the inner membrane protein SieA interferes with the assembly or function of the periplasmic gp20 and membrane-bound gp16 DNA delivery conduit.
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Affiliation(s)
- Justin C. Leavitt
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112 USA
- Current address: Green Raccoon Scientific, Gunlock UT 84733 USA
| | - Brianna M. Woodbury
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
- Current address: York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Eddie B. Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
- Current address: Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, UT 84112 USA
| | - Charles M. Bridges
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Carolyn M. Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
- Department of Chemistry, University of Connecticut, Storrs, CT 06269 USA
| | - Sherwood R. Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112 USA
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112 USA
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34
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Wang HM, Qiao YY, Cai BY, Tan J, Na L, Wang Y, Lu H, Tang YD. Genome editing of pseudorabies virus in the CRISPR/Cas9 era: a mini-review. Front Vet Sci 2023; 10:1237186. [PMID: 37476821 PMCID: PMC10354360 DOI: 10.3389/fvets.2023.1237186] [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: 06/09/2023] [Accepted: 06/22/2023] [Indexed: 07/22/2023] Open
Abstract
Pseudorabies virus (PRV) is an important swine virus that has a significant impact on the global swine industry. PRV is a member of the herpesvirus family, specifically the alphaherpesvirus subfamily, and has been extensively utilized as a prototype herpesvirus. Notably, recent studies have reported that PRV sporadically spills over into humans. The PRV genome is approximately 150 kb in size and is difficult to manipulate at the genomic level. The development of clustered regularly interspaced short palindromic repeat-associated protein (CRISPR/Cas9) technology has revolutionized PRV genome editing. CRISPR/Cas9 has been widely used in the construction of reporter viruses, knock-out/knock-in of genes of interest, single virus tracking and antiviral strategies. Most importantly, for vaccine development, virulence gene knockout PRV vaccine candidates can be obtained within 2 weeks using CRISPR/Cas9. In this mini-review, we provide a concise overview of the application of CRISPR/Cas9 in PRV research and mainly share our experience with methods for efficiently editing the PRV genome. Through this review, we hope to give researchers better insight into the genome editing of pseudorabies virus.
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Affiliation(s)
- Hai-Ming Wang
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Yang-Yang Qiao
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Bing-Yan Cai
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Ju Tan
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Lei Na
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Vocational College Agriculture and Forestry, Taizhou, Jiangsu, China
| | - Yu Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hui Lu
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Yan-Dong Tang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Provincial Research Center for Veterinary Biomedicine, Harbin, China
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35
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Vasquez OE, Allen AM, So AKC, Nguyen QH, Krause HM, Levine JD, Sokolowski MB. Characterizing the Protein Isoforms of foraging ( for), the PKGI Ortholog in Drosophila melanogaster. Int J Mol Sci 2023; 24:10219. [PMID: 37373366 DOI: 10.3390/ijms241210219] [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: 04/26/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The foraging (for) gene of Drosophila melanogaster encodes a cGMP-dependent protein kinase (PKG), which is a major effector of the cGMP signaling pathway involved in the regulation of behaviour and metabolic traits. Despite being well studied at the transcript level, little is known about the for gene at the protein level. Here, we provide a detailed characterization of the for gene protein (FOR) products and present new tools for their study, including five isoform-specific antibodies and a transgenic strain that carries an HA-labelled for allele (forBAC::HA). Our results showed that multiple FOR isoforms were expressed in the larval and adult stages of D. melanogaster and that the majority of whole-body FOR expression arises from three (P1, P1α, and P3) of eight putative protein isoforms. We found that FOR expression differed between the larval and adult stages and between the dissected larval organs we analyzed, which included the central nervous system (CNS), fat body, carcass, and intestine. Moreover, we showed that the FOR expression differed between two allelic variants of the for gene, namely, fors (sitter) and forR (rover), that are known to differ in many food-related traits. Together, our in vivo identification of FOR isoforms and the existence of temporal, spatial, and genetic differences in their expression lay the groundwork for determining their functional significance.
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Affiliation(s)
- Oscar E Vasquez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Aaron M Allen
- Centre for Neural Circuits and Behaviour, Oxford University, Oxford OX1 3SR, UK
| | - Anthony K-C So
- Department of Biology, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Quynh H Nguyen
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Henry M Krause
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Joel D Levine
- Department of Biology, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
| | - Marla B Sokolowski
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
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36
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Lee J, Ha J, Kim JH, Seo D, Kim M, Lee Y, Park SS, Choi D, Park JS, Lee YJ, Yang S, Yang KM, Jung SM, Hong S, Koo SH, Bae YS, Kim SJ, Park SH. Peli3 ablation ameliorates acetaminophen-induced liver injury through inhibition of GSK3β phosphorylation and mitochondrial translocation. Exp Mol Med 2023; 55:1218-1231. [PMID: 37258579 PMCID: PMC10318043 DOI: 10.1038/s12276-023-01009-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/07/2023] [Accepted: 03/15/2023] [Indexed: 06/02/2023] Open
Abstract
The signaling pathways governing acetaminophen (APAP)-induced liver injury have been extensively studied. However, little is known about the ubiquitin-modifying enzymes needed for the regulation of APAP-induced liver injury. Here, we examined whether the Pellino3 protein, which has E3 ligase activity, is needed for APAP-induced liver injury and subsequently explored its molecular mechanism. Whole-body Peli3-/- knockout (KO) and adenovirus-mediated Peli3 knockdown (KD) mice showed reduced levels of centrilobular cell death, infiltration of immune cells, and biomarkers of liver injury, such as alanine aminotransferase (ALT) and aspartate aminotransferase (AST), upon APAP treatment compared to wild-type (WT) mice. Peli3 deficiency in primary hepatocytes decreased mitochondrial and lysosomal damage and reduced the mitochondrial reactive oxygen species (ROS) levels. In addition, the levels of phosphorylation at serine 9 in the cytoplasm and mitochondrial translocation of GSK3β were decreased in primary hepatocytes obtained from Peli3-/- KO mice, and these reductions were accompanied by decreases in JNK phosphorylation and mitochondrial translocation. Pellino3 bound more strongly to GSK3β compared with JNK1 and JNK2 and induced the lysine 63 (K63)-mediated polyubiquitination of GSK3β. In rescue experiments, the ectopic expression of wild-type Pellino3 in Peli3-/- KO hepatocytes restored the mitochondrial translocation of GSK3β, but this restoration was not obtained with expression of a catalytically inactive mutant of Pellino3. These findings are the first to suggest a mechanistic link between Pellino3 and APAP-induced liver injury through the modulation of GSK3β polyubiquitination.
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Affiliation(s)
- Jaewon Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jihoon Ha
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jun-Hyeong Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- KoBio Labs, Seongnam, 13488, Republic of Korea
| | - Dongyeob Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Minbeom Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yerin Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seong Shil Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Dahee Choi
- Department of Life Science, Korea University, Seoul, 02841, Republic of Korea
| | - Jin Seok Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Young Jae Lee
- Department of Biochemistry, Gachon University School of Medicine, Incheon, 21999, Republic of Korea
| | - Siyoung Yang
- Department of Pharmacology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
- SRC Center for Immune Research on Non-lymphoid Organs, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | | | - Su Myung Jung
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Suntaek Hong
- Department of Biochemistry, Gachon University School of Medicine, Incheon, 21999, Republic of Korea
| | - Seung-Hoi Koo
- Department of Life Science, Korea University, Seoul, 02841, Republic of Korea
| | - Yong-Soo Bae
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- SRC Center for Immune Research on Non-lymphoid Organs, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seong-Jin Kim
- Medpacto Inc., Seoul, 06668, Republic of Korea.
- GILO Institute, GILO Foundation, Seoul, 06668, Republic of Korea.
| | - Seok Hee Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- SRC Center for Immune Research on Non-lymphoid Organs, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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37
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Russo L, Capra E, Franceschi V, Cavazzini D, Sala R, Lazzari B, Cavirani S, Donofrio G. Characterization of BoHV-4 ORF45. Front Microbiol 2023; 14:1171770. [PMID: 37234529 PMCID: PMC10206056 DOI: 10.3389/fmicb.2023.1171770] [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: 02/22/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Bovine herpesvirus 4 (BoHV-4) is a Gammaherpesvirus belonging to the Rhadinovirus genus. The bovine is BoHV-4's natural host, and the African buffalo is BoHV-4's natural reservoir. In any case, BoHV-4 infection is not associated with a specific disease. Genome structure and genes are well-conserved in Gammaherpesvirus, and the orf 45 gene and its product, ORF45, are one of those. BoHV-4 ORF45 has been suggested to be a tegument protein; however, its structure and function have not yet been experimentally characterized. The present study shows that BoHV-4 ORF45, despite its poor homology with other characterized Rhadinovirus ORF45s, is structurally related to Kaposi's sarcoma-associated herpesvirus (KSHV), is a phosphoprotein, and localizes in the host cell nuclei. Through the generation of an ORF45-null mutant BoHV-4 and its pararevertant, it was possible to demonstrate that ORF45 is essential for BoHV-4 lytic replication and is associated with the viral particles, as for the other characterized Rhadinovirus ORF45s. Finally, the impact of BoHV-4 ORF45 on cellular transcriptome was investigated, an aspect poorly explored or not at all for other Gammaherpesvirus. Many cellular transcriptional pathways were found to be altered, mainly those involving p90 ribosomal S6 kinase (RSK) and signal-regulated kinase (ERK) complex (RSK/ERK). It was concluded that BoHV-4 ORF45 has similar characteristics to those of KSHV ORF45, and its unique and incisive impact on the cell transcriptome paves the way for further investigations.
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Affiliation(s)
- Luca Russo
- Dipartimento di Scienze Medico Veterinarie, Università di Parma, Parma, Italy
| | - Emanuele Capra
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, Lodi, Italy
| | | | - Davide Cavazzini
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parma, Italy
| | - Roberto Sala
- Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy
| | - Barbara Lazzari
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, Lodi, Italy
| | - Sandro Cavirani
- Dipartimento di Scienze Medico Veterinarie, Università di Parma, Parma, Italy
| | - Gaetano Donofrio
- Dipartimento di Scienze Medico Veterinarie, Università di Parma, Parma, Italy
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Downton P, Bagnall JS, England H, Spiller DG, Humphreys NE, Jackson DA, Paszek P, White MRH, Adamson AD. Overexpression of IκB⍺ modulates NF-κB activation of inflammatory target gene expression. Front Mol Biosci 2023; 10:1187187. [PMID: 37228587 PMCID: PMC10203502 DOI: 10.3389/fmolb.2023.1187187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Cells respond to inflammatory stimuli such as cytokines by activation of the nuclear factor-κB (NF-κB) signalling pathway, resulting in oscillatory translocation of the transcription factor p65 between nucleus and cytoplasm in some cell types. We investigate the relationship between p65 and inhibitor-κB⍺ (IκBα) protein levels and dynamic properties of the system, and how this interaction impacts on the expression of key inflammatory genes. Using bacterial artificial chromosomes, we developed new cell models of IκB⍺-eGFP protein overexpression in a pseudo-native genomic context. We find that cells with high levels of the negative regulator IκBα remain responsive to inflammatory stimuli and maintain dynamics for both p65 and IκBα. In contrast, canonical target gene expression is dramatically reduced by overexpression of IκBα, but can be partially rescued by overexpression of p65. Treatment with leptomycin B to promote nuclear accumulation of IκB⍺ also suppresses canonical target gene expression, suggesting a mechanism in which nuclear IκB⍺ accumulation prevents productive p65 interaction with promoter binding sites. This causes reduced target promoter binding and gene transcription, which we validate by chromatin immunoprecipitation and in primary cells. Overall, we show how inflammatory gene transcription is modulated by the expression levels of both IκB⍺ and p65. This results in an anti-inflammatory effect on transcription, demonstrating a broad mechanism to modulate the strength of inflammatory response.
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Affiliation(s)
- Polly Downton
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James S. Bagnall
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Hazel England
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David G. Spiller
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Neil E. Humphreys
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Dean A. Jackson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Pawel Paszek
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Michael R. H. White
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Antony D. Adamson
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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39
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Ourahmane A, Hertel L, McVoy MA. The RL13 Temperance Factor Represses Replication of the Highly Cell Culture-Adapted Towne Strain of Human Cytomegalovirus. Viruses 2023; 15:1023. [PMID: 37113003 PMCID: PMC10142520 DOI: 10.3390/v15041023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 04/06/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Human cytomegalovirus (CMV) has evolved to replicate while causing minimal damage, maintain life-long latency, reactivate sub-clinically, and, in spite of robust host immunity, produce and shed infectious virus in order to transmit to new hosts. The CMV temperance factor RL13 may contribute to this strategy of coexistence with the host by actively restricting viral replication and spread. Viruses with an intact RL13 gene grow slowly in cell culture, release little extracellular virus, and form small foci. By contrast, viruses carrying disruptive mutations in the RL13 gene form larger foci and release higher amounts of cell-free infectious virions. Such mutations invariably arise during cell culture passage of clinical isolates and are consistently found in highly adapted strains. The potential existence in such strains of other mutations with roles in mitigating RL13's restrictive effects, however, has not been explored. To this end, a mutation that frame shifts the RL13 gene in the highly cell culture-adapted laboratory strain Towne was repaired, and a C-terminal FLAG epitope was added. Compared to the frame-shifted parental virus, viruses encoding wild-type or FLAG-tagged wild-type RL13 produced small foci and replicated poorly. Within six to ten cell culture passages, mutations emerged in RL13 that restored replication and focus size to those of the RL13-frame-shifted parental virus, implying that none of the numerous adaptive mutations acquired by strain Towne during more than 125 cell culture passages mitigate the temperance activity of RL13. Whilst RL13-FLAG expressed by passage zero stocks was localized exclusively within the virion assembly compartment, RL13-FLAG with a E208K substitution that emerged in one lineage was mostly dispersed into the cytoplasm, suggesting that localization to the virion assembly compartment is likely required for RL13 to exert its growth-restricting activities. Changes in localization also provided a convenient way to assess the emergence of RL13 mutations during serial passage, highlighting the usefulness of RL13-FLAG Towne variants for elucidating the mechanisms underlying RL13's temperance functions.
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Affiliation(s)
- Amine Ourahmane
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Laura Hertel
- Department of Pediatrics, University of California San Francisco, Oakland, CA 94609, USA;
| | - Michael A. McVoy
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA 23298, USA
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Martín-González N, Gómez-González A, Hernando-Pérez M, Bauer M, Greber UF, San Martín C, de Pablo PJ. Adenovirus core protein V reinforces the capsid and enhances genome release from disrupted particles. SCIENCE ADVANCES 2023; 9:eade9910. [PMID: 37027464 PMCID: PMC10081844 DOI: 10.1126/sciadv.ade9910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Out of the three core proteins in human adenovirus, protein V is believed to connect the inner capsid surface to the outer genome layer. Here, we explored mechanical properties and in vitro disassembly of particles lacking protein V (Ad5-ΔV). Ad5-ΔV particles were softer and less brittle than the wild-type ones (Ad5-wt), but they were more prone to release pentons under mechanical fatigue. In Ad5-ΔV, core components did not readily diffuse out of partially disrupted capsids, and the core appeared more condensed than in Ad5-wt. These observations suggest that instead of condensing the genome, protein V antagonizes the condensing action of the other core proteins. Protein V provides mechanical reinforcement and facilitates genome release by keeping DNA connected to capsid fragments that detach during disruption. This scenario is in line with the location of protein V in the virion and its role in Ad5 cell entry.
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Affiliation(s)
- Natalia Martín-González
- Departament of Condensed Matter Physics, Universidad Autónoma de Madrid and Institute of Condensed Matter Physics (IFIMAC), 28049 Madrid, Spain
| | - Alfonso Gómez-González
- Department of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | - Mercedes Hernando-Pérez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | - Carmen San Martín
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Pedro J. de Pablo
- Departament of Condensed Matter Physics, Universidad Autónoma de Madrid and Institute of Condensed Matter Physics (IFIMAC), 28049 Madrid, Spain
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41
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Onuchic L, Padovano V, Schena G, Rajendran V, Dong K, Shi X, Pandya R, Rai V, Gresko NP, Ahmed O, Lam TT, Wang W, Shen H, Somlo S, Caplan MJ. The C-terminal tail of polycystin-1 suppresses cystic disease in a mitochondrial enzyme-dependent fashion. Nat Commun 2023; 14:1790. [PMID: 36997516 PMCID: PMC10063565 DOI: 10.1038/s41467-023-37449-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 03/17/2023] [Indexed: 04/03/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most prevalent potentially lethal monogenic disorder. Mutations in the PKD1 gene, which encodes polycystin-1 (PC1), account for approximately 78% of cases. PC1 is a large 462-kDa protein that undergoes cleavage in its N and C-terminal domains. C-terminal cleavage produces fragments that translocate to mitochondria. We show that transgenic expression of a protein corresponding to the final 200 amino acid (aa) residues of PC1 in two Pkd1-KO orthologous murine models of ADPKD suppresses cystic phenotype and preserves renal function. This suppression depends upon an interaction between the C-terminal tail of PC1 and the mitochondrial enzyme Nicotinamide Nucleotide Transhydrogenase (NNT). This interaction modulates tubular/cyst cell proliferation, the metabolic profile, mitochondrial function, and the redox state. Together, these results suggest that a short fragment of PC1 is sufficient to suppress cystic phenotype and open the door to the exploration of gene therapy strategies for ADPKD.
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Affiliation(s)
- Laura Onuchic
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Valeria Padovano
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Giorgia Schena
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Vanathy Rajendran
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ke Dong
- Department of Internal Medicine and Division of Nephrology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Xiaojian Shi
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Systems Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Raj Pandya
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Victoria Rai
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Nikolay P Gresko
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Omair Ahmed
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06510, USA
- Keck Mass Spectrometry & Proteomics Resource, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Weiwei Wang
- Keck Mass Spectrometry & Proteomics Resource, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Hongying Shen
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Systems Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Stefan Somlo
- Department of Internal Medicine and Division of Nephrology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Michael J Caplan
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, 06510, USA.
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Liu Y, Yamazaki S, Ojika M. Heterologous Biosynthesis of Myxobacterial Antibiotic Miuraenamide A. Molecules 2023; 28:molecules28062815. [PMID: 36985787 PMCID: PMC10051162 DOI: 10.3390/molecules28062815] [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: 02/15/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
The hard-to-culture slightly halophilic myxobacterium "Paraliomyxa miuraensis" SMH-27-4 produces antifungal cyclodepsipeptide miuraenamide A (1). Herein, the region (85.9 kbp) containing the biosynthetic gene cluster (BGC) coding the assembly of 1 was identified and heterologously expressed in Myxococcus xanthus. A biosynthetic pathway proposed using in silico analysis was verified through the gene disruption of the heterologous transformant. In addition to the core polyketide synthase (PKS) and nonribosomal peptide synthase (NRPS) genes, tyrosine halogenase and O-methyltransferase genes participated in the biosynthesis of 1 as their gene-disrupted mutants produced a new congener, debromomiuraenamide A (4), and a previously isolated congener, miuraenamide E (3), respectively. Multigene disruption provided a heterologous mutant that produced 1 with the highest yield among the prepared mutants. When fed on 3-bromo-L-tyrosine, this mutant produced more 1 in the yield of 1.21 mg/L, which was 20 times higher than that produced by the initially prepared heterologous transformant. Although this yield was comparable to that of the original producer SMH-27-4 (1 mg/L), the culture time was 4.5 times shorter than that of SMH-27-4, indicating a five-fold efficiency in productivity. The results indicate the great potential of the miuraenamide BGC for the future contribution to drug development through logical gene manipulation.
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Affiliation(s)
- Ying Liu
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Satoshi Yamazaki
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Makoto Ojika
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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43
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Hao M, Tang J, Ge S, Li T, Xia N. Bacterial-Artificial-Chromosome-Based Genome Editing Methods and the Applications in Herpesvirus Research. Microorganisms 2023; 11:microorganisms11030589. [PMID: 36985163 PMCID: PMC10056367 DOI: 10.3390/microorganisms11030589] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Herpesviruses are major pathogens that infect humans and animals. Manipulating the large genome is critical for exploring the function of specific genes and studying the pathogenesis of herpesviruses and developing novel anti-viral vaccines and therapeutics. Bacterial artificial chromosome (BAC) technology significantly advanced the capacity of herpesviruses researchers to manipulate the virus genomes. In the past years, advancements in BAC-based genome manipulating and screening strategies of recombinant BACs have been achieved, which has promoted the study of the herpes virus. This review summarizes the advances in BAC-based gene editing technology and selection strategies. The merits and drawbacks of BAC-based herpesvirus genome editing methods and the application of BAC-based genome manipulation in viral research are also discussed. This review provides references relevant for researchers in selecting gene editing methods in herpes virus research. Despite the achievements in the genome manipulation of the herpes viruses, the efficiency of BAC-based genome manipulation is still not satisfactory. This review also highlights the need for developing more efficient genome-manipulating methods for herpes viruses.
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Affiliation(s)
- Mengling Hao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Jiabao Tang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- Xiang An Biomedicine Laboratory, Xiamen 361102, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Tingdong Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- Xiang An Biomedicine Laboratory, Xiamen 361102, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, Xiamen 361102, China
- Correspondence:
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- Xiang An Biomedicine Laboratory, Xiamen 361102, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, Xiamen 361102, China
- The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen 361102, China
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44
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Thomason LC, Costantino N, Li X, Court DL. Recombineering: Genetic Engineering in Escherichia coli Using Homologous Recombination. Curr Protoc 2023; 3:e656. [PMID: 36779782 PMCID: PMC10037674 DOI: 10.1002/cpz1.656] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
The bacterial chromosome and bacterial plasmids can be engineered in vivo by homologous recombination using either PCR products or synthetic double-stranded DNA (dsDNA) or single-stranded DNA as substrates. Multiple linear dsDNA molecules can be assembled into an intact plasmid. The technology of recombineering is possible because bacteriophage-encoded recombination proteins efficiently recombine sequences with homologies as short as 35 to 50 bases. Recombineering allows DNA sequences to be inserted or deleted without regard to the location of restriction sites and can also be used in combination with CRISPR/Cas targeting systems. © 2023 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Basic Protocol: Making electrocompetent cells and transforming with linear DNA Support Protocol 1: Selection/counter-selections for genome engineering Support Protocol 2: Creating and screening for oligo recombinants by PCR Support Protocol 3: Other methods of screening for unselected recombinants Support Protocol 4: Curing recombineering plasmids containing a temperature-sensitive replication function Support Protocol 5: Removal of the prophage by recombineering Alternate Protocol 1: Using CRISPR/Cas9 as a counter-selection following recombineering Alternate Protocol 2: Assembly of linear dsDNA fragments into functional plasmids Alternate Protocol 3: Retrieval of alleles onto a plasmid by gap repair Alternate Protocol 4: Modifying multicopy plasmids with recombineering Support Protocol 6: Screening for unselected plasmid recombinants Alternate Protocol 5: Recombineering with an intact λ prophage Alternate Protocol 6: Targeting an infecting λ phage with the defective prophage strains.
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Affiliation(s)
- Lynn C. Thomason
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Nina Costantino
- formerly with Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Xintian Li
- Armata Pharmaceuticals, 4503 Glencoe Avenue, Marina del Rey, CA 90292
| | - Donald L. Court
- Emeritus, Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
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45
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Venken KJ, Matinyan N, Gonzalez Y, Dierick HA. Serial Recombineering Cloning to Build Selectable and Tagged Genomic P[acman] BAC Clones for Selection Transgenesis and Functional Gene Analysis using Drosophila melanogaster. Curr Protoc 2023; 3:e675. [PMID: 36757632 PMCID: PMC9923880 DOI: 10.1002/cpz1.675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Transgenes with genomic DNA fragments that encompass genes of interest are the gold standard for complementing null alleles in rescue experiments in the fruit fly Drosophila melanogaster. Of particular interest are genomic DNA clones available as bacterial artificial chromosomes (BACs) or fosmids from publicly available genomic DNA libraries. Genes contained within BAC and fosmid clones can be easily modified by recombineering cloning to insert peptide or protein tags to localize, visualize, or manipulate gene products, and to create point mutations or deletions for structure-function analysis of the inserted genes. However, since transgenesis efficiency is inversely correlated with transgene size, obtaining transgenic animals for increasingly larger BAC and fosmid clones requires increasingly laborious screening efforts using the transgenesis marker commonly used for these transgenes, the dominant eye color marker white+ . We recently described a drug-based selectable genetic platform for Drosophila melanogaster, which included four resistance markers that allow direct selection of transgenic animals, eliminating the need to identify transgenic progeny by laborious phenotypic screening. By integrating these resistance markers into BAC transgenes, we were able to isolate animals containing large transgenes by direct selection, avoiding laborious screening. Here we present procedures on how to upgrade BAC clones by serial recombineering cloning to build both selectable and tagged BAC transgenes, for selection transgenesis and functional gene analysis, respectively. We illustrate these procedures using a BAC clone encompassing the gene encoding the synaptic vesicle protein, cysteine string protein. We demonstrate that the modified BAC clone, serially recombineered with a selectable marker for selection transgenesis and an N-terminal green fluorescent protein tag for gene expression analysis, is functional by showing the expression pattern obtained after successful selection transgenesis. The protocols cover: (1) cloning and preparation of the recombineering templates needed for serial recombineering cloning to incorporate selectable markers and protein tags; (2) preparing electrocompetent cells needed to perform serial recombineering cloning; and (3) the serial recombineering workflow to generate both selectable and tagged genomic BAC reporter transgenes for selection transgenesis and functional gene analysis in Drosophila melanogaster. The protocols we describe can be easily adapted to incorporate any of four selectable markers, protein tags, or any other modification for structure-function analysis of the genes present within any of the BAC or fosmid clones. A protocol for generating transgenic animals using serially recombineered BAC clones is presented in an accompanying Current Protocols article (Venken, Matinyan, Gonzalez, & Dierick, 2023a). © 2023 Wiley Periodicals LLC. Basic Protocol 1: Cloning and preparation of recombineering templates used for serial recombineering cloning. Basic Protocol 2: Making electrocompetent cells of the bacterial strains used to perform serial recombineering cloning or induction of plasmid copy number. Basic Protocol 3: Serial recombineering cloning to generate both selectable and tagged genomic P[acman] BAC reporter transgenes for selection transgenesis and gene expression analysis in Drosophila melanogaster.
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Affiliation(s)
- Koen J.T. Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nick Matinyan
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Herman A. Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
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Moy MA, Collins-McMillen D, Crawford L, Parkins C, Zeltzer S, Caviness K, Caposio P, Goodrum F. UL135 and UL136 Epistasis Controls Reactivation of Human Cytomegalovirus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525282. [PMID: 36747736 PMCID: PMC9900790 DOI: 10.1101/2023.01.24.525282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Human cytomegalovirus (HCMV) is beta herpesvirus that persists indefinitely in the human host through a protracted, latent infection. The polycistronic UL133-UL138 gene locus of HCMV encodes genes regulating latency and reactivation. While UL138 is pro-latency, restricting virus replication in CD34+ hematopoietic progenitor cells (HPCs), UL135 overcomes this restriction for reactivation. By contrast, UL136 is expressed with later kinetics and encodes multiple protein isoforms with differential roles in latency and reactivation. Like UL135, the largest UL136 isoform, UL136p33, is required for reactivation from latency in hematopoietic cells. Furthermore, UL136p33 is unstable, and its instability is important for the establishment of latency and sufficient accumulation of UL136p33 is a checkpoint for reactivation. We hypothesized that stabilizing UL136p33 might overcome the requirement of UL135 for reactivation. To test this, we generated recombinant viruses lacking UL135 that expressed a stabilized variant of UL136p33. Stabilizing UL136p33 did not impact replication of the UL135-mutant virus in fibroblasts. However, in the context of infection in hematopoietic cells, stabilization of UL136p33 strikingly compensated for the loss of UL135, resulting in increased replication in CD34+ HPCs and in humanized NOD- scid IL2Rγ c null (NSG) mice. This finding suggests that while UL135 is essential for reactivation, it functions at steps preceding the accumulation of UL136p33 and that stabilized expression of UL136p33 largely overcomes the requirement for UL135 in reactivation. Taken together, our genetic evidence indicates an epistatic relationship between UL136p33 and UL135 whereby UL135 may initiate events early in reactivation that will result in the accumulation of UL136p33 to a threshold required for productive reactivation. SIGNIFICANCE Human cytomegalovirus (HCMV) is one of nine human herpesviruses and a significant human pathogen. While HCMV establishes a life-long latent infection that is typically asymptomatic in healthy individuals, its reactivation from latency can have devastating consequences in the immune compromised. Defining virus-host and virus-virus interactions important for HCMV latency, reactivation and replication is critical to defining the molecular basis of latent and replicative states and in controlling infection and CMV disease. Here we define a genetic relationship between two viral genes in controlling virus reactivation from latency using primary human hematopoietic progenitor cell and humanized mouse models.
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Sallard E, Zhang W, Aydin M, Schröer K, Ehrhardt A. The Adenovirus Vector Platform: Novel Insights into Rational Vector Design and Lessons Learned from the COVID-19 Vaccine. Viruses 2023; 15:204. [PMID: 36680244 PMCID: PMC9862123 DOI: 10.3390/v15010204] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 01/13/2023] Open
Abstract
The adenovirus vector platform remains one of the most efficient toolboxes for generation of transfer vehicles used in gene therapy and virotherapy to treat tumors, as well as vaccines to protect from infectious diseases. The adenovirus genome and capsids can be modified using highly efficient techniques, and vectors can be produced at high titers, which facilitates their rapid adaptation to current needs and disease applications. Over recent years, the adenovirus vector platform has been in the center of attention for vaccine development against the ongoing coronavirus SARS-CoV-2/COVID-19 pandemic. The worldwide deployment of these vaccines has greatly deepened the knowledge on virus-host interactions and highlighted the need to further improve the effectiveness and safety not only of adenovirus-based vaccines but also of gene therapy and oncolytic virotherapy vectors. Based on the current evidence, we discuss here how adenoviral vectors can be further improved by intelligent molecular design. This review covers the full spectrum of state-of-the-art strategies to avoid vector-induced side effects ranging from the vectorization of non-canonical adenovirus types to novel genome engineering techniques.
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Affiliation(s)
- Erwan Sallard
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), School of Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Wenli Zhang
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), School of Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Malik Aydin
- Laboratory of Experimental Pediatric Pneumology and Allergology, Center for Biomedical Education and Research, School of Life Sciences (ZBAF), Faculty of Health, Witten/Herdecke University, 58455 Witten, Germany
| | - Katrin Schröer
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), School of Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Anja Ehrhardt
- Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), School of Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
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48
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Xia Y, Duca S, Perder B, Dündar F, Zumbo P, Qiu M, Yao J, Cao Y, Harrison MRM, Zangi L, Betel D, Cao J. Activation of a transient progenitor state in the epicardium is required for zebrafish heart regeneration. Nat Commun 2022; 13:7704. [PMID: 36513650 PMCID: PMC9747719 DOI: 10.1038/s41467-022-35433-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The epicardium, a mesothelial cell tissue that encompasses vertebrate hearts, supports heart regeneration after injury through paracrine effects and as a source of multipotent progenitors. However, the progenitor state in the adult epicardium has yet to be defined. Through single-cell RNA-sequencing of isolated epicardial cells from uninjured and regenerating adult zebrafish hearts, we define the epithelial and mesenchymal subsets of the epicardium. We further identify a transiently activated epicardial progenitor cell (aEPC) subpopulation marked by ptx3a and col12a1b expression. Upon cardiac injury, aEPCs emerge from the epithelial epicardium, migrate to enclose the wound, undergo epithelial-mesenchymal transition (EMT), and differentiate into mural cells and pdgfra+hapln1a+ mesenchymal epicardial cells. These EMT and differentiation processes are regulated by the Tgfβ pathway. Conditional ablation of aEPCs blocks heart regeneration through reduced nrg1 expression and mesenchymal cell number. Our findings identify a transient progenitor population of the adult epicardium that is indispensable for heart regeneration and highlight it as a potential target for enhancing cardiac repair.
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Affiliation(s)
- Yu Xia
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Sierra Duca
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Björn Perder
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Applied Bioinformatics Core, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Applied Bioinformatics Core, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Miaoyan Qiu
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Jun Yao
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Yingxi Cao
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Michael R M Harrison
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Lior Zangi
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Institute for Computational Biomedicine, Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA.
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49
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Xiong F, Yang H, Song YG, Qin HB, Zhang QY, Huang X, Jing W, Deng M, Liu Y, Liu Z, Shen Y, Han Y, Lu Y, Xu X, Holmes TC, Luo M, Zhao F, Luo MH, Zeng WB. An HSV-1-H129 amplicon tracer system for rapid and efficient monosynaptic anterograde neural circuit tracing. Nat Commun 2022; 13:7645. [PMID: 36496505 PMCID: PMC9741617 DOI: 10.1038/s41467-022-35355-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Monosynaptic viral tracers are essential tools for dissecting neuronal connectomes and for targeted delivery of molecular sensors and effectors. Viral toxicity and complex multi-injection protocols are major limiting application barriers. To overcome these barriers, we developed an anterograde monosynaptic H129Amp tracer system based on HSV-1 strain H129. The H129Amp tracer system consists of two components: an H129-dTK-T2-pacFlox helper which assists H129Amp tracer's propagation and transneuronal monosynaptic transmission. The shared viral features of tracer/helper allow for simultaneous single-injection and subsequent high expression efficiency from multiple-copy of expression cassettes in H129Amp tracer. These improvements of H129Amp tracer system shorten experiment duration from 28-day to 5-day for fast-bright monosynaptic tracing. The lack of toxic viral genes in the H129Amp tracer minimizes toxicity in postsynaptic neurons, thus offering the potential for functional anterograde mapping and long-term tracer delivery of genetic payloads. The H129Amp tracer system is a powerful tracing tool for revealing neuronal connectomes.
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Affiliation(s)
- Feng Xiong
- grid.9227.e0000000119573309State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.9227.e0000000119573309Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Hong Yang
- grid.9227.e0000000119573309State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Yi-Ge Song
- grid.33199.310000 0004 0368 7223Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hai-Bin Qin
- grid.9227.e0000000119573309State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Qing-Yang Zhang
- grid.9227.e0000000119573309State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xian Huang
- grid.33199.310000 0004 0368 7223Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Jing
- grid.33199.310000 0004 0368 7223Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Manfei Deng
- grid.33199.310000 0004 0368 7223Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Liu
- grid.410717.40000 0004 0644 5086National Institute of Biological Sciences, Beijing, China
| | - Zhixiang Liu
- grid.410717.40000 0004 0644 5086National Institute of Biological Sciences, Beijing, China
| | - Yin Shen
- grid.49470.3e0000 0001 2331 6153Eye Center, Renmin Hospital, Wuhan University, Wuhan, China
| | - Yunyun Han
- grid.49470.3e0000 0001 2331 6153Eye Center, Renmin Hospital, Wuhan University, Wuhan, China
| | - Youming Lu
- grid.33199.310000 0004 0368 7223Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangmin Xu
- grid.266093.80000 0001 0668 7243Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA USA ,grid.266093.80000 0001 0668 7243Center for Neural Circuit Mapping, School of Medicine, University of California, Irvine, CA USA
| | - Todd C. Holmes
- grid.266093.80000 0001 0668 7243Center for Neural Circuit Mapping, School of Medicine, University of California, Irvine, CA USA ,grid.266093.80000 0001 0668 7243Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA USA
| | - Minmin Luo
- grid.410717.40000 0004 0644 5086National Institute of Biological Sciences, Beijing, China ,grid.510934.a0000 0005 0398 4153Chinese Institute for Brain Research, Beijing, China
| | - Fei Zhao
- grid.510934.a0000 0005 0398 4153Chinese Institute for Brain Research, Beijing, China ,grid.24696.3f0000 0004 0369 153XSchool of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Min-Hua Luo
- grid.9227.e0000000119573309State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China ,grid.9227.e0000000119573309Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China ,grid.266093.80000 0001 0668 7243Center for Neural Circuit Mapping, School of Medicine, University of California, Irvine, CA USA
| | - Wen-Bo Zeng
- grid.9227.e0000000119573309State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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50
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Dicks MD, Rose LM, Russell RA, Bowman LA, Graham C, Jimenez-Guardeño JM, Doores KJ, Malim MH, Draper SJ, Howarth M, Biswas S. Modular capsid decoration boosts adenovirus vaccine-induced humoral immunity against SARS-CoV-2. Mol Ther 2022; 30:3639-3657. [PMID: 35949171 PMCID: PMC9364715 DOI: 10.1016/j.ymthe.2022.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Adenovirus vector vaccines have been widely and successfully deployed in response to coronavirus disease 2019 (COVID-19). However, despite inducing potent T cell immunity, improvement of vaccine-specific antibody responses upon homologous boosting is modest compared with other technologies. Here, we describe a system enabling modular decoration of adenovirus capsid surfaces with antigens and demonstrate potent induction of humoral immunity against these displayed antigens. Ligand attachment via a covalent bond was achieved using a protein superglue, DogTag/DogCatcher (similar to SpyTag/SpyCatcher), in a rapid and spontaneous reaction requiring only co-incubation of ligand and vector components. DogTag was inserted into surface-exposed loops in the adenovirus hexon protein to allow attachment of DogCatcher-fused ligands on virus particles. Efficient coverage of the capsid surface was achieved using various ligands, with vector infectivity retained in each case. Capsid decoration shielded particles from vector neutralizing antibodies. In prime-boost regimens, adenovirus vectors decorated with the receptor-binding domain of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike induced >10-fold higher SARS-CoV-2 neutralization titers compared with an undecorated vector encoding spike. Importantly, decorated vectors achieved equivalent or superior T cell immunogenicity against encoded antigens compared with undecorated vectors. We propose capsid decoration using protein superglues as a novel strategy to improve efficacy and boostability of adenovirus-based vaccines and therapeutics.
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Affiliation(s)
- Matthew D.J. Dicks
- SpyBiotech Ltd, 7600 The Quorum, Oxford Business Park North, Oxford, OX4 2JZ, UK,Corresponding author: Matthew D. J. Dicks, SpyBiotech Ltd, 7600 The Quorum, Oxford Business Park North, Oxford, OX4 2JZ, UK.
| | - Louisa M. Rose
- SpyBiotech Ltd, 7600 The Quorum, Oxford Business Park North, Oxford, OX4 2JZ, UK
| | - Rebecca A. Russell
- SpyBiotech Ltd, 7600 The Quorum, Oxford Business Park North, Oxford, OX4 2JZ, UK
| | - Lesley A.H. Bowman
- SpyBiotech Ltd, 7600 The Quorum, Oxford Business Park North, Oxford, OX4 2JZ, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London SE1 9RT, UK
| | - Jose M. Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London SE1 9RT, UK
| | - Katie J. Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London SE1 9RT, UK
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King’s College London, London SE1 9RT, UK
| | - Simon J. Draper
- SpyBiotech Ltd, 7600 The Quorum, Oxford Business Park North, Oxford, OX4 2JZ, UK,Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark Howarth
- SpyBiotech Ltd, 7600 The Quorum, Oxford Business Park North, Oxford, OX4 2JZ, UK,Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Sumi Biswas
- SpyBiotech Ltd, 7600 The Quorum, Oxford Business Park North, Oxford, OX4 2JZ, UK,The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
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