1
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Thalmann L, Martin-Gonzalez N, Brücher D, Plückthun A, de Pablo PJ, Suomalainen M, Greber UF. Gutless Helper-Dependent and First-Generation HAdV5 Vectors Have Similar Mechanical Properties and Common Transduction Mechanisms. Hum Gene Ther 2024; 35:163-176. [PMID: 38386500 DOI: 10.1089/hum.2023.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
Delivering vectorized information into cells with the help of viruses has been of high interest to fundamental and applied science, and bears significant therapeutic promise. Human adenoviruses (HAdVs) have been at the forefront of gene delivery for many years, and the subject of intensive development resulting in several generations of agents, including replication-competent, -defective or retargeted vectors, and recently also helper-dependent (HD), so-called gutless vectors lacking any viral protein coding information. While it is possible to produce HD-AdVs in significant amounts, physical properties of these virus-like particles and their efficiency of transduction have not been addressed. Here, we used single-cell and single virus particle assays to probe the effect of genome length on HAdV-C5 vector transduction. Our results demonstrate that first-generation C5 vectors lacking the E1/E3 regions of the viral genome as well as HD-AdV-C5 particles with a wild type (wt) ∼36 kbp or an undersized double-strand DNA genome are similar to human adenovirus C5 (HAdV-C5) wt regarding attachment to human lung epithelial cells, endocytic uptake, endosome penetration and dependency on the E3 RING ubiquitin ligase Mind Bomb 1 for DNA uncoating at the nuclear pore complex. Atomic force microscopy measurements of single virus particles indicated that small changes in the genome length from 94% to 103% of HAdV-C5 have no major impact on physical and mechanical features of AdV vectors. In contrast, an HD-AdV-C5 with ∼30 kbp genome was slightly stiffer and less heat-resistant than the other particles, despite comparable entry and transduction efficiencies in tissue culture cell lines, including murine alveolar macrophage-like Max-Planck-Institute (MPI)-2 cells. Together, our in vitro studies reinforce the use of HD-AdV vectors for effective single round gene delivery. The results illustrate how physical properties and cell entry behavior of single virus particles can provide functional information for anticipated therapeutic vector applications.
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Affiliation(s)
- Lars Thalmann
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | | | - Dominik Brücher
- Department of Condensed Matter Physics and IFIMAC, Universidad Autónoma de Madrid, Madrid, Spain
| | - Andreas Plückthun
- Department of Condensed Matter Physics and IFIMAC, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pedro J de Pablo
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
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2
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Jetzer T, Studer L, Bieri M, Greber UF, Hemmi S. Engineered Human Adenoviruses of Species B and C Report Early, Intermediate Early, and Late Viral Gene Expression. Hum Gene Ther 2023; 34:1230-1247. [PMID: 37725579 DOI: 10.1089/hum.2023.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
Adenoviruses (AdVs) are being developed for oncolytic or vaccination therapy against existing and emerging conditions. Well-characterized replication-competent human and human primate AdVs expressing multiple payloads are desirable, but their replication in rodent models is limited. To score the timing of adenoviral gene expression in cell cultures, we developed fully replication-competent transcriptional reporter viruses for HAdV-C5, -B3, and -B35. The picornavirus-derived 2A sequence, which induces cotranslational peptide splitting and reinitiation (skipping), was linked to GFP and the fused sequence was inserted C-terminal of the early gene E1A, the intermediate early gene protein IX and the late fiber gene. The 2A peptide induced ribosomal skipping during translation of the messenger RNA (mRNA) and gave rise to GFP from the corresponding viral promoters, as shown by immunoblotting and flow cytometry analyses of human and rodent cells. In human cells, both species B and C AdV exhibited highest reporter expression for fiber, followed by protein IX and lowest for E1A. Inoculation with either HAdV-C5 or -B3/35 viruses encoding protein IX- or fiber-GFP gave rise to higher GFP levels in hamster than mouse cells. Remarkably, despite rather low 2A ribosomal skipping efficiency of ∼50% for E1A-2A-GFP, protein IX-2A-GFP, and fiber-2A-GFP, unprocessed protein IX-2A-GFP and fiber-2A-GFP fusion proteins were efficiently incorporated into HAdV-B3 virions, respectively. These data indicate that the B3 C-termini of protein IX and fiber can be considered for retargeting engineered oncolytic or vaccination vectors, or for antigen display. The variable expression levels of transgenes from different subviral promoters may be used to improve oncolytic AdV vectors expressing therapeutic genes.
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Affiliation(s)
- Tania Jetzer
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Lukas Studer
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Manuela Bieri
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Molecular Life Science Program, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Silvio Hemmi
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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3
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Petkidis A, Andriasyan V, Greber UF. Machine learning for cross-scale microscopy of viruses. Cell Rep Methods 2023; 3:100557. [PMID: 37751685 PMCID: PMC10545915 DOI: 10.1016/j.crmeth.2023.100557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/05/2023] [Accepted: 07/20/2023] [Indexed: 09/28/2023]
Abstract
Despite advances in virological sciences and antiviral research, viruses continue to emerge, circulate, and threaten public health. We still lack a comprehensive understanding of how cells and individuals remain susceptible to infectious agents. This deficiency is in part due to the complexity of viruses, including the cell states controlling virus-host interactions. Microscopy samples distinct cellular infection stages in a multi-parametric, time-resolved manner at molecular resolution and is increasingly enhanced by machine learning and deep learning. Here we discuss how state-of-the-art artificial intelligence (AI) augments light and electron microscopy and advances virological research of cells. We describe current procedures for image denoising, object segmentation, tracking, classification, and super-resolution and showcase examples of how AI has improved the acquisition and analyses of microscopy data. The power of AI-enhanced microscopy will continue to help unravel virus infection mechanisms, develop antiviral agents, and improve viral vectors.
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Affiliation(s)
- Anthony Petkidis
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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4
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Petkidis A, Andriasyan V, Greber UF. Label-free microscopy for virus infections. Microscopy (Oxf) 2023:7133758. [PMID: 37079744 DOI: 10.1093/jmicro/dfad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 04/22/2023] Open
Abstract
Microscopy has been essential to elucidate micro- and nano-scale processes in space and time, and has provided insight into cell and organismic function. It is widely employed in cell biology, microbiology, physiology, clinical sciences and virology. While label-dependent microscopy, such as fluorescence microscopy, provides molecular specificity, it has remained difficult to multiplex in live samples. In contrast, label-free microscopy reports on overall features of the specimen at minimal perturbation. Here, we discuss modalities of label-free imaging at the molecular, cellular and tissue levels, including transmitted light microscopy, quantitative phase imaging, cryogenic electron microscopy or tomography, and atomic force microscopy. We highlight how label-free microscopy is used to probe the structural organization and mechanical properties of viruses, including virus particles and infected cells across a wide range of spatial scales. We discuss the working principles of imaging procedures and analyses, and showcase how they open new avenues in virology. Finally, we discuss orthogonal approaches that enhance and complement label-free microscopy techniques. Mini Abstract Label-free imaging gives unprecedented insight into viruses at macroscopic, molecular and atomic levels. We present the major label-free imaging techniques and discuss how they are used for virus particles and infected cells. The power of label-free microscopy promises to enhance discovery of unknown aspects of infectious and therapeutic agents.
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Affiliation(s)
- Anthony Petkidis
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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5
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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. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Pelisek J, Reutersberg B, Greber UF, Zimmermann A. Vascular dysfunction in COVID-19 patients: update on SARS-CoV-2 infection of endothelial cells and the role of long non-coding RNAs. Clin Sci (Lond) 2022; 136:1571-1590. [PMID: 36367091 PMCID: PMC9652506 DOI: 10.1042/cs20220235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 08/16/2023]
Abstract
Although COVID-19 is primarily a respiratory disease, it may affect also the cardiovascular system. COVID-19 patients with cardiovascular disorder (CVD) develop a more severe disease course with a significantly higher mortality rate than non-CVD patients. A common denominator of CVD is the dysfunction of endothelial cells (ECs), increased vascular permeability, endothelial-to-mesenchymal transition, coagulation, and inflammation. It has been assumed that clinical complications in COVID-19 patients suffering from CVD are caused by SARS-CoV-2 infection of ECs through the angiotensin-converting enzyme 2 (ACE2) receptor and the cellular transmembrane protease serine 2 (TMPRSS2) and the consequent dysfunction of the infected vascular cells. Meanwhile, other factors associated with SARS-CoV-2 entry into the host cells have been described, including disintegrin and metalloproteinase domain-containing protein 17 (ADAM17), the C-type lectin CD209L or heparan sulfate proteoglycans (HSPG). Here, we discuss the current data about the putative entry of SARS-CoV-2 into endothelial and smooth muscle cells. Furthermore, we highlight the potential role of long non-coding RNAs (lncRNAs) affecting vascular permeability in CVD, a process that might exacerbate disease in COVID-19 patients.
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Affiliation(s)
- Jaroslav Pelisek
- Department of Vascular Surgery, University Hospital Zürich, Zürich, Switzerland
| | | | - Urs F Greber
- Department of Molecular Life Sciences, University of Zürich, Switzerland
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7
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Olszewski D, Georgi F, Murer L, Andriasyan V, Kuttler F, Petkidis A, Witte R, Yakimovich A, Fischer L, Rozanova A, Yamauchi Y, Turcatti G, Greber UF. High-content, arrayed compound screens with rhinovirus, influenza A virus and herpes simplex virus infections. Sci Data 2022; 9:610. [PMID: 36209289 PMCID: PMC9547564 DOI: 10.1038/s41597-022-01733-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Viruses are genetically and structurally diverse, and outnumber cells by orders of magnitude. They can cause acute and chronic infections, suppress, or exacerbate immunity, or dysregulate survival and growth of cells. To identify chemical agents with pro- or antiviral effects we conducted arrayed high-content image-based multi-cycle infection screens of 1,280 mainly FDA-approved compounds with three human viruses, rhinovirus (RV), influenza A virus (IAV), and herpes simplex virus (HSV) differing in genome organization, composition, presence of an envelope, and tropism. Based on Z’-factors assessing screening quality and Z-scores ranking individual compounds, we identified potent inhibitors and enhancers of infection: the RNA mutagen 5-Azacytidine against RV-A16; the broad-spectrum antimycotic drug Clotrimazole inhibiting IAV-WSN; the chemotherapeutic agent Raltitrexed blocking HSV-1; and Clobetasol enhancing HSV-1. Remarkably, the topical antiseptic compound Aminacrine, which is clinically used against bacterial and fungal agents, inhibited all three viruses. Our data underscore the versatility and potency of image-based, full cycle virus propagation assays in cell-based screenings for antiviral agents. Measurement(s) | transmission of virus • drug toxicity | Technology Type(s) | fluorescence microscopy | Factor Type(s) | virus genotype • cell line • incubation temperature • number of cells seeded/ seeding density • inoculation time • virus input FFU • drug concentration | Sample Characteristic - Organism | Homo sapiens • Rhinovirus A • Influenza A virus • Human alphaherpesvirus 1 | Sample Characteristic - Environment | epithelium | Sample Characteristic - Location | Switzerland |
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Affiliation(s)
- Dominik Olszewski
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Luca Murer
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Fabien Kuttler
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale (EPFL) de Lausanne, Station 15, Lausanne, 1015, Switzerland
| | - Anthony Petkidis
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Robert Witte
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Artur Yakimovich
- Center for Advanced Systems Understanding (CASUS), Helmholtz Center Dresden-Rossendorf, Untermarkt 20, 82026, Görlitz, Germany.,Bladder Infection and Immunity Group (BIIG), Department of Renal Medicine, Division of Medicine, University College London, Royal Free Hospital Campus, London, NW3 2PF, United Kingdom
| | - Lucy Fischer
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Alina Rozanova
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland.,University of Bristol, Bristol, BS8 1TH, United Kingdom
| | - Yohei Yamauchi
- University of Bristol, Bristol, BS8 1TH, United Kingdom.,Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Gerardo Turcatti
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale (EPFL) de Lausanne, Station 15, Lausanne, 1015, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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8
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Greber UF, Suomalainen M. Adenovirus entry: Stability, uncoating, and nuclear import. Mol Microbiol 2022; 118:309-320. [PMID: 35434852 PMCID: PMC9790413 DOI: 10.1111/mmi.14909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 12/30/2022]
Abstract
Adenoviruses (AdVs) are widespread in vertebrates. They infect the respiratory and gastrointestinal tracts, the eyes, heart, liver, and kidney, and are lethal to immunosuppressed people. Mastadenoviruses infecting mammals comprise several hundred different types, and many specifically infect humans. Human adenoviruses are the most widely used vectors in clinical applications, including cancer treatment and COVID-19 vaccination. AdV vectors are physically and genetically stable and generally safe in humans. The particles have an icosahedral coat and a nucleoprotein core with a DNA genome. We describe the concept of AdV cell entry and highlight recent advances in cytoplasmic transport, uncoating, and nuclear import of the viral DNA. We highlight a recently discovered "linchpin" function of the virion protein V ensuring cytoplasmic particle stability, which is relaxed at the nuclear pore complex by cues from the E3 ubiquitin ligase Mind bomb 1 (MIB1) and the proteasome triggering disruption. Capsid disruption by kinesin motor proteins and microtubules exposes the linchpin and renders protein V a target for MIB1 ubiquitination, which dissociates V from viral DNA and enhances DNA nuclear import. These advances uncover mechanisms controlling capsid stability and premature uncoating and provide insight into nuclear transport of nucleic acids.
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Affiliation(s)
- Urs F. Greber
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Maarit Suomalainen
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
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9
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Kannan A, Suomalainen M, Volle R, Bauer M, Amsler M, Trinh HV, Vavassori S, Schmid JP, Vilhena G, Marín-González A, Perez R, Franceschini A, von Mering C, Hemmi S, Greber UF. Sequence-Specific Features of Short Double-Strand, Blunt-End RNAs Have RIG-I- and Type 1 Interferon-Dependent or -Independent Anti-Viral Effects. Viruses 2022; 14:v14071407. [PMID: 35891387 PMCID: PMC9322957 DOI: 10.3390/v14071407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 02/08/2023] Open
Abstract
Pathogen-associated molecular patterns, including cytoplasmic DNA and double-strand (ds)RNA trigger the induction of interferon (IFN) and antiviral states protecting cells and organisms from pathogens. Here we discovered that the transfection of human airway cell lines or non-transformed fibroblasts with 24mer dsRNA mimicking the cellular micro-RNA (miR)29b-1* gives strong anti-viral effects against human adenovirus type 5 (AdV-C5), influenza A virus X31 (H3N2), and SARS-CoV-2. These anti-viral effects required blunt-end complementary RNA strands and were not elicited by corresponding single-strand RNAs. dsRNA miR-29b-1* but not randomized miR-29b-1* mimics induced IFN-stimulated gene expression, and downregulated cell adhesion and cell cycle genes, as indicated by transcriptomics and IFN-I responsive Mx1-promoter activity assays. The inhibition of AdV-C5 infection with miR-29b-1* mimic depended on the IFN-alpha receptor 2 (IFNAR2) and the RNA-helicase retinoic acid-inducible gene I (RIG-I) but not cytoplasmic RNA sensors MDA5 and ZNFX1 or MyD88/TRIF adaptors. The antiviral effects of miR29b-1* were independent of a central AUAU-motif inducing dsRNA bending, as mimics with disrupted AUAU-motif were anti-viral in normal but not RIG-I knock-out (KO) or IFNAR2-KO cells. The screening of a library of scrambled short dsRNA sequences identified also anti-viral mimics functioning independently of RIG-I and IFNAR2, thus exemplifying the diverse anti-viral mechanisms of short blunt-end dsRNAs.
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Affiliation(s)
- Abhilash Kannan
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Neurimmune AG, Wagistrasse 18, 8952 Schlieren, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Romain Volle
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Marco Amsler
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Hung V. Trinh
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Genezen, 9900 Westpoint Dr, Suite 128, Indianapolis, IN 46256, USA
| | - Stefano Vavassori
- Division of Immunology, University Children’s Hospital Zürich, 8032 Zürich, Switzerland; (S.V.); (J.P.S.)
| | - Jana Pachlopnik Schmid
- Division of Immunology, University Children’s Hospital Zürich, 8032 Zürich, Switzerland; (S.V.); (J.P.S.)
- Faculty of Medicine, University of Zürich, 8006 Zürich, Switzerland
| | - Guilherme Vilhena
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain; (G.V.); (R.P.)
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Alberto Marín-González
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Cantoblanco, E-28049 Madrid, Spain;
| | - Ruben Perez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain; (G.V.); (R.P.)
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Andrea Franceschini
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Silvio Hemmi
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Correspondence:
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10
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Murer L, Petkidis A, Vallet T, Vignuzzi M, Greber UF. Chemical Evolution of Rhinovirus Identifies Capsid-Destabilizing Mutations Driving Low-pH-Independent Genome Uncoating. J Virol 2022; 96:e0106021. [PMID: 34705560 PMCID: PMC8791267 DOI: 10.1128/jvi.01060-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/20/2021] [Indexed: 12/24/2022] Open
Abstract
Rhinoviruses (RVs) cause recurrent infections of the nasal and pulmonary tracts, life-threatening conditions in chronic respiratory illness patients, predisposition of children to asthmatic exacerbation, and large economic cost. RVs are difficult to treat. They rapidly evolve resistance and are genetically diverse. Here, we provide insight into RV drug resistance mechanisms against chemical compounds neutralizing low pH in endolysosomes. Serial passaging of RV-A16 in the presence of the vacuolar proton ATPase inhibitor bafilomycin A1 (BafA1) or the endolysosomotropic agent ammonium chloride (NH4Cl) promoted the emergence of resistant virus populations. We found two reproducible point mutations in viral proteins 1 and 3 (VP1 and VP3), A2526G (serine 66 to asparagine [S66N]), and G2274U (cysteine 220 to phenylalanine [C220F]), respectively. Both mutations conferred cross-resistance to BafA1, NH4Cl, and the protonophore niclosamide, as identified by massive parallel sequencing and reverse genetics, but not the double mutation, which we could not rescue. Both VP1-S66 and VP3-C220 locate at the interprotomeric face, and their mutations increase the sensitivity of virions to low pH, elevated temperature, and soluble intercellular adhesion molecule 1 receptor. These results indicate that the ability of RV to uncoat at low endosomal pH confers virion resistance to extracellular stress. The data endorse endosomal acidification inhibitors as a viable strategy against RVs, especially if inhibitors are directly applied to the airways. IMPORTANCE Rhinoviruses (RVs) are the predominant agents causing the common cold. Anti-RV drugs and vaccines are not available, largely due to rapid evolutionary adaptation of RVs giving rise to resistant mutants and an immense diversity of antigens in more than 160 different RV types. In this study, we obtained insight into the cell biology of RVs by harnessing the ability of RVs to evolve resistance against host-targeting small chemical compounds neutralizing endosomal pH, an important cue for uncoating of normal RVs. We show that RVs grown in cells treated with inhibitors of endolysosomal acidification evolved capsid mutations yielding reduced virion stability against elevated temperature, low pH, and incubation with recombinant soluble receptor fragments. This fitness cost makes it unlikely that RV mutants adapted to neutral pH become prevalent in nature. The data support the concept of host-directed drug development against respiratory viruses in general, notably at low risk of gain-of-function mutations.
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Affiliation(s)
- Luca Murer
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Anthony Petkidis
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Thomas Vallet
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Department of Virology, CNRS UMR 3569, Paris, France
| | - Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Department of Virology, CNRS UMR 3569, Paris, France
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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11
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Murer L, Volle R, Andriasyan V, Petkidis A, Gomez-Gonzalez A, Yang L, Meili N, Suomalainen M, Bauer M, Policarpo Sequeira D, Olszewski D, Georgi F, Kuttler F, Turcatti G, Greber UF. Identification of broad anti-coronavirus chemical agents for repurposing against SARS-CoV-2 and variants of concern. Curr Res Virol Sci 2022; 3:100019. [PMID: 35072124 PMCID: PMC8760634 DOI: 10.1016/j.crviro.2022.100019] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 01/18/2023]
Abstract
Endemic human coronaviruses (hCoVs) 229E and OC43 cause respiratory disease with recurrent infections, while severe acute respiratory syndrome (SARS)-CoV-2 spreads across the world with impact on health and societies. Here, we report an image-based multicycle infection procedure with α-coronavirus hCoV-229E-eGFP in an arrayed chemical library screen of 5440 clinical and preclinical compounds. Toxicity counter selection and challenge with the β-coronaviruses OC43 and SARS-CoV-2 in tissue culture and human airway epithelial explant cultures (HAEEC) identified four FDA-approved compounds with oral availability. Methylene blue (MB, used for the treatment of methemoglobinemia), Mycophenolic acid (MPA, used in organ transplantation) and the anti-fungal agent Posaconazole (POS) had the broadest anti-CoV spectrum. They inhibited the shedding of SARS-CoV-2 and variants-of-concern (alpha, beta, gamma, delta) from HAEEC in either pre- or post exposure regimens at clinically relevant concentrations. Co-treatment of cultured cells with MB and the FDA-approved SARS-CoV-2 RNA-polymerase inhibitor Remdesivir reduced the effective anti-viral concentrations of MB by 2-fold, and Remdesivir by 4 to 10-fold, indicated by BLISS independence synergy modelling. Neither MB, nor MPA, nor POS affected the cell delivery of SARS-CoV-2 or OC43 (+)sense RNA, but blocked subsequent viral RNA accumulation in cells. Unlike Remdesivir, MB, MPA or POS did not reduce the release of viral RNA in post exposure regimen, thus indicating infection inhibition at a post-replicating step as well. In summary, the data emphasize the power of unbiased, full cycle compound screens to identify and repurpose broadly acting drugs against coronaviruses.
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Affiliation(s)
- Luca Murer
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Romain Volle
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Anthony Petkidis
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Alfonso Gomez-Gonzalez
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Liliane Yang
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Nicole Meili
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Daniela Policarpo Sequeira
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Dominik Olszewski
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Fabien Kuttler
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 15, 1015, Lausanne, Switzerland
| | - Gerardo Turcatti
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 15, 1015, Lausanne, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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12
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Bauer M, Gomez-Gonzalez A, Suomalainen M, Schilling N, Hemmi S, Greber UF. A viral ubiquitination switch attenuates innate immunity and triggers nuclear import of virion DNA and infection. Sci Adv 2021; 7:eabl7150. [PMID: 34919430 PMCID: PMC8682987 DOI: 10.1126/sciadv.abl7150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Antiviral defense and virus exclusion from the cell nucleus restrict foreign nucleic acid influx and infection. How the genomes of DNA viruses evade cytosolic pattern recognition and cross the nuclear envelope is incompletely understood. Here, we show that the virion protein V of adenovirus functions as a linchpin between the genome and the capsid, thereby securing particle integrity. Absence of protein V destabilizes cytoplasmic particles and promotes premature genome release, raising cytokine levels through the DNA sensor cGAS. Non-ubiquitinable V yields stable virions, genome misdelivery to the cytoplasm, and increased cytokine levels. In contrast, normal protein V is ubiquitinated at the nuclear pore complex, dissociates from the virion depending on the E3 ubiquitin ligase Mib1 and the proteasome, and allows genome delivery into the nucleus for infection. Our data uncover previously unknown cellular and viral mechanisms of viral DNA nuclear import in pathogenesis, vaccination, gene therapy, and synthetic biology.
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Affiliation(s)
- Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich CH8057, Switzerland
| | - Alfonso Gomez-Gonzalez
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich CH8057, Switzerland
- Life Science Zurich Graduate School, ETH and University of Zurich, Zurich 8057, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich CH8057, Switzerland
| | - Nicolas Schilling
- Center for Microscopy and Image Analysis, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Silvio Hemmi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich CH8057, Switzerland
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich CH8057, Switzerland
- Corresponding author.
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13
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Bieri M, Hendrickx R, Bauer M, Yu B, Jetzer T, Dreier B, Mittl PRE, Sobek J, Plückthun A, Greber UF, Hemmi S. The RGD-binding integrins αvβ6 and αvβ8 are receptors for mouse adenovirus-1 and -3 infection. PLoS Pathog 2021; 17:e1010083. [PMID: 34910784 PMCID: PMC8673666 DOI: 10.1371/journal.ppat.1010083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022] Open
Abstract
Mammalian adenoviruses (AdVs) comprise more than ~350 types including over 100 human (HAdVs) and just three mouse AdVs (MAdVs). While most HAdVs initiate infection by high affinity/avidity binding of their fiber knob (FK) protein to either coxsackievirus AdV receptor (CAR), CD46 or desmoglein (DSG)-2, MAdV-1 (M1) infection requires arginine-glycine-aspartate (RGD) binding integrins. To identify the receptors mediating MAdV infection we generated five novel reporter viruses for MAdV-1/-2/-3 (M1, M2, M3) transducing permissive murine (m) CMT-93 cells, but not B16 mouse melanoma cells expressing mCAR, human (h) CD46 or hDSG-2. Recombinant M1 or M3 FKs cross-blocked M1 and M3 but not M2 infections. Profiling of murine and human cells expressing RGD-binding integrins suggested that αvβ6 and αvβ8 heterodimers are associated with M1 and M3 infections. Ectopic expression of mβ6 in B16 cells strongly enhanced M1 and M3 binding, infection, and progeny production comparable with mαvβ6-positive CMT-93 cells, whereas mβ8 expressing cells were more permissive to M1 than M3. Anti-integrin antibodies potently blocked M1 and M3 binding and infection of CMT-93 cells and hαvβ8-positive M000216 cells. Soluble integrin αvβ6, and synthetic peptides containing the RGDLXXL sequence derived from FK-M1, FK-M3 and foot and mouth disease virus coat protein strongly interfered with M1/M3 infections, in agreement with high affinity interactions of FK-M1/FK-M3 with αvβ6/αvβ8, determined by surface plasmon resonance measurements. Molecular docking simulations of ternary complexes revealed a bent conformation of RGDLXXL-containing FK-M3 peptides on the subunit interface of αvβ6/β8, where the distal leucine residue dips into a hydrophobic pocket of β6/8, the arginine residue ionically engages αv aspartate215, and the aspartate residue coordinates a divalent cation in αvβ6/β8. Together, the RGDLXXL-bearing FKs are part of an essential mechanism for M1/M3 infection engaging murine and human αvβ6/8 integrins. These integrins are highly conserved in other mammals, and may favour cross-species virus transmission.
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Affiliation(s)
- Manuela Bieri
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Molecular Life Sciences Graduate School, ETH and University Of Zurich, Switzerland
| | - Rodinde Hendrickx
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Molecular Life Sciences Graduate School, ETH and University Of Zurich, Switzerland
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Bin Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Tania Jetzer
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Peer R. E. Mittl
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Jens Sobek
- Functional Genomics Center Zurich, Eidgenössische Technische Hochschule (ETH) Zurich and University of Zurich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Silvio Hemmi
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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14
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Abstract
The 2019 outbreak of coronavirus disease (COVID‐19) in Wuhan (Hubei province of China) has given rise to a pandemic spread of virus, more than 240 million incidences and a death toll larger than 5 million people. COVID‐19 has set off large efforts in research, therapy and patient care, as well as public and private debates in every imaginable form. A number of scientists used the publication platforms provided by the Federation of the European Biochemical Societies (FEBS) to present their research data, reviews, opinions and other contributions relating to COVID‐19 and severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Here, I highlight the recent COVID‐19 papers which have been published and collected in a Virtual Issue in FEBS Letters, and discuss their implications towards understanding the molecular, biochemical and cellular mechanisms of SARS‐CoV‐2 infections, vaccine development and antiviral discovery strategies.
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Affiliation(s)
- Urs F Greber
- Department of Molecular Life Sciences, University of Zürich, Switzerland
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15
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Abstract
Cell-to-cell variability of infection has long been known, yet it has remained one of the least understood phenomena in infection research. It impacts on disease onset and development, yet only recently underlying mechanisms have been studied in clonal cell cultures by single-virion immunofluorescence microscopy and flow cytometry. In this review, we showcase how single-cell RNA sequencing (scRNA-seq), single-molecule RNA-fluorescence in situ hybridization (FISH), and copper(I)-catalyzed azide-alkyne cycloaddition (click) with alkynyl-tagged viral genomes dissect infection variability in human and mouse cells. We show how the combined use of scRNA-FISH and click-chemistry reveals highly variable onsets of adenoviral gene expression, and how single live cell plaques reveal lytic and nonlytic adenovirus transmissions. The review highlights how scRNA-seq profiling and scRNA-FISH of coxsackie, influenza, dengue, zika, and herpes simplex virus infections uncover transcriptional variability, and how the host interferon response tunes influenza and sendai virus infections. We introduce the concept of "cell state" in infection variability, and conclude with advances by single-cell simultaneous measurements of chromatin accessibility and mRNA counts at high-throughput. Such technology will further dissect the sequence of events in virus infection and pathology, and better characterize the genetic and genomic stability of viruses, cell autonomous innate immune responses, and mechanisms of tissue injury.
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Affiliation(s)
- Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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16
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Höller C, Schnoering G, Eghlidi H, Suomalainen M, Greber UF, Poulikakos D. On-chip transporting arresting and characterizing individual nano-objects in biological ionic liquids. Sci Adv 2021; 7:7/27/eabd8758. [PMID: 34215575 DOI: 10.1126/sciadv.abd8758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
Understanding and controlling the individual behavior of nanoscopic matter in liquids, the environment in which many such entities are functioning, is both inherently challenging and important to many natural and man-made applications. Here, we transport individual nano-objects, from an assembly in a biological ionic solution, through a nanochannel network and confine them in electrokinetic nanovalves, created by the collaborative effect of an applied ac electric field and a rationally engineered nanotopography, locally amplifying this field. The motion of so-confined fluorescent nano-objects is tracked, and its kinetics provides important information, enabling the determination of their particle diffusion coefficient, hydrodynamic radius, and electrical conductivity, which are elucidated for artificial polystyrene nanospheres and subsequently for sub-100-nm conjugated polymer nanoparticles and adenoviruses. The on-chip, individual nano-object resolution method presented here is a powerful approach to aid research and development in broad application areas such as medicine, chemistry, and biology.
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Affiliation(s)
- Christian Höller
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Sonneggstrasse 3, Zurich, Switzerland
| | - Gabriel Schnoering
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Sonneggstrasse 3, Zurich, Switzerland
| | - Hadi Eghlidi
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Sonneggstrasse 3, Zurich, Switzerland
| | - Maarit Suomalainen
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Dimos Poulikakos
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Sonneggstrasse 3, Zurich, Switzerland.
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17
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Andriasyan V, Yakimovich A, Petkidis A, Georgi F, Witte R, Puntener D, Greber UF. Microscopy deep learning predicts virus infections and reveals mechanics of lytic-infected cells. iScience 2021; 24:102543. [PMID: 34151222 PMCID: PMC8192562 DOI: 10.1016/j.isci.2021.102543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/07/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Imaging across scales reveals disease mechanisms in organisms, tissues, and cells. Yet, particular infection phenotypes, such as virus-induced cell lysis, have remained difficult to study. Here, we developed imaging modalities and deep learning procedures to identify herpesvirus and adenovirus (AdV) infected cells without virus-specific stainings. Fluorescence microscopy of vital DNA-dyes and live-cell imaging revealed learnable virus-specific nuclear patterns transferable to related viruses of the same family. Deep learning predicted two major AdV infection outcomes, non-lytic (nonspreading) and lytic (spreading) infections, up to about 20 hr prior to cell lysis. Using these predictive algorithms, lytic and non-lytic nuclei had the same levels of green fluorescent protein (GFP)-tagged virion proteins but lytic nuclei enriched the virion proteins faster, and collapsed more extensively upon laser-rupture than non-lytic nuclei, revealing impaired mechanical properties of lytic nuclei. Our algorithms may be used to infer infection phenotypes of emerging viruses, enhance single cell biology, and facilitate differential diagnosis of non-lytic and lytic infections. Artificial intelligence identifies HSV- and AdV-infected cells without specific probes. Imaging lytic-infected cells reveals nuclear envelope rupture and AdV dissemination. Live cell imaging and neural networks presciently pinpoint lytic-infected cells. Lytic-infected cell nuclei have mechanical properties distinct from non-lytic nuclei.
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Affiliation(s)
- Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Artur Yakimovich
- Department of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland.,University College London, London WC1E 6BT, UK.,Artificial Intelligence for Life Sciences CIC, London N8 7FJ, UK
| | - Anthony Petkidis
- Department of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Robert Witte
- Department of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
| | - Daniel Puntener
- Department of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland.,Roche Diagnostics International Ltd, Rotkreuz 6343, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zürich, Zürich 8057, Switzerland
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18
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Prasad V, Greber UF. The endoplasmic reticulum unfolded protein response - homeostasis, cell death and evolution in virus infections. FEMS Microbiol Rev 2021; 45:6188392. [PMID: 33765123 PMCID: PMC8498563 DOI: 10.1093/femsre/fuab016] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023] Open
Abstract
Viruses elicit cell and organismic stress, and offset homeostasis. They trigger intrinsic, innate and adaptive immune responses, which limit infection. Viruses restore homeostasis by harnessing evolutionary conserved stress responses, such as the endoplasmic reticulum (ER) unfolded protein response (UPRER). The canonical UPRER restores homeostasis based on a cell-autonomous signalling network modulating transcriptional and translational output. The UPRER remedies cell damage, but upon severe and chronic stress leads to cell death. Signals from the UPRER flow along three branches with distinct stress sensors, the inositol requiring enzyme (Ire) 1, protein kinase R (PKR)-like ER kinase (PERK), and the activating transcription factor 6 (ATF6). This review shows how both enveloped and non-enveloped viruses use the UPRER to control cell stress and metabolic pathways, and thereby enhance infection and progeny formation, or undergo cell death. We highlight how the Ire1 axis bypasses apoptosis, boosts viral transcription and maintains dormant viral genomes during latency and persistence periods concurrent with long term survival of infected cells. These considerations open new options for oncolytic virus therapies against cancer cells where the UPRER is frequently upregulated. We conclude with a discussion of the evolutionary impact that viruses, in particular retroviruses, and anti-viral defense has on the UPRER.
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Affiliation(s)
- Vibhu Prasad
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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19
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Brücher D, Kirchhammer N, Smith SN, Schumacher J, Schumacher N, Kolibius J, Freitag PC, Schmid M, Weiss F, Keller C, Grove M, Greber UF, Zippelius A, Plückthun A. iMATCH: an integrated modular assembly system for therapeutic combination high-capacity adenovirus gene therapy. Mol Ther Methods Clin Dev 2021; 20:572-586. [PMID: 33665227 PMCID: PMC7890373 DOI: 10.1016/j.omtm.2021.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/14/2021] [Indexed: 12/11/2022]
Abstract
Adenovirus-mediated combination gene therapies have shown promising results in vaccination or treating malignant and genetic diseases. Nevertheless, an efficient system for the rapid assembly and incorporation of therapeutic genes into high-capacity adenoviral vectors (HCAdVs) is still missing. In this study, we developed the iMATCH (integrated modular assembly for therapeutic combination HCAdVs) platform, which enables the generation and production of HCAdVs encoding therapeutic combinations in high quantity and purity within 3 weeks. Our modular cloning system facilitates the efficient combination of up to four expression cassettes and the rapid integration into HCAdV genomes with defined sizes. Helper viruses (HVs) and purification protocols were optimized to produce HCAdVs with distinct capsid modifications and unprecedented purity (0.1 ppm HVs). The constitution of HCAdVs, with adapters for targeting and a shield of trimerized single-chain variable fragment (scFv) for reduced liver clearance, mediated cell- and organ-specific targeting of HCAdVs. As proof of concept, we show that a single HCAdV encoding an anti PD-1 antibody, interleukin (IL)-12, and IL-2 produced all proteins, and it led to tumor regression and prolonged survival in tumor models, comparable to a mixture of single payload HCAdVs in vitro and in vivo. Therefore, the iMATCH system provides a versatile platform for the generation of high-capacity gene therapy vectors with a high potential for clinical development.
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Affiliation(s)
- Dominik Brücher
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Nicole Kirchhammer
- Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland
| | - Sheena N. Smith
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jatina Schumacher
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Nina Schumacher
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jonas Kolibius
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Patrick C. Freitag
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Markus Schmid
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Fabian Weiss
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Pharmacology, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland
| | - Corina Keller
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Melanie Grove
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Alfred Zippelius
- Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031 Basel, Switzerland
- Medical Oncology, University Hospital Basel, 4031 Basel, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Corresponding author: Andreas Plückthun, Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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20
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Marin-Gonzalez A, Aicart-Ramos C, Marin-Baquero M, Martín-González A, Suomalainen M, Kannan A, Vilhena JG, Greber UF, Moreno-Herrero F, Pérez R. Double-stranded RNA bending by AU-tract sequences. Nucleic Acids Res 2021; 48:12917-12928. [PMID: 33245767 PMCID: PMC7736806 DOI: 10.1093/nar/gkaa1128] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 10/08/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
Sequence-dependent structural deformations of the DNA double helix (dsDNA) have been extensively studied, where adenine tracts (A-tracts) provide a striking example for global bending in the molecule. However, in contrast to dsDNA, sequence-dependent structural features of dsRNA have received little attention. In this work, we demonstrate that the nucleotide sequence can induce a bend in a canonical Watson-Crick base-paired dsRNA helix. Using all-atom molecular dynamics simulations, we identified a sequence motif consisting of alternating adenines and uracils, or AU-tracts, that strongly bend the RNA double-helix. This finding was experimentally validated using atomic force microscopy imaging of dsRNA molecules designed to display macroscopic curvature via repetitions of phased AU-tract motifs. At the atomic level, this novel phenomenon originates from a localized compression of the dsRNA major groove and a large propeller twist at the position of the AU-tract. Moreover, the magnitude of the bending can be modulated by changing the length of the AU-tract. Altogether, our results demonstrate the possibility of modifying the dsRNA curvature by means of its nucleotide sequence, which may be exploited in the emerging field of RNA nanotechnology and might also constitute a natural mechanism for proteins to achieve recognition of specific dsRNA sequences.
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Affiliation(s)
- Alberto Marin-Gonzalez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Mikel Marin-Baquero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Alejandro Martín-González
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Abhilash Kannan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - J G Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland.,Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.,IFIMAC - Condensed Matter Physics Center, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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21
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Daly JL, Simonetti B, Klein K, Chen KE, Williamson MK, Antón-Plágaro C, Shoemark DK, Simón-Gracia L, Bauer M, Hollandi R, Greber UF, Horvath P, Sessions RB, Helenius A, Hiscox JA, Teesalu T, Matthews DA, Davidson AD, Collins BM, Cullen PJ, Yamauchi Y. Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science 2020; 370:861-865. [PMID: 33082294 DOI: 10.1101/2020.06.05.134114] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/12/2020] [Indexed: 05/20/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), uses the viral spike (S) protein for host cell attachment and entry. The host protease furin cleaves the full-length precursor S glycoprotein into two associated polypeptides: S1 and S2. Cleavage of S generates a polybasic Arg-Arg-Ala-Arg carboxyl-terminal sequence on S1, which conforms to a C-end rule (CendR) motif that binds to cell surface neuropilin-1 (NRP1) and NRP2 receptors. We used x-ray crystallography and biochemical approaches to show that the S1 CendR motif directly bound NRP1. Blocking this interaction by RNA interference or selective inhibitors reduced SARS-CoV-2 entry and infectivity in cell culture. NRP1 thus serves as a host factor for SARS-CoV-2 infection and may potentially provide a therapeutic target for COVID-19.
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Affiliation(s)
- James L Daly
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Boris Simonetti
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.
| | - Katja Klein
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Kai-En Chen
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Carlos Antón-Plágaro
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Deborah K Shoemark
- School of Biochemistry and BrisSynBio Centre, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Lorena Simón-Gracia
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Reka Hollandi
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), Szeged, Hungary
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), Szeged, Hungary
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Richard B Sessions
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Ari Helenius
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Singapore Immunology Network, Agency for Science, Technology, and Research, 138648, Singapore
| | - Tambet Teesalu
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - David A Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Brett M Collins
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Peter J Cullen
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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22
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Suomalainen M, Prasad V, Kannan A, Greber UF. Cell-to-cell and genome-to-genome variability of adenovirus transcription tuned by the cell cycle. J Cell Sci 2020; 134:jcs252544. [PMID: 32917739 DOI: 10.1242/jcs.252544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/27/2020] [Indexed: 12/11/2022] Open
Abstract
In clonal cultures, not all cells are equally susceptible to virus infection, and the mechanisms underlying this are poorly understood. Here, we developed image-based single-cell measurements to scrutinize the heterogeneity of adenovirus (AdV) infection. AdV delivers, transcribes and replicates a linear double-stranded DNA genome in the nucleus. We measured the abundance of viral transcripts using single-molecule RNA fluorescence in situ hybridization (FISH) and the incoming 5-ethynyl-2'-deoxycytidine (EdC)-tagged viral genomes using a copper(I)-catalyzed azide-alkyne cycloaddition (click) reaction. Surprisingly, expression of the immediate early gene E1A only moderately correlated with the number of viral genomes in the cell nucleus. Intranuclear genome-to-genome heterogeneity was found at the level of viral transcription and, in accordance, individual genomes exhibited heterogeneous replication activity. By analyzing the cell cycle state, we found that G1 cells exhibited the highest E1A gene expression and displayed increased correlation between E1A gene expression and viral genome copy numbers. The combined image-based single-molecule procedures described here are ideally suited to explore the cell-to-cell variability in viral gene expression in a range of different settings, including the innate immune response.
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Affiliation(s)
- Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Vibhu Prasad
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Abhilash Kannan
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
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23
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Daly JL, Simonetti B, Klein K, Chen KE, Williamson MK, Antón-Plágaro C, Shoemark DK, Simón-Gracia L, Bauer M, Hollandi R, Greber UF, Horvath P, Sessions RB, Helenius A, Hiscox JA, Teesalu T, Matthews DA, Davidson AD, Collins BM, Cullen PJ, Yamauchi Y. Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science 2020; 370:861-865. [PMID: 33082294 DOI: 10.1126/science.abd3072] [Citation(s) in RCA: 845] [Impact Index Per Article: 211.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), uses the viral spike (S) protein for host cell attachment and entry. The host protease furin cleaves the full-length precursor S glycoprotein into two associated polypeptides: S1 and S2. Cleavage of S generates a polybasic Arg-Arg-Ala-Arg carboxyl-terminal sequence on S1, which conforms to a C-end rule (CendR) motif that binds to cell surface neuropilin-1 (NRP1) and NRP2 receptors. We used x-ray crystallography and biochemical approaches to show that the S1 CendR motif directly bound NRP1. Blocking this interaction by RNA interference or selective inhibitors reduced SARS-CoV-2 entry and infectivity in cell culture. NRP1 thus serves as a host factor for SARS-CoV-2 infection and may potentially provide a therapeutic target for COVID-19.
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Affiliation(s)
- James L Daly
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Boris Simonetti
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.
| | - Katja Klein
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Kai-En Chen
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Carlos Antón-Plágaro
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Deborah K Shoemark
- School of Biochemistry and BrisSynBio Centre, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Lorena Simón-Gracia
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Reka Hollandi
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), Szeged, Hungary
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Centre (BRC), Szeged, Hungary.,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Richard B Sessions
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Ari Helenius
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.,Singapore Immunology Network, Agency for Science, Technology, and Research, 138648, Singapore
| | - Tambet Teesalu
- Laboratory of Cancer Biology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - David A Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Brett M Collins
- Institute for Molecular Bioscience, the University of Queensland, St. Lucia, QLD 4072, Australia
| | - Peter J Cullen
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK. .,Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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24
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Bauer M, Flatt JW, Seiler D, Cardel B, Emmenlauer M, Boucke K, Suomalainen M, Hemmi S, Greber UF. The E3 Ubiquitin Ligase Mind Bomb 1 Controls Adenovirus Genome Release at the Nuclear Pore Complex. Cell Rep 2020; 29:3785-3795.e8. [PMID: 31851912 DOI: 10.1016/j.celrep.2019.11.064] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/15/2019] [Accepted: 11/14/2019] [Indexed: 01/06/2023] Open
Abstract
Adenoviruses (AdVs) cause respiratory, ocular, and gastrointestinal tract infection and inflammation in immunocompetent people and life-threatening disease upon immunosuppression. AdV vectors are widely used in gene therapy and vaccination. Incoming particles attach to nuclear pore complexes (NPCs) of post-mitotic cells, then rupture and deliver viral DNA (vDNA) to the nucleus or misdeliver to the cytosol. Our genome-wide RNAi screen in AdV-infected cells identified the RING-type E3 ubiquitin ligase Mind bomb 1 (Mib1) as a proviral host factor for AdV infection. Mib1 is implicated in Notch-Delta signaling, ciliary biogenesis, and RNA innate immunity. Mib1 depletion arrested incoming AdVs at NPCs. Induced expression of full-length but not ligase-defective Mib1 in knockout cells triggered vDNA uncoating from NPC-tethered virions, nuclear import, misdelivery of vDNA, and vDNA expression. Mib1 is an essential host factor for AdV uncoating in human cells, and it provides a new concept for licensing virion DNA delivery through the NPC.
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Affiliation(s)
- Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, ETH and University of Zurich, 8057 Zurich, Switzerland
| | - Justin W Flatt
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland; Department of Biosciences, University of Helsinki, 00790 Helsinki, Finland
| | - Daria Seiler
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Bettina Cardel
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | | | - Karin Boucke
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Silvio Hemmi
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.
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25
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Georgi F, Andriasyan V, Witte R, Murer L, Hemmi S, Yu L, Grove M, Meili N, Kuttler F, Yakimovich A, Turcatti G, Greber UF. The FDA-Approved Drug Nelfinavir Inhibits Lytic Cell-Free but Not Cell-Associated Nonlytic Transmission of Human Adenovirus. Antimicrob Agents Chemother 2020; 64:e01002-20. [PMID: 32601166 PMCID: PMC7449217 DOI: 10.1128/aac.01002-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
Adenoviruses (AdVs) are prevalent and give rise to chronic and recurrent disease. Human AdV (HAdV) species B and C, such as HAdV-C2, -C5, and -B14, cause respiratory disease and constitute a health threat for immunocompromised individuals. HAdV-Cs are well known for lysing cells owing to the E3 CR1-β-encoded adenovirus death protein (ADP). We previously reported a high-throughput image-based screening framework and identified an inhibitor of HAdV-C2 multiround infection, nelfinavir mesylate. Nelfinavir is the active ingredient of Viracept, an FDA-approved inhibitor of human immunodeficiency virus (HIV) aspartyl protease that is used to treat AIDS. It is not effective against single-round HAdV infections. Here, we show that nelfinavir inhibits lytic cell-free transmission of HAdV, indicated by the suppression of comet-shaped infection foci in cell culture. Comet-shaped foci occur upon convection-based transmission of cell-free viral particles from an infected cell to neighboring uninfected cells. HAdV lacking ADP was insensitive to nelfinavir but gave rise to comet-shaped foci, indicating that ADP enhances but is not required for cell lysis. This was supported by the notion that HAdV-B14 and -B14p1 lacking ADP were highly sensitive to nelfinavir, although HAdV-A31, -B3, -B7, -B11, -B16, -B21, -D8, -D30, and -D37 were less sensitive. Conspicuously, nelfinavir uncovered slow-growing round HAdV-C2 foci, independent of neutralizing antibodies in the medium, indicative of nonlytic cell-to-cell transmission. Our study demonstrates the repurposing potential of nelfinavir with postexposure efficacy against different HAdVs and describes an alternative nonlytic cell-to-cell transmission mode of HAdV.
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Affiliation(s)
- Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Luca Murer
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Silvio Hemmi
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Lisa Yu
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Melanie Grove
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Nicole Meili
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Fabien Kuttler
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Artur Yakimovich
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Artificial Intelligence for Life Sciences CIC, London, United Kingdom
| | - Gerardo Turcatti
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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26
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Georgi F, Kuttler F, Murer L, Andriasyan V, Witte R, Yakimovich A, Turcatti G, Greber UF. A high-content image-based drug screen of clinical compounds against cell transmission of adenovirus. Sci Data 2020; 7:265. [PMID: 32788590 PMCID: PMC7423605 DOI: 10.1038/s41597-020-00604-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/16/2020] [Indexed: 12/21/2022] Open
Abstract
Human adenoviruses (HAdVs) are fatal to immuno-suppressed individuals, but no effective anti-HAdV therapy is available. Here, we present a novel image-based high-throughput screening (HTS) platform, which scores the full viral replication cycle from virus entry to dissemination of progeny and second-round infections. We analysed 1,280 small molecular weight compounds of the Prestwick Chemical Library (PCL) for interference with HAdV-C2 infection in a quadruplicate, blinded format, and performed robust image analyses and hit filtering. We present the entire set of the screening data including all images, image analyses and data processing pipelines. The data are made available at the Image Data Resource (IDR, idr0081). Our screen identified Nelfinavir mesylate as an inhibitor of HAdV-C2 multi-round plaque formation, but not single round infection. Nelfinavir has been FDA-approved for anti-retroviral therapy in humans. Our results underscore the power of image-based full cycle infection assays in identifying viral inhibitors with clinical potential.
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Affiliation(s)
- Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse, 190, 8057, Zurich, Switzerland
| | - Fabien Kuttler
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 15, Lausanne, 1015, Switzerland
| | - Luca Murer
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse, 190, 8057, Zurich, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse, 190, 8057, Zurich, Switzerland
| | - Robert Witte
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse, 190, 8057, Zurich, Switzerland
| | - Artur Yakimovich
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St, London, WC1E 6BT, United Kingdom
- Artificial Intelligence for Life Sciences CIC, 40 Gowers walk, London, E1 8BH, United Kingdom
| | - Gerardo Turcatti
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 15, Lausanne, 1015, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse, 190, 8057, Zurich, Switzerland.
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27
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Georgi F, Greber UF. The Adenovirus Death Protein - a small membrane protein controls cell lysis and disease. FEBS Lett 2020; 594:1861-1878. [PMID: 32472693 DOI: 10.1002/1873-3468.13848] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/16/2022]
Abstract
Human adenoviruses (HAdVs) cause widespread acute and persistent infections. Infections are usually mild and controlled by humoral and cell-based immunity. Reactivation of persistently infected immune cells can lead to a life-threatening disease in immunocompromised individuals, especially children and transplant recipients. To date, no effective therapy or vaccine against HAdV disease is available to the public. HAdV-C2 and C5 are the best-studied of more than 100 HAdV types. They persist in infected cells and release their progeny by host cell lysis to neighbouring cells and fluids, a process facilitated by the adenovirus death protein (ADP). ADP consists of about 100 amino acids and harbours a single membrane-spanning domain. It undergoes post-translational processing in endoplasmic reticulum and Golgi compartments, before localizing to the inner nuclear membrane. Here, we discuss the current knowledge on how ADP induces membrane rupture. Membrane rupture is essential for both progression of disease and efficacy of therapeutic viruses in clinical applications, in particular oncolytic therapy.
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Affiliation(s)
- Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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28
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Abstract
Both well-known and emerging viruses increasingly affect humans and cause disease, sometimes with devastating impact on society. The viruses present in the biosphere are the top predators in the life chain, virtually without enemies, except perhaps the immune system, and harsh environmental physicochemical conditions restricting their dissemination. We know a lot about viruses, but do we know enough? This series of reviews is dedicated to adenoviruses (AdVs), a family of nonenveloped DNA viruses occurring in vertebrates, including humans. AdVs have been the focus of intense research for more than 67 years. Besides causing disease, they have immensely contributed to the advance of life sciences and medicine over the past decades. Recently, AdVs have been widely used as vehicles in gene therapy and vaccination. They continue to provide fundamental insights into virus-host interactions in cells, tissues and organisms, as well as systems and metabolic networks. This special issue of FEBS Letters presents a unique collection of 23 state-of-the-art review articles by leading adenovirologists. In this prelude, I present the chapters, which provide a solid basis for further exploring the rich heritage in adenovirus molecular cell biology, structural biology, genetics, immunology, gene therapy and epidemiology. I conclude with an essential discussion of six blind spots in adenovirology.
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Affiliation(s)
- Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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29
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Lang J, Bohn P, Bhat H, Jastrow H, Walkenfort B, Cansiz F, Fink J, Bauer M, Olszewski D, Ramos-Nascimento A, Duhan V, Friedrich SK, Becker KA, Krawczyk A, Edwards MJ, Burchert A, Huber M, Friebus-Kardash J, Göthert JR, Hardt C, Probst HC, Schumacher F, Köhrer K, Kleuser B, Babiychuk EB, Sodeik B, Seibel J, Greber UF, Lang PA, Gulbins E, Lang KS. Acid ceramidase of macrophages traps herpes simplex virus in multivesicular bodies and protects from severe disease. Nat Commun 2020; 11:1338. [PMID: 32165633 PMCID: PMC7067866 DOI: 10.1038/s41467-020-15072-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/17/2020] [Indexed: 12/20/2022] Open
Abstract
Macrophages have important protective functions during infection with herpes simplex virus type 1 (HSV-1). However, molecular mechanisms that restrict viral propagation and protect from severe disease are unclear. Here we show that macrophages take up HSV-1 via endocytosis and transport the virions into multivesicular bodies (MVBs). In MVBs, acid ceramidase (aCDase) converts ceramide into sphingosine and increases the formation of sphingosine-rich intraluminal vesicles (ILVs). Once HSV-1 particles reach MVBs, sphingosine-rich ILVs bind to HSV-1 particles, which restricts fusion with the limiting endosomal membrane and prevents cellular infection. Lack of aCDase in macrophage cultures or in Asah1-/- mice results in replication of HSV-1 and Asah1-/- mice die soon after systemic or intravaginal inoculation. The treatment of macrophages with sphingosine enhancing compounds blocks HSV-1 propagation, suggesting a therapeutic potential of this pathway. In conclusion, aCDase loads ILVs with sphingosine, which prevents HSV-1 capsids from penetrating into the cytosol.
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Affiliation(s)
- Judith Lang
- Institute of Immunology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Patrick Bohn
- Institute of Immunology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Hilal Bhat
- Institute of Immunology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Holger Jastrow
- Institute of Anatomy, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany.,Institut for Experimental Immunology and Imaging, Imaging Center Essen, Electron Microscopy Unit, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Bernd Walkenfort
- Institut for Experimental Immunology and Imaging, Imaging Center Essen, Electron Microscopy Unit, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Feyza Cansiz
- Institute of Immunology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Julian Fink
- Institute of Organic Chemistry, Julius-Maximilians University of Würzburg, Am Hubland, Würzburg, D-97074, Germany
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstr. 190, CH-8057, Zurich, Switzerland
| | - Dominik Olszewski
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstr. 190, CH-8057, Zurich, Switzerland
| | - Ana Ramos-Nascimento
- Institute of Virology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, D-30625, Germany
| | - Vikas Duhan
- Institute of Immunology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Sarah-Kim Friedrich
- Institute of Immunology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Katrin Anne Becker
- Institute of Molecular Biology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Adalbert Krawczyk
- Institute for Virology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany.,Department of Infectious Diseases, University Hospital of Essen, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Michael J Edwards
- Department of Surgery, University of Cincinnati, Cincinnati, OH, USA
| | - Andreas Burchert
- Department of Hematology, Oncology and Immunology, University Hospital Giessen and Marburg, Campus Marburg, Baldingerstr., Marburg, D-35043, Germany
| | - Magdalena Huber
- Institute of Medical Microbiology and Hospital Hygiene, Philipps-University Marburg, Hans-Meerwein Str. 2, Marburg, D-35043, Germany
| | - Justa Friebus-Kardash
- Institute of Immunology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Joachim R Göthert
- Department of Hematology, West German Cancer Center, University Hospital of Essen, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Cornelia Hardt
- Institute of Immunology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany
| | - Hans Christian Probst
- Institute of Immunology, University Medical Center Mainz, Langenbeckstr. 1, Mainz, D-55131, Germany
| | - Fabian Schumacher
- Institute of Molecular Biology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany.,Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert Allee 114-116, Nuthetal, D-14558, Germany
| | - Karl Köhrer
- Biological and Medical Research Center (BMFZ), Heinrich-Heine-University, Universitätsstr. 1, Düsseldorf, D-40225, Germany
| | - Burkhard Kleuser
- Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert Allee 114-116, Nuthetal, D-14558, Germany
| | - Eduard B Babiychuk
- Institute of Anatomy, University of Bern, Baltzerstr. 4, CH-3012, Bern, Switzerland
| | - Beate Sodeik
- Institute of Virology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, D-30625, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, D-30625, Germany
| | - Jürgen Seibel
- Institute of Organic Chemistry, Julius-Maximilians University of Würzburg, Am Hubland, Würzburg, D-97074, Germany
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstr. 190, CH-8057, Zurich, Switzerland
| | - Philipp A Lang
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, D-40225, Germany
| | - Erich Gulbins
- Institute of Molecular Biology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany.,Department of Surgery, University of Cincinnati, Cincinnati, OH, USA
| | - Karl S Lang
- Institute of Immunology, University of Duisburg-Essen, Hufelandstr. 55, Essen, D-45147, Germany.
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Abstract
Virus particles, 'virions', range in size from nano-scale to micro-scale. They have many different shapes and are composed of proteins, sugars, nucleic acids, lipids, water and solutes. Virions are autonomous entities and affect all forms of life in a parasitic relationship. They infect prokaryotic and eukaryotic cells. The physical properties of virions are tuned to the way they interact with cells. When virions interact with cells, they gain huge complexity and give rise to an infected cell, also known as 'virus'. Virion-cell interactions entail the processes of entry, replication and assembly, as well as egress from the infected cell. Collectively, these steps can result in progeny virions, which is a productive infection, or in silencing of the virus, an abortive or latent infection. This book explores facets of the physical nature of virions and viruses and the impact of mechanical properties on infection processes at the cellular and subcellular levels.
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Affiliation(s)
- Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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31
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Daga N, Eicher S, Kannan A, Casanova A, Low SH, Kreibich S, Andritschke D, Emmenlauer M, Jenkins JL, Hardt WD, Greber UF, Dehio C, von Mering C. Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition. Nucleic Acids Res 2019; 46:9309-9320. [PMID: 30215772 PMCID: PMC6182159 DOI: 10.1093/nar/gky798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 09/10/2018] [Indexed: 01/17/2023] Open
Abstract
Perturbation of gene expression by means of synthetic small interfering RNAs (siRNAs) is a powerful way to uncover gene function. However, siRNA technology suffers from sequence-specific off-target effects and from limitations in knock-down efficiency. In this study, we assess a further problem: unintended effects of siRNA transfections on cellular fitness/proliferation. We show that the nucleotide compositions of siRNAs at specific positions have reproducible growth-restricting effects on mammalian cells in culture. This is likely distinct from hybridization-dependent off-target effects, since each nucleotide residue is seen to be acting independently and additively. The effect is robust and reproducible across different siRNA libraries and also across various cell lines, including human and mouse cells. Analyzing the growth inhibition patterns in correlation to the nucleotide sequence of the siRNAs allowed us to build a predictor that can estimate growth-restricting effects for any arbitrary siRNA sequence. Competition experiments with co-transfected siRNAs further suggest that the growth-restricting effects might be linked to an oversaturation of the cellular miRNA machinery, thus disrupting endogenous miRNA functions at large. We caution that competition between siRNA molecules could complicate the interpretation of double-knockdown or epistasis experiments, and potential interactions with endogenous miRNAs can be a factor when assaying cell growth or viability phenotypes.
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Affiliation(s)
- Neha Daga
- Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland.,Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | - Simone Eicher
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Abhilash Kannan
- Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | - Alain Casanova
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Shyan H Low
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Saskia Kreibich
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Daniel Andritschke
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | | | - Jeremy L Jenkins
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Christian von Mering
- Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland.,Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
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32
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Abstract
More than 80 different adenovirus (AdV) types infect humans through the respiratory, ocular, or gastrointestinal tracts. They cause acute clinical mani-festations or persist under humoral and cell-based immunity. Immuno-suppressed individuals are at risk of death from an AdV infection. Concepts about cell entry of AdV build on strong foundations from molecular and cellular biology-and increasingly physical virology. Here, we discuss how virions enter and deliver their genome into the nucleus of epithelial cells. This process breaks open the virion at distinct sites because the particle has nonisometric mechanical strength and reacts to specific host factors along the entry pathway. We further describe how macrophages and dendritic cells resist AdV infection yet enhance productive entry into polarized epithelial cells. A deep understanding of the viral mechanisms and cell biological and biophysical principles will continue to unravel how epithelial and antigen-presenting cells respond to AdVs and control inflammation and persistence in pathology and therapy.
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Affiliation(s)
- Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland;
| | - Justin W Flatt
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, 00790 Helsinki, Finland;
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33
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Greber UF. Correction to: Physical Virology. Advances in Experimental Medicine and Biology 2019. [DOI: 10.1007/978-3-030-14741-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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34
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Eberle P, Höller C, Müller P, Suomalainen M, Greber UF, Eghlidi H, Poulikakos D. Single entity resolution valving of nanoscopic species in liquids. Nat Nanotechnol 2018; 13:578-582. [PMID: 29784963 DOI: 10.1038/s41565-018-0150-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
Investigating biological and synthetic nanoscopic species in liquids, at the ultimate resolution of single entity, is important in diverse fields1-5. Progress has been made6-10, but significant barriers need to be overcome such as the need for intense fields, the lack of versatility in operating conditions and the limited functionality in solutions of high ionic strength for biological applications. Here, we demonstrate switchable electrokinetic nanovalving able to confine and guide single nano-objects, including macromolecules, with sizes down to around 10 nanometres, in a lab-on-chip environment. The nanovalves are based on spatiotemporal tailoring of the potential energy landscape of nano-objects using an electric field, modulated collaboratively by wall nanotopography and by embedded electrodes in a nanochannel system. We combine nanovalves to isolate single entities from an ensemble, and demonstrate their guiding, confining, releasing and sorting. We show on-demand motion control of single immunoglobulin G molecules, quantum dots, adenoviruses, lipid vesicles, dielectric and metallic particles, suspended in electrolytes with a broad range of ionic strengths, up to biological levels. Such systems can enable nanofluidic, large-scale integration and individual handling of multiple entities in applications ranging from single species characterization and screening to in situ chemical or biochemical synthesis in continuous on-chip processes.
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Affiliation(s)
- Patric Eberle
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Zurich, Switzerland
| | - Christian Höller
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Zurich, Switzerland
| | - Philipp Müller
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Zurich, Switzerland
| | - Maarit Suomalainen
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Hadi Eghlidi
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Zurich, Switzerland.
| | - Dimos Poulikakos
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Zurich, Switzerland.
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35
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Affiliation(s)
- Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. E-mail: .,Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69198 Heidelberg, Germany. E-mail:
| | - Ralf Bartenschlager
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. E-mail: .,Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69198 Heidelberg, Germany. E-mail:
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36
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Witte R, Andriasyan V, Georgi F, Yakimovich A, Greber UF. Concepts in Light Microscopy of Viruses. Viruses 2018; 10:E202. [PMID: 29670029 PMCID: PMC5923496 DOI: 10.3390/v10040202] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses threaten humans, livestock, and plants, and are difficult to combat. Imaging of viruses by light microscopy is key to uncover the nature of known and emerging viruses in the quest for finding new ways to treat viral disease and deepening the understanding of virus–host interactions. Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research.
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Affiliation(s)
- Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Artur Yakimovich
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St., London WC1E 6BT, UK.
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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37
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Stichling N, Suomalainen M, Flatt JW, Schmid M, Pacesa M, Hemmi S, Jungraithmayr W, Maler MD, Freudenberg MA, Plückthun A, May T, Köster M, Fejer G, Greber UF. Lung macrophage scavenger receptor SR-A6 (MARCO) is an adenovirus type-specific virus entry receptor. PLoS Pathog 2018. [PMID: 29522575 PMCID: PMC5862501 DOI: 10.1371/journal.ppat.1006914] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Macrophages are a diverse group of phagocytic cells acting in host protection against stress, injury, and pathogens. Here, we show that the scavenger receptor SR-A6 is an entry receptor for human adenoviruses in murine alveolar macrophage-like MPI cells, and important for production of type I interferon. Scavenger receptors contribute to the clearance of endogenous proteins, lipoproteins and pathogens. Knockout of SR-A6 in MPI cells, anti-SR-A6 antibody or the soluble extracellular SR-A6 domain reduced adenovirus type-C5 (HAdV-C5) binding and transduction. Expression of murine SR-A6, and to a lower extent human SR-A6 boosted virion binding to human cells and transduction. Virion clustering by soluble SR-A6 and proximity localization with SR-A6 on MPI cells suggested direct adenovirus interaction with SR-A6. Deletion of the negatively charged hypervariable region 1 (HVR1) of hexon reduced HAdV-C5 binding and transduction, implying that the viral ligand for SR-A6 is hexon. SR-A6 facilitated macrophage entry of HAdV-B35 and HAdV-D26, two important vectors for transduction of hematopoietic cells and human vaccination. The study highlights the importance of scavenger receptors in innate immunity against human viruses. Macrophages are a diverse group of phagocytic cells acting in host protection against stress, injury, and pathogens. They phenotypically and functionally adapt to their local environment, for example, peritoneal macrophages are distinct from brain-resident microglia, from liver-resident Kupffer cells or lung macrophages in the lung. Airway macrophages are among the first cells to encounter human respiratory viruses, such as adenoviruses. They release pro-inflammatory cytokines, kill pathogens, present antigens, and restore tissues. Yet, interactions of viruses with lung macrophages are poorly understood, and it is unclear, how they lead to infection or virus clearance. Here we identified the murine scavenger receptor SR-A6 as a receptor for a subset of human adenoviruses on alveolar macrophage-like cells, so-called MPI cells. Scavenger receptors comprise a large family of trans-membrane proteins, and contribute to the clearance of endogenous proteins, lipoproteins and pathogens. In a series of robust experimentation, we show that adenoviruses use SR-A6 as an entry receptor for infection of MPI cells, and production of type I interferon. MPI cells are non-transformed, self-renewing macrophages derived from fetal murine liver, and closely resemble adult alveolar macrophages. The results demonstrate that SR-A6 binds virions on the surface of alveolar macrophage-like cells, and leads to infection.
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MESH Headings
- Adenoviridae Infections/immunology
- Adenoviridae Infections/metabolism
- Adenoviridae Infections/virology
- Adenoviruses, Human/immunology
- Animals
- Humans
- Immunity, Innate
- Lung/immunology
- Lung/metabolism
- Lung/virology
- Macrophages/immunology
- Macrophages/metabolism
- Macrophages/virology
- Macrophages, Alveolar/immunology
- Macrophages, Alveolar/metabolism
- Macrophages, Alveolar/virology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Knockout
- Protein Binding
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, Immunologic/physiology
- Virus Internalization
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Affiliation(s)
- Nicole Stichling
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Molecular Life Sciences Graduate School, ETH and University of Zurich, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Justin W. Flatt
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Markus Schmid
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Martin Pacesa
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Silvio Hemmi
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Wolfgang Jungraithmayr
- University Hospital Zurich, Institute of Thorax Surgery, Zurich, Switzerland
- present address: Department of Thoracic Surgery, Medical University Brandenburg, Neuruppin, Germany
| | - Mareike D. Maler
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Allergy Research Group, Department of Dermatology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Marina A. Freudenberg
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität, Freiburg, Germany
- Department of Pneumology, Medical Center–University of Freiburg and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Tobias May
- Inscreenex GmbH, Inhoffenstr. Brunswick, Germany
| | - Mario Köster
- Helmholtz-Zentrum für Infektionsforschung GmbH, Braunschweig, Germany
| | - György Fejer
- School of Biomedical and Healthcare Sciences, Peninsula Schools of Medicine and Dentistry, University of Plymouth, Plymouth, United Kingdom
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- * E-mail:
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38
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Lötzerich M, Roulin PS, Boucke K, Witte R, Georgiev O, Greber UF. Rhinovirus 3C protease suppresses apoptosis and triggers caspase-independent cell death. Cell Death Dis 2018; 9:272. [PMID: 29449668 PMCID: PMC5833640 DOI: 10.1038/s41419-018-0306-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/29/2017] [Accepted: 01/04/2018] [Indexed: 12/14/2022]
Abstract
Apoptosis and programmed necrosis (necroptosis) determine cell fate, and antagonize infection. Execution of these complementary death pathways involves the formation of receptor-interacting protein kinase 1 (RIPK1) containing complexes. RIPK1 binds to adaptor proteins, such as TRIF (Toll-IL-1 receptor-domain-containing-adaptor-inducing interferon-beta factor), FADD (Fas-associated-protein with death domain), NEMO (NF-κB regulatory subunit IKKγ), SQSTM1 (sequestosome 1/p62), or RIPK3 (receptor-interacting protein kinase 3), which are involved in RNA sensing, NF-κB signaling, autophagosome formation, apoptosis, and necroptosis. We report that a range of rhinoviruses impair apoptosis and necroptosis in epithelial cells late in infection. Unlike the double-strand (ds) RNA mimetic poly I:C (polyinosinic:polycytidylic acid), the exposure of dsRNA to toll-like receptor 3 (TLR3) in rhinovirus-infected cells did not lead to apoptosis execution. Accordingly, necroptosis and the production of ROS (reactive oxygen species) were not observed late in infection, when RIPK3 was absent. Instead, a virus-induced alternative necrotic cell death pathway proceeded, which led to membrane rupture, indicated by propidium iodide staining. The impairment of dsRNA-induced apoptosis late in infection was controlled by the viral 3C-protease (3Cpro), which disrupted RIPK1-TRIF/FADD /SQSTM1 immune-complexes. 3Cpro and 3C precursors were found to coimmuno-precipitate with RIPK1, cleaving the RIPK1 death-domain, and generating N-terminal RIPK1 fragments. The depletion of RIPK1 or chemical inhibition of its kinase at the N-terminus did not interfere with virus progeny formation or cell fate. The data show that rhinoviruses suppress apoptosis and necroptosis, and release progeny by an alternative cell death pathway, which is controlled by viral proteases modifying innate immune complexes.
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Affiliation(s)
- Mark Lötzerich
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Hussman Institute for Autism, 801 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Pascal S Roulin
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Karin Boucke
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Oleg Georgiev
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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39
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Schmid M, Ernst P, Honegger A, Suomalainen M, Zimmermann M, Braun L, Stauffer S, Thom C, Dreier B, Eibauer M, Kipar A, Vogel V, Greber UF, Medalia O, Plückthun A. Adenoviral vector with shield and adapter increases tumor specificity and escapes liver and immune control. Nat Commun 2018; 9:450. [PMID: 29386504 PMCID: PMC5792622 DOI: 10.1038/s41467-017-02707-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/20/2017] [Indexed: 01/16/2023] Open
Abstract
Most systemic viral gene therapies have been limited by sequestration and degradation of virions, innate and adaptive immunity, and silencing of therapeutic genes within the target cells. Here we engineer a high-affinity protein coat, shielding the most commonly used vector in clinical gene therapy, human adenovirus type 5. Using electron microscopy and crystallography we demonstrate a massive coverage of the virion surface through the hexon-shielding scFv fragment, trimerized to exploit the hexon symmetry and gain avidity. The shield reduces virion clearance in the liver. When the shielded particles are equipped with adaptor proteins, the virions deliver their payload genes into human cancer cells expressing HER2 or EGFR. The combination of shield and adapter also increases viral gene delivery to xenografted tumors in vivo, reduces liver off-targeting and immune neutralization. Our study highlights the power of protein engineering for viral vectors overcoming the challenges of local and systemic viral gene therapies. Viral gene therapy can be limited by the efficacy of virion sequestration, immune responses and the silencing of genetic payloads. Here the authors engineer an advenovirus protein coat which shields the virion from the immune system while targeting cancer cells.
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Affiliation(s)
- Markus Schmid
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Annemarie Honegger
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Science, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Martina Zimmermann
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Lukas Braun
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland
| | - Sarah Stauffer
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Cristian Thom
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Matthias Eibauer
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Anja Kipar
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, 8057, Zurich, Switzerland
| | - Viola Vogel
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Science, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland.,Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva, 84105, Israel
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland.
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40
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Pacesa M, Hendrickx R, Bieri M, Flatt JW, Greber UF, Hemmi S. Small-size recombinant adenoviral hexon protein fragments for the production of virus-type specific antibodies. Virol J 2017; 14:158. [PMID: 28821267 PMCID: PMC5563037 DOI: 10.1186/s12985-017-0822-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/08/2017] [Indexed: 12/30/2022] Open
Abstract
Background Adenoviruses are common pathogens infecting animals and humans. They are classified based on serology, or genome sequence information. These methods have limitations due to lengthy procedures or lack of infectivity data. Adenoviruses are easy to produce and amenable to genetic and biochemical modifications, which makes them a powerful tool for biological studies, and clinical gene-delivery and vaccine applications. Antibodies directed against adenoviral proteins are important diagnostic tools for virus identification in vivo and in vitro, and are used to elucidate infection mechanisms, often in combination with genomic sequencing and type specific information from hyper-variable regions of structural proteins. Results Here we describe a novel and readily useable method for cloning, expressing and purifying small fragments of hyper-variable regions 1-6 of the adenoviral hexon protein. We used these polypeptides as antigens for generating polyclonal rabbit antibodies against human adenovirus 3 (HAdV-B3), mouse adenovirus 1 (MAdV-1) and MAdV-2 hexon. In Western immunoblots with lysates from cells infected from thirteen human and three mouse viruses, these antibodies bound to homologous full-length hexon protein and revealed variable levels of cross-reactivity to heterologous hexons. Results from immuno-fluorescence and electron microscopy studies indicated that HAdV-B3 and MAdV-2 hexon antibodies recognized native forms of hexon. Conclusions The procedure described here can in principle be applied to any adenovirus for which genome sequence information is available. It provides a basis for generating novel type-specific tools in diagnostics and research, and extends beyond the commonly used anti-viral antibodies raised against purified viruses or subviral components. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0822-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Pacesa
- Institute of Molecular Life Sciences, University of Zurich, CH-8057, Zurich, Switzerland
| | - Rodinde Hendrickx
- Institute of Molecular Life Sciences, University of Zurich, CH-8057, Zurich, Switzerland.,Molecular Life Sciences Graduate School, Eidgenössische Technische Hochschule and University of Zurich, CH-8057, Zurich, Switzerland
| | - Manuela Bieri
- Institute of Molecular Life Sciences, University of Zurich, CH-8057, Zurich, Switzerland.,Molecular Life Sciences Graduate School, Eidgenössische Technische Hochschule and University of Zurich, CH-8057, Zurich, Switzerland
| | - Justin W Flatt
- Institute of Molecular Life Sciences, University of Zurich, CH-8057, Zurich, Switzerland
| | - Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, CH-8057, Zurich, Switzerland
| | - Silvio Hemmi
- Institute of Molecular Life Sciences, University of Zurich, CH-8057, Zurich, Switzerland.
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41
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Wang IH, Burckhardt CJ, Yakimovich A, Morf MK, Greber UF. The nuclear export factor CRM1 controls juxta-nuclear microtubule-dependent virus transport. J Cell Sci 2017; 130:2185-2195. [PMID: 28515232 DOI: 10.1242/jcs.203794] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/12/2017] [Indexed: 12/26/2022] Open
Abstract
Transport of large cargo through the cytoplasm requires motor proteins and polarized filaments. Viruses that replicate in the nucleus of post-mitotic cells use microtubules and the dynein-dynactin motor to traffic to the nuclear membrane and deliver their genome through nuclear pore complexes (NPCs) into the nucleus. How virus particles (virions) or cellular cargo are transferred from microtubules to the NPC is unknown. Here, we analyzed trafficking of incoming cytoplasmic adenoviruses by single-particle tracking and super-resolution microscopy. We provide evidence for a regulatory role of CRM1 (chromosome-region-maintenance-1; also known as XPO1, exportin-1) in juxta-nuclear microtubule-dependent adenovirus transport. Leptomycin B (LMB) abolishes nuclear targeting of adenovirus. It binds to CRM1, precludes CRM1-cargo binding and blocks signal-dependent nuclear export. LMB-inhibited CRM1 did not compete with adenovirus for binding to the nucleoporin Nup214 at the NPC. Instead, CRM1 inhibition selectively enhanced virion association with microtubules, and boosted virion motions on microtubules less than ∼2 µm from the nuclear membrane. The data show that the nucleus provides positional information for incoming virions to detach from microtubules, engage a slower microtubule-independent motility to the NPC and enhance infection.
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Affiliation(s)
- I-Hsuan Wang
- Department of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland
| | - Christoph J Burckhardt
- Department of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland
- Department of Bioinformatics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Artur Yakimovich
- Department of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland
| | - Matthias K Morf
- Department of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland
- Molecular Life Sciences Graduate School, ETH and University of Zürich, 8057 Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zürich, 8057 Zurich, Switzerland
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Abstract
Human adenoviruses (HAdVs) infect respiratory, gastrointestinal, and urinary tracts and give rise to eye infections and epidemic keratoconjunctivitis (EKC). They persist in lymphoid tissue and cause morbidity and mortality in immunocompromised people. Treatments with significant postexposure efficacy are not available. Here, we report that inhibition of the cell cycle-dependent kinase 9 (Cdk9) by RNA interference, or the compound flavopiridol, blocked infections with HAdV-C2/5, EKC-causing HAdV-D8/37, and progeny formation in human corneal epithelial and cancer cells. Flavopiridol abrogated the production of the immediate early viral transactivating protein E1A without affecting nuclear import of viral DNA. In morphometric plaque assays, the compound exhibited antiviral efficacy in both pre- and postexposure regimens with therapeutic indexes exceeding 10. The study identifies Cdk9 as a postexposure drug target against adenovirus infections in vitro and suggests that the clinically tested anticancer drug flavopiridol is a candidate for treating adenoviral EKC or adenovirus emergence upon immune suppression.
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Affiliation(s)
- Vibhu Prasad
- Institute of Molecular
Life Sciences, University of Zurich, Zurich, Switzerland
- Molecular Life Sciences Graduate School, ETH and University of Zurich, Zurich, Switzerland
| | - Maarit Suomalainen
- Institute of Molecular
Life Sciences, University of Zurich, Zurich, Switzerland
| | - Silvio Hemmi
- Institute of Molecular
Life Sciences, University of Zurich, Zurich, Switzerland
| | - Urs F. Greber
- Institute of Molecular
Life Sciences, University of Zurich, Zurich, Switzerland
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43
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Flatt JW, Greber UF. Viral mechanisms for docking and delivering at nuclear pore complexes. Semin Cell Dev Biol 2017; 68:59-71. [PMID: 28506891 DOI: 10.1016/j.semcdb.2017.05.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 05/11/2017] [Indexed: 12/22/2022]
Abstract
Some viruses possess the remarkable ability to transport their genomes across nuclear pore complexes (NPCs) for replication inside the host cell's intact nuclear compartment. Viral mechanisms for crossing the restrictive NPC passageway are highly complex and astonishingly diverse, requiring in each case stepwise interaction between incoming virus particles and components of the nuclear transport machinery. Exactly how a large viral genome loaded with accessory proteins is able to pass through the relatively narrow central channel of the NPC without causing catastrophic structural damage is not yet fully understood. It appears likely, however, that the overall structure of the NPC changes in response to the cargo. Translocation may result in nucleic acids being misdelivered to the cytoplasm. Here we consider in detail the diverse strategies that viruses have evolved to target and subvert NPCs during infection. For decades, this process has both captivated and confounded researchers in the fields of virology, cell biology, and structural biology.
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Affiliation(s)
- Justin W Flatt
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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44
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Abstract
Viruses are spherical or complex shaped carriers of proteins, nucleic acids and sometimes lipids and sugars. They are metastable and poised for structural changes. These features allow viruses to communicate with host cells during entry, and to release the viral genome, a process known as uncoating. Studies have shown that hundreds of host factors directly or indirectly support this process. The cell provides molecules that promote stepwise virus uncoating, and direct the virus to the site of replication. It acts akin to a snooker player who delivers accurate and timely shots (cues) to the ball (virus) to score. The viruses, on the other hand, trick (snooker) the host, hijack its homeostasis systems, and dampen innate immune responses directed against danger signals. In this review, we discuss how cellular cues, facilitators, and built‐in viral mechanisms promote uncoating. Cues come from receptors, enzymes and chemicals that act directly on the virus particle to alter its structure, trafficking and infectivity. Facilitators are defined as host factors that are involved in processes which indirectly enhance entry or uncoating. Unraveling the mechanisms of virus uncoating will continue to enhance understanding of cell functions, and help counteracting infections with chemicals and vaccines.
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Affiliation(s)
- Yohei Yamauchi
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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45
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Gschweitl M, Ulbricht A, Barnes CA, Enchev RI, Stoffel-Studer I, Meyer-Schaller N, Huotari J, Yamauchi Y, Greber UF, Helenius A, Peter M. A SPOPL/Cullin-3 ubiquitin ligase complex regulates endocytic trafficking by targeting EPS15 at endosomes. eLife 2016; 5:e13841. [PMID: 27008177 PMCID: PMC4846373 DOI: 10.7554/elife.13841] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/23/2016] [Indexed: 01/01/2023] Open
Abstract
Cullin-3 (CUL3)-based ubiquitin ligases regulate endosome maturation and trafficking of endocytic cargo to lysosomes in mammalian cells. Here, we report that these functions depend on SPOPL, a substrate-specific CUL3 adaptor. We find that SPOPL associates with endosomes and is required for both the formation of multivesicular bodies (MVBs) and the endocytic host cell entry of influenza A virus. In SPOPL-depleted cells, endosomes are enlarged and fail to acquire intraluminal vesicles (ILVs). We identify a critical substrate ubiquitinated by CUL3-SPOPL as EPS15, an endocytic adaptor that also associates with the ESCRT-0 complex members HRS and STAM on endosomes. Indeed, EPS15 is ubiquitinated in a SPOPL-dependent manner, and accumulates with HRS in cells lacking SPOPL. Together, our data indicates that a CUL3-SPOPL E3 ubiquitin ligase complex regulates endocytic trafficking and MVB formation by ubiquitinating and degrading EPS15 at endosomes, thereby influencing influenza A virus infection as well as degradation of EGFR and other EPS15 targets. DOI:http://dx.doi.org/10.7554/eLife.13841.001 Individual cells can move material, collectively referred to as cargo, from the outside environment into the cell interior via a process known as endocytosis. The cell then has different routes to transport the packages of cargo, called endocytic vesicles, to specific locations within the cell. Protein-based molecular machines move the cargo and control how it is selected and targeted to different destinations. For example, a molecular machine that contains a protein called CUL3 labels other components of the system with a chemical tag to regulate the route cargo takes in mammalian cells. However, it was not clear how CUL3 can selectively attach the chemical labels. Gschweitl, Ulbricht et al. have now found that another protein called SPOPL provides selectivity for the CUL3-based machine during endocytosis in human cells. The experiments show that SPOPL attaches to endocytic vesicles, and that CUL3 and SPOPL work together to label a specific component of these vesicles called EPS15. The label changes how EPS15 interacts with other proteins. When SPOPL is not present in a cell, EPS15 is unnaturally stable and occupies many of the routes used by endocytic cargos. The cargo directly interacting with EPS15 is then routed on the fast lane to its destination, while other cargo accumulate in a kind of molecular traffic jam. Other proteins like SPOPL are specific for the endocytic system. Exchange of SPOPL with these similar proteins in the CUL3 machine is likely to chemically label a different set of endocytic proteins. Gschweitl, Ulbricht et al.’s next challenge is to identify the selectivity, targeting and coordination of these exchangeable components in the endocytic system. DOI:http://dx.doi.org/10.7554/eLife.13841.002
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Affiliation(s)
- Michaela Gschweitl
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Anna Ulbricht
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Christopher A Barnes
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Radoslav I Enchev
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Ingrid Stoffel-Studer
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Nathalie Meyer-Schaller
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Jatta Huotari
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Yohei Yamauchi
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ari Helenius
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
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Ortega-Esteban A, Bodensiek K, San Martín C, Suomalainen M, Greber UF, de Pablo PJ, Schaap IAT. Fluorescence Tracking of Genome Release during Mechanical Unpacking of Single Viruses. ACS Nano 2015; 9:10571-10579. [PMID: 26381363 DOI: 10.1021/acsnano.5b03020] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Viruses package their genome in a robust protein coat to protect it during transmission between cells and organisms. In a reaction termed uncoating, the virus is progressively weakened during entry into cells. At the end of the uncoating process the genome separates, becomes transcriptionally active, and initiates the production of progeny. Here, we triggered the disruption of single human adenovirus capsids with atomic force microscopy and followed genome exposure by single-molecule fluorescence microscopy. This method allowed the comparison of immature (noninfectious) and mature (infectious) adenovirus particles. We observed two condensation states of the fluorescently labeled genome, a feature of the virus that may be related to infectivity. Beyond tracking the unpacking of virus genomes, this approach may find application in testing the cargo release of bioinspired delivery vehicles.
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Affiliation(s)
| | - Kai Bodensiek
- III. Physikalisches Institut, Georg August Universität , Göttingen, Germany
| | - Carmen San Martín
- Department of Macromolecular Structures and NanoBioMedicine Initiative, Centro Nacional de Biotecnología (CNB-CSIC) , Madrid, Spain
| | - Maarit Suomalainen
- Institute of Molecular Life Sciences, University of Zürich , Zürich, Switzerland
| | - Urs F Greber
- Institute of Molecular Life Sciences, University of Zürich , Zürich, Switzerland
| | | | - Iwan A T Schaap
- III. Physikalisches Institut, Georg August Universität , Göttingen, Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB) , Göttingen, Germany
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47
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Yakimovich A, Andriasyan V, Witte R, Wang IH, Prasad V, Suomalainen M, Greber UF. Plaque2.0-A High-Throughput Analysis Framework to Score Virus-Cell Transmission and Clonal Cell Expansion. PLoS One 2015; 10:e0138760. [PMID: 26413745 PMCID: PMC4587671 DOI: 10.1371/journal.pone.0138760] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 08/24/2015] [Indexed: 01/17/2023] Open
Abstract
Classical plaque assay measures the propagation of infectious agents across a monolayer of cells. It is dependent on cell lysis, and limited by user-specific settings and low throughput. Here, we developed Plaque2.0, a broadly applicable, fluorescence microscopy-based high-throughput method to mine patho-biological clonal cell features. Plaque2.0 is an open source framework to extract information from chemically fixed cells by immuno-histochemistry or RNA in situ hybridization, or from live cells expressing GFP transgene. Multi-parametric measurements include infection density, intensity, area, shape or location information at single plaque or population levels. Plaque2.0 distinguishes lytic and non-lytic spread of a variety of DNA and RNA viruses, including vaccinia virus, adenovirus and rhinovirus, and can be used to visualize simultaneous plaque formation from co-infecting viruses. Plaque2.0 also analyzes clonal growth of cancer cells, which is relevant for cell migration and metastatic invasion studies. Plaque2.0 is suitable to quantitatively analyze virus infections, vector properties, or cancer cell phenotypes.
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Affiliation(s)
- Artur Yakimovich
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vardan Andriasyan
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Robert Witte
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - I-Hsuan Wang
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vibhu Prasad
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Maarit Suomalainen
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Urs F. Greber
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- * E-mail:
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48
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Greber UF. How cells tune viral mechanics--insights from biophysical measurements of influenza virus. Biophys J 2015; 106:2317-21. [PMID: 24896110 DOI: 10.1016/j.bpj.2014.04.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/10/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022] Open
Abstract
During replication, the physical state of a virus is controlled by assembly and disassembly processes, when particles are put together and dismantled by cellular cues, respectively. A fundamental question has been how a cell can assemble an infectious virus, and dismantle a virus entering an uninfected cell and thereby trigger a new round of infection. This apparent paradox might be explained by considering that infected and uninfected cells are functionally different, or that assembly and disassembly take place along different cellular pathways. A third possibility is that the physical properties of newly assembled viruses are different from the infection-ready viruses. Recent biophysical experiments measured the stiffness of single Influenza viruses and combined this with biochemical measurements and cell biological assays. Besides inducing the fusogenic state of hemagglutinin, low pH cues softened the virus and precluded aggregation of viral ribonucleoprotein particles with the matrix protein M1. The recent experiments suggest a two-step model for Influenza virus entry and uncoating involving low pH in early and late endosomes, respectively. I conclude with a short outlook into how combined biophysical and cell biological approaches might lead to the identification of new cellular cues controlling viral uncoating and infection.
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Affiliation(s)
- Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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49
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Ingold E, Vom Berg-Maurer CM, Burckhardt CJ, Lehnherr A, Rieder P, Keller PJ, Stelzer EH, Greber UF, Neuhauss SCF, Gesemann M. Proper migration and axon outgrowth of zebrafish cranial motoneuron subpopulations require the cell adhesion molecule MDGA2A. Biol Open 2015; 4:146-54. [PMID: 25572423 PMCID: PMC4365483 DOI: 10.1242/bio.20148482] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The formation of functional neuronal circuits relies on accurate migration and proper axonal outgrowth of neuronal precursors. On the route to their targets migrating cells and growing axons depend on both, directional information from neurotropic cues and adhesive interactions mediated via extracellular matrix molecules or neighbouring cells. The inactivation of guidance cues or the interference with cell adhesion can cause severe defects in neuronal migration and axon guidance. In this study we have analyzed the function of the MAM domain containing glycosylphosphatidylinositol anchor 2A (MDGA2A) protein in zebrafish cranial motoneuron development. MDGA2A is prominently expressed in distinct clusters of cranial motoneurons, especially in the ones of the trigeminal and facial nerves. Analyses of MDGA2A knockdown embryos by light sheet and confocal microscopy revealed impaired migration and aberrant axonal outgrowth of these neurons; suggesting that adhesive interactions mediated by MDGA2A are required for the proper arrangement and outgrowth of cranial motoneuron subtypes.
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Affiliation(s)
- Esther Ingold
- Brain Research Institute of the University Zurich and Swiss Federal Institute of Technology (ETH), Department of Biology, 8057 Zurich, Switzerland
| | | | | | - André Lehnherr
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Philip Rieder
- Brain Research Institute of the University Zurich and Swiss Federal Institute of Technology (ETH), Department of Biology, 8057 Zurich, Switzerland
| | - Philip J Keller
- EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Ernst H Stelzer
- EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Stephan C F Neuhauss
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Matthias Gesemann
- Brain Research Institute of the University Zurich and Swiss Federal Institute of Technology (ETH), Department of Biology, 8057 Zurich, Switzerland Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
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50
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Wang IH, Suomalainen M, Andriasyan V, Kilcher S, Mercer J, Neef A, Luedtke NW, Greber UF. Tracking viral genomes in host cells at single-molecule resolution. Cell Host Microbe 2014; 14:468-80. [PMID: 24139403 DOI: 10.1016/j.chom.2013.09.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/07/2013] [Accepted: 09/04/2013] [Indexed: 01/01/2023]
Abstract
Viral DNA trafficking in cells has large impacts on physiology and disease development. Current methods lack the resolution and accuracy to visualize and quantify viral DNA trafficking at single-molecule resolution. We developed a noninvasive protocol for accurate quantification of viral DNA-genome (vDNA) trafficking in single cells. Ethynyl-modified nucleosides were used to metabolically label newly synthesized adenovirus, herpes virus, and vaccinia virus vDNA, without affecting infectivity. Superresolution microscopy and copper(I)-catalyzed azide-alkyne cycloaddition (click) reactions allowed visualization of infection at single vDNA resolution within mammalian cells. Analysis of adenovirus infection revealed that a large pool of capsid-free vDNA accumulated in the cytosol upon virus uncoating, indicating that nuclear import of incoming vDNA is a bottleneck. The method described here is applicable for the entire replication cycle of DNA viruses and offers opportunities to localize cellular and viral effector machineries on newly replicated viral DNA, or innate immune sensors on cytoplasmic viral DNA.
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Affiliation(s)
- I-Hsuan Wang
- Institute of Molecular Life Sciences, University of Zürich, CH-8057 Zurich, Switzerland; Molecular Life Sciences Graduate School, ETH and University of Zürich, CH-8057 Zurich, Switzerland
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