1
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Petkidis A, Suomalainen M, Andriasyan V, Singh A, Greber UF. Preexisting cell state rather than stochastic noise confers high or low infection susceptibility of human lung epithelial cells to adenovirus. mSphere 2024; 9:e0045424. [PMID: 39315811 PMCID: PMC11542551 DOI: 10.1128/msphere.00454-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 08/20/2024] [Indexed: 09/25/2024] Open
Abstract
Viruses display large variability across all stages of their life cycle, including entry, gene expression, replication, assembly, and egress. We previously reported that the immediate early adenovirus (AdV) E1A transcripts accumulate in human lung epithelial A549 cancer cells with high variability, mostly independent of the number of incoming viral genomes, but somewhat correlated to the cell cycle state at the time of inoculation. Here, we leveraged the classical Luria-Delbrück fluctuation analysis to address whether infection variability primarily arises from the cell state or stochastic noise. The E1A expression was measured by the expression of green fluorescent protein (GFP) from the endogenous E1A promoter in AdV-C5_E1A-FS2A-GFP and found to be highly correlated with the viral plaque formation, indicating reliability of the reporter virus. As an ensemble, randomly picked clonal A549 cell isolates displayed significantly higher coefficients of variation in the E1A expression than technical noise, indicating a phenotypic variability larger than noise. The underlying cell state determining infection variability was maintained for at least 9 weeks of cell cultivation. Our results indicate that preexisting cell states tune adenovirus infection in favor of the cell or the virus. These findings have implications for antiviral strategies and gene therapy applications.IMPORTANCEViral infections are known for their variability. Underlying mechanisms are still incompletely understood but have been associated with particular cell states, for example, the eukaryotic cell division cycle in DNA virus infections. A cell state is the collective of biochemical, morphological, and contextual features owing to particular conditions or at random. It affects how intrinsic or extrinsic cues trigger a response, such as cell division or anti-viral state. Here, we provide evidence that cell states with a built-in memory confer high or low susceptibility of clonal human epithelial cells to adenovirus infection. Results are reminiscent of the Luria-Delbrück fluctuation test with bacteriophage infections back in 1943, which demonstrated that mutations, in the absence of selective pressure prior to infection, cause infection resistance rather than being a consequence of infection. Our findings of dynamic cell states conferring adenovirus infection susceptibility uncover new challenges for the prediction and treatment of viral infections.
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Affiliation(s)
- Anthony Petkidis
- Department of
Molecular Life Sciences, Universitat
Zurich, Zurich,
Switzerland
| | - Maarit Suomalainen
- Department of
Molecular Life Sciences, Universitat
Zurich, Zurich,
Switzerland
| | - Vardan Andriasyan
- Department of
Molecular Life Sciences, Universitat
Zurich, Zurich,
Switzerland
| | - Abhyudai Singh
- Department of
Electrical and Computer Engineering, University of
Delaware, Newark,
Delaware, USA
| | - Urs F. Greber
- Department of
Molecular Life Sciences, Universitat
Zurich, Zurich,
Switzerland
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2
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Hofmann N, Bartkuhn M, Becker S, Biedenkopf N, Böttcher-Friebertshäuser E, Brinkrolf K, Dietzel E, Fehling SK, Goesmann A, Heindl MR, Hoffmann S, Karl N, Maisner A, Mostafa A, Kornecki L, Müller-Kräuter H, Müller-Ruttloff C, Nist A, Pleschka S, Sauerhering L, Stiewe T, Strecker T, Wilhelm J, Wuerth JD, Ziebuhr J, Weber F, Schmitz ML. Distinct negative-sense RNA viruses induce a common set of transcripts encoding proteins forming an extensive network. J Virol 2024; 98:e0093524. [PMID: 39283124 PMCID: PMC11494938 DOI: 10.1128/jvi.00935-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/14/2024] [Indexed: 10/23/2024] Open
Abstract
The large group of negative-strand RNA viruses (NSVs) comprises many important pathogens. To identify conserved patterns in host responses, we systematically compared changes in the cellular RNA levels after infection of human hepatoma cells with nine different NSVs of different virulence degrees. RNA sequencing experiments indicated that the amount of viral RNA in host cells correlates with the number of differentially expressed host cell transcripts. Time-resolved differential gene expression analysis revealed a common set of 178 RNAs that are regulated by all NSVs analyzed. A newly developed open access web application allows downloads and visualizations of all gene expression comparisons for individual viruses over time or between several viruses. Most of the genes included in the core set of commonly differentially expressed genes (DEGs) encode proteins that serve as membrane receptors, signaling proteins and regulators of transcription. They mainly function in signal transduction and control immunity, metabolism, and cell survival. One hundred sixty-five of the DEGs encode host proteins from which 47 have already been linked to the regulation of viral infections in previous studies and 89 proteins form a complex interaction network that may function as a core hub to control NSV infections.IMPORTANCEThe infection of cells with negative-strand RNA viruses leads to the differential expression of many host cell RNAs. The differential spectrum of virus-regulated RNAs reflects a large variety of events including anti-viral responses, cell remodeling, and cell damage. Here, these virus-specific differences and similarities in the regulated RNAs were measured in a highly standardized model. A newly developed app allows interested scientists a wide range of comparisons and visualizations.
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Affiliation(s)
- Nina Hofmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine Science Unit for Basic and Clinical Medicine, Justus Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University Giessen, Giessen, Germany
| | - Stephan Becker
- Institute of Virology, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | - Nadine Biedenkopf
- Institute of Virology, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | | | - Karina Brinkrolf
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Erik Dietzel
- Institute of Virology, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | | | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Miriam Ruth Heindl
- Institute of Virology, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | - Simone Hoffmann
- Institute for Virology, FB10-Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Nadja Karl
- Institute of Medical Virology, FB11-Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Andrea Maisner
- Institute of Virology, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | - Ahmed Mostafa
- Institute of Medical Virology, FB11-Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Laura Kornecki
- Institute of Virology, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | - Helena Müller-Kräuter
- Institute of Virology, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | - Christin Müller-Ruttloff
- Institute of Medical Virology, FB11-Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Philipps University of Marburg, Marburg, Germany
| | - Stephan Pleschka
- Institute of Medical Virology, FB11-Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Lucie Sauerhering
- Institute of Virology, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Philipps University of Marburg, Marburg, Germany
| | - Thomas Strecker
- Institute of Virology, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg, Germany
| | - Jochen Wilhelm
- Institute for Lung Health (ILH), Justus Liebig University Giessen, Giessen, Germany
| | - Jennifer D. Wuerth
- Institute for Virology, FB10-Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - John Ziebuhr
- Institute of Medical Virology, FB11-Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - M. Lienhard Schmitz
- Institute of Biochemistry, FB11-Medicine, Justus Liebig University Giessen, Giessen, Germany
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3
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Chen S, Zhu J, Hua C, Feng C, Wu X, Zhou C, Chen X, Zhang B, Xu Y, Ma Z, He J, Jin N, Song Y, van der Veen S, Cheng H. Single-cell RNA sequencing reveals the diversity of the immunological landscape response to genital herpes. Virol Sin 2024:S1995-820X(24)00152-4. [PMID: 39426602 DOI: 10.1016/j.virs.2024.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 10/12/2024] [Indexed: 10/21/2024] Open
Abstract
Genital herpes (GH) is a common sexually transmitted disease, which is primarily caused by herpes simplex virus type 2 (HSV-2), and continues to be a global health concern. Although our understanding of the alterations in immune cell populations and immunomodulation in GH patients is still limited, it is evident that systemic intrinsic immunity, innate immunity, and adaptive immunity play crucial roles during HSV-2 infection and GH reactivation. To investigate the mechanisms underlying HSV-2 infection and recurrence, single-cell RNA sequencing (scRNA-seq) was performed on immune cells isolated from the peripheral blood of both healthy individuals and patients with recurrent GH. Furthermore, the systemic immune response in patients with recurrent GH showed activation of classical monocytes, CD4+ T cells, natural killer cells (NK cells), and plasmacytoid dendritic cells (pDCs), especially of genes associated with the Toll-like receptor signaling pathway and T cell activation. Circulating immune cells in GH patients show higher expression of genes associated with inflammation and antiviral responses both in the scRNA-Seq data set and in independent quantitative real-time polymerase chain reaction (qRT-PCR) analysis and ELISA experiments. This study demonstrated that localized genital herpes, resulting from HSV reactivation, may influence the functionality of circulating immune cells, suggesting a potential avenue for future research into the role of systemic immunity during HSV infection and recurrence.
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Affiliation(s)
- Siji Chen
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Jiang Zhu
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Chunting Hua
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Chenxi Feng
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Xia Wu
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Can Zhou
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Xianzhen Chen
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Boya Zhang
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Yaohan Xu
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Zeyu Ma
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Jianping He
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Na Jin
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Yinjing Song
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.
| | - Stijn van der Veen
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China; Department of Microbiology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Hao Cheng
- Department of Dermatology and Venereology, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.
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4
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Štimac I, Marcelić M, Radić B, Viduka I, Blagojević Zagorac G, Lukanović Jurić S, Rožmanić C, Messerle M, Brizić I, Lučin P, Mahmutefendić Lučin H. SNX27:Retromer:ESCPE-1-mediated early endosomal tubulation impacts cytomegalovirus replication. Front Cell Infect Microbiol 2024; 14:1399761. [PMID: 39359939 PMCID: PMC11445146 DOI: 10.3389/fcimb.2024.1399761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/23/2024] [Indexed: 10/04/2024] Open
Abstract
Introduction Cytomegaloviruses (CMVs) extensively reorganize the membrane system of the cell and establish a new structure as large as the cell nucleus called the assembly compartment (AC). Our previous studies on murine CMV (MCMV)-infected fibroblasts indicated that the inner part of the AC contains rearranged early endosomes, recycling endosomes, endosomal recycling compartments and trans-Golgi membrane structures that are extensively tubulated, including the expansion and retention of tubular Rab10 elements. An essential process that initiates Rab10-associated tubulation is cargo sorting and retrieval mediated by SNX27, Retromer, and ESCPE-1 (endosomal SNX-BAR sorting complex for promoting exit 1) complexes. Objective The aim of this study was to investigate the role of SNX27:Retromer:ESCPE-1 complexes in the biogenesis of pre-AC in MCMV-infected cells and subsequently their role in secondary envelopment and release of infectious virions. Results Here we show that SNX27:Retromer:ESCPE1-mediated tubulation is essential for the establishment of a Rab10-decorated subset of membranes within the pre-AC, a function that requires an intact F3 subdomain of the SNX27 FERM domain. Suppression of SNX27-mediated functions resulted in an almost tenfold decrease in the release of infectious virions. However, these effects cannot be directly linked to the contribution of SNX27:Retromer:ESCPE-1-dependent tubulation to the secondary envelopment, as suppression of these components, including the F3-FERM domain, led to a decrease in MCMV protein expression and inhibited the progression of the replication cycle. Conclusion This study demonstrates a novel and important function of membrane tubulation within the pre-AC associated with the control of viral protein expression.
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Affiliation(s)
- Igor Štimac
- Department of Physiology, Immunology and Pathophysiology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Marina Marcelić
- Department of Physiology, Immunology and Pathophysiology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Barbara Radić
- Department of Physiology, Immunology and Pathophysiology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ivona Viduka
- Department of Physiology, Immunology and Pathophysiology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Gordana Blagojević Zagorac
- Department of Physiology, Immunology and Pathophysiology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- University North, University Center Varaždin, Varaždin, Croatia
| | - Silvija Lukanović Jurić
- Department of Physiology, Immunology and Pathophysiology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Carmen Rožmanić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Martin Messerle
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Ilija Brizić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Pero Lučin
- Department of Physiology, Immunology and Pathophysiology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- University North, University Center Varaždin, Varaždin, Croatia
| | - Hana Mahmutefendić Lučin
- Department of Physiology, Immunology and Pathophysiology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- University North, University Center Varaždin, Varaždin, Croatia
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5
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Bost P, Drayman N. Dissecting viral infections, one cell at a time, by single-cell technologies. Microbes Infect 2024; 26:105268. [PMID: 38008398 PMCID: PMC11161131 DOI: 10.1016/j.micinf.2023.105268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/22/2023] [Accepted: 11/21/2023] [Indexed: 11/28/2023]
Abstract
The meteoric rise of single-cell genomic technologies, especially of single-cell RNA-sequencing (scRNA-seq), has revolutionized several fields of cellular biology, especially immunology, oncology, neuroscience and developmental biology. While the field of virology has been relatively slow to adopt these technological advances, many works have shed new light on the fascinating interactions of viruses with their hosts using single cell technologies. One clear example is the multitude of studies dissecting viral infections by single-cell sequencing technologies during the recent COVID-19 pandemic. In this review we will detail the advantages of studying viral infections at a single-cell level, how scRNA-seq technologies can be used to achieve this goal and the associated technical limitations, challenges and solutions. We will highlight recent biological discoveries and breakthroughs in virology enabled by single-cell analyses and will end by discussing possible future directions of the field. Given the rate of publications in this exciting new frontier of virology, we have likely missed some important works and we apologize in advance to the researchers whose work we have failed to cite.
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Affiliation(s)
- Pierre Bost
- University of Zurich, Department of Quantitative Biomedicine, Zurich, 8057, Switzerland; ETH Zurich, Institute for Molecular Health Sciences, Zurich, 8093 Switzerland.
| | - Nir Drayman
- The Department of Molecular Biology and Biochemistry, The Center for Virus Research and The Center for Complex Biological Systems, The University of California, Irvine, CA, 92697, USA
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6
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Howell LM, Gracie NP, Newsome TP. Single-cell analysis of VACV infection reveals pathogen-driven timing of early and late phases and host-limited dynamics of virus production. PLoS Pathog 2024; 20:e1012423. [PMID: 39093901 PMCID: PMC11347022 DOI: 10.1371/journal.ppat.1012423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 08/26/2024] [Accepted: 07/15/2024] [Indexed: 08/04/2024] Open
Abstract
The extent and origin of variation in the replication dynamics of complex DNA viruses is not well-defined. Here, we investigate the vaccinia virus (VACV) infection cycle at the single-cell level, quantifying the temporal dynamics of early and post(dna)-replicative phase gene expression across thousands of infections. We found that viral factors determine the initiation time of these phases, and this is influenced by the multiplicity of infection (MOI). In contrast, virus production dynamics are largely constrained by the host cell. Additionally, between-cell variability in infection start time and virus production rate were strongly influenced by MOI, providing evidence for cooperativity between infecting virions. Blocking programmed cell death by pan-caspase inhibition increased infection frequency but not virus production at the population level due to a concurrent attenuation of per-cell virus yield, suggesting a dual role for caspase signaling in VACV infection. Our findings provide key insights into the pivotal factors influencing heterogeneity in the infection cycle of a large DNA virus at the single-cell level.
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Affiliation(s)
- Liam Michael Howell
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Nicholas Peter Gracie
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Timothy Peter Newsome
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, Australia
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7
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Adams SK, Ducharme GE, Loveday EK. All the single cells: if you like it then you should put some virus on it. J Virol 2024; 98:e0127323. [PMID: 38904395 PMCID: PMC11324023 DOI: 10.1128/jvi.01273-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Abstract
Across a rich 70-year history, single-cell virology has revealed the impact of host and pathogen heterogeneity during virus infections. Recent technological innovations have enabled higher-resolution analyses of cellular and viral heterogeneity. Furthermore, single-cell analysis has revealed extreme phenotypes and provided additional insights into host-pathogen dynamics. Using a single-cell approach to explore fundamental virology questions, contemporary researchers have contributed to a revival of interest in single-cell virology with increased insights and enthusiasm.
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Affiliation(s)
- Sophia K. Adams
- Department of
Chemistry and Biochemistry, Montana State
University, Bozeman,
Montana, USA
- Center for Biofilm
Engineering, Montana State University,
Bozeman, Montana, USA
| | - Grace E. Ducharme
- Center for Biofilm
Engineering, Montana State University,
Bozeman, Montana, USA
- Department of Chemical
and Biological Engineering, Montana State
University, Bozeman,
Montana, USA
| | - Emma K. Loveday
- Center for Biofilm
Engineering, Montana State University,
Bozeman, Montana, USA
- Department of Chemical
and Biological Engineering, Montana State
University, Bozeman,
Montana, USA
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8
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Petkidis A, Andriasyan V, Murer L, Volle R, Greber UF. A versatile automated pipeline for quantifying virus infectivity by label-free light microscopy and artificial intelligence. Nat Commun 2024; 15:5112. [PMID: 38879641 PMCID: PMC11180103 DOI: 10.1038/s41467-024-49444-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 06/03/2024] [Indexed: 06/19/2024] Open
Abstract
Virus infectivity is traditionally determined by endpoint titration in cell cultures, and requires complex processing steps and human annotation. Here we developed an artificial intelligence (AI)-powered automated framework for ready detection of virus-induced cytopathic effect (DVICE). DVICE uses the convolutional neural network EfficientNet-B0 and transmitted light microscopy images of infected cell cultures, including coronavirus, influenza virus, rhinovirus, herpes simplex virus, vaccinia virus, and adenovirus. DVICE robustly measures virus-induced cytopathic effects (CPE), as shown by class activation mapping. Leave-one-out cross-validation in different cell types demonstrates high accuracy for different viruses, including SARS-CoV-2 in human saliva. Strikingly, DVICE exhibits virus class specificity, as shown with adenovirus, herpesvirus, rhinovirus, vaccinia virus, and SARS-CoV-2. In sum, DVICE provides unbiased infectivity scores of infectious agents causing CPE, and can be adapted to laboratory diagnostics, drug screening, serum neutralization or clinical samples.
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Affiliation(s)
- Anthony Petkidis
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Life Science Zurich Graduate School, ETH and University of Zürich, 8057, Zurich, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Luca Murer
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Roche Diagnostics, Forrenstrasse 2, 6343, Rotkreuz, Switzerland
| | - Romain Volle
- 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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9
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Uribe FR, González VPI, Kalergis AM, Soto JA, Bohmwald K. Understanding the Neurotrophic Virus Mechanisms and Their Potential Effect on Systemic Lupus Erythematosus Development. Brain Sci 2024; 14:59. [PMID: 38248274 PMCID: PMC10813552 DOI: 10.3390/brainsci14010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/24/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Central nervous system (CNS) pathologies are a public health concern, with viral infections one of their principal causes. These viruses are known as neurotropic pathogens, characterized by their ability to infiltrate the CNS and thus interact with various cell populations, inducing several diseases. The immune response elicited by neurotropic viruses in the CNS is commanded mainly by microglia, which, together with other local cells, can secrete inflammatory cytokines to fight the infection. The most relevant neurotropic viruses are adenovirus (AdV), cytomegalovirus (CMV), enterovirus (EV), Epstein-Barr Virus (EBV), herpes simplex virus type 1 (HSV-1), and herpes simplex virus type 2 (HSV-2), lymphocytic choriomeningitis virus (LCMV), and the newly discovered SARS-CoV-2. Several studies have associated a viral infection with systemic lupus erythematosus (SLE) and neuropsychiatric lupus (NPSLE) manifestations. This article will review the knowledge about viral infections, CNS pathologies, and the immune response against them. Also, it allows us to understand the relevance of the different viral proteins in developing neuronal pathologies, SLE and NPSLE.
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Affiliation(s)
- Felipe R. Uribe
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Valentina P. I. González
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8330025, Chile;
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Jorge A. Soto
- Millennium Institute on Immunology and Immunotherapy, Laboratorio de Inmunología Traslacional, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile; (F.R.U.); (V.P.I.G.)
| | - Karen Bohmwald
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma, Santiago 8910060, Chile
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10
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Dutta P, Mäkinen K. Absolute and Relative Quantification of Single-Stranded Positive-Sense RNA Viruses from Plant Tissue. Methods Mol Biol 2024; 2724:81-91. [PMID: 37987900 DOI: 10.1007/978-1-0716-3485-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Reverse transcription quantitative PCR (RT-qPCR) allows sensitive and specific measurement of mRNA transcripts from a given sample in a short period of time. Relative and absolute RT-qPCR are two strategies that could be used to quantify mRNA transcripts, based on the goal of the experiment. Here, we describe the protocol for the quantification of plant viral RNA transcripts from an infected sample using both strategies.
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Affiliation(s)
- Pinky Dutta
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Kristiina Mäkinen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
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11
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Wyler E. Single-Cell RNA-Sequencing of RVFV Infection. Methods Mol Biol 2024; 2824:361-372. [PMID: 39039423 DOI: 10.1007/978-1-0716-3926-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
On the RNA level, viral infections are characterized by perturbations in the host cell transcriptome as well as the development of viral genetic information. Investigating the abundance and dynamic of RNA molecules can provide ample information to understand many aspects of the infection, from viral replication to pathogenesis. A key aspect therein is the resolution of the data, as infections are generally highly heterogeneous. Even in simple model systems such as cell lines, viral infections happen in a very asynchronous way. Quantifying RNAs at single-cell resolution can therefore substantially increase our understanding of these processes.Whereas measuring the RNA in bulk, that is, in samples containing thousands to hundreds of thousands of cells, is established and widely used since many years, methods for studying not only just a few different RNAs in individual cells became widely available only recently. Here, I outline and compare current concepts and methodologies for using single-cell RNA-sequencing to study virus infections. This covers sample preparation, cell preservation, biosafety considerations, and various experimental methods, with a special focus on the aspects that are important for studying virus infections. Since there is not "the one" method for doing single-cell RNA-sequencing, I will not provide a detailed protocol. Rather, this chapter should serve as a primer for getting started with single-cell RNA-sequencing experiments of virus infections and discusses the criteria that allow readers to choose the best procedures for their specific research question.
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Affiliation(s)
- Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Helmholtz Association, Berlin, Germany.
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12
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Chuapoco MR, Flytzanis NC, Goeden N, Christopher Octeau J, Roxas KM, Chan KY, Scherrer J, Winchester J, Blackburn RJ, Campos LJ, Man KNM, Sun J, Chen X, Lefevre A, Singh VP, Arokiaraj CM, Shay TF, Vendemiatti J, Jang MJ, Mich JK, Bishaw Y, Gore BB, Omstead V, Taskin N, Weed N, Levi BP, Ting JT, Miller CT, Deverman BE, Pickel J, Tian L, Fox AS, Gradinaru V. Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain. NATURE NANOTECHNOLOGY 2023; 18:1241-1251. [PMID: 37430038 PMCID: PMC10575780 DOI: 10.1038/s41565-023-01419-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/15/2023] [Indexed: 07/12/2023]
Abstract
Crossing the blood-brain barrier in primates is a major obstacle for gene delivery to the brain. Adeno-associated viruses (AAVs) promise robust, non-invasive gene delivery from the bloodstream to the brain. However, unlike in rodents, few neurotropic AAVs efficiently cross the blood-brain barrier in non-human primates. Here we report on AAV.CAP-Mac, an engineered variant identified by screening in adult marmosets and newborn macaques, which has improved delivery efficiency in the brains of multiple non-human primate species: marmoset, rhesus macaque and green monkey. CAP-Mac is neuron biased in infant Old World primates, exhibits broad tropism in adult rhesus macaques and is vasculature biased in adult marmosets. We demonstrate applications of a single, intravenous dose of CAP-Mac to deliver functional GCaMP for ex vivo calcium imaging across multiple brain areas, or a cocktail of fluorescent reporters for Brainbow-like labelling throughout the macaque brain, circumventing the need for germline manipulations in Old World primates. As such, CAP-Mac is shown to have potential for non-invasive systemic gene transfer in the brains of non-human primates.
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Affiliation(s)
- Miguel R Chuapoco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Nicholas C Flytzanis
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Capsida Biotherapeutics, Thousand Oaks, CA, USA.
| | - Nick Goeden
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Capsida Biotherapeutics, Thousand Oaks, CA, USA
| | | | | | - Ken Y Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Stanley Center for Psychiatric Research at Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | - Lillian J Campos
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Psychology and the California National Primate Research Center, University of California Davis, Davis, CA, USA
| | - Kwun Nok Mimi Man
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - Junqing Sun
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Arthur Lefevre
- Cortical Systems and Behavior Laboratory, University of California San Diego, San Diego, CA, USA
| | - Vikram Pal Singh
- Cortical Systems and Behavior Laboratory, University of California San Diego, San Diego, CA, USA
| | - Cynthia M Arokiaraj
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Timothy F Shay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Julia Vendemiatti
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Min J Jang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - John K Mich
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Bryan B Gore
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Natalie Weed
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Cory T Miller
- Cortical Systems and Behavior Laboratory, University of California San Diego, San Diego, CA, USA
| | - Benjamin E Deverman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Stanley Center for Psychiatric Research at Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James Pickel
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Lin Tian
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - Andrew S Fox
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Psychology and the California National Primate Research Center, University of California Davis, Davis, CA, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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13
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Petkidis A, Andriasyan V, Greber UF. Machine learning for cross-scale microscopy of viruses. CELL REPORTS 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] [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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14
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Petkidis A, Andriasyan V, Greber UF. Label-free microscopy for virus infections. Microscopy (Oxf) 2023; 72:204-212. [PMID: 37079744 PMCID: PMC10250014 DOI: 10.1093/jmicro/dfad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [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 insights into cell and organismic functions. 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.
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Affiliation(s)
- Anthony Petkidis
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, Zürich 8057, Switzerland
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15
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Song B, Sheng X, Justice JL, Lum KK, Metzger PJ, Cook KC, Kostas JC, Cristea IM. Intercellular communication within the virus microenvironment affects the susceptibility of cells to secondary viral infections. SCIENCE ADVANCES 2023; 9:eadg3433. [PMID: 37163594 PMCID: PMC10171814 DOI: 10.1126/sciadv.adg3433] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/07/2023] [Indexed: 05/12/2023]
Abstract
Communication between infected cells and cells in the surrounding tissue is a determinant of viral spread. However, it remains unclear how cells in close or distant proximity to an infected cell respond to primary or secondary infections. We establish a cell-based system to characterize a virus microenvironment, distinguishing infected, neighboring, and distal cells. Cell sorting, microscopy, proteomics, and cell cycle assays allow resolving cellular features and functional consequences of proximity to infection. We show that human cytomegalovirus (HCMV) infection primes neighboring cells for both subsequent HCMV infections and secondary infections with herpes simplex virus 1 and influenza A. Neighboring cells exhibit mitotic arrest, dampened innate immunity, and altered extracellular matrix. Conversely, distal cells are poised to slow viral spread due to enhanced antiviral responses. These findings demonstrate how infection reshapes the microenvironment through intercellular signaling to facilitate spread and how spatial proximity to an infection guides cell fate.
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Affiliation(s)
| | | | - Joshua L. Justice
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | | | - Peter J. Metzger
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | | | - James C. Kostas
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
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16
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Silvano M, Virgolini N, Correia R, Clarke C, Isidro IA, Alves PM, Roldão A. Dissecting insect cell heterogeneity during influenza VLP production using single-cell transcriptomics. Front Bioeng Biotechnol 2023; 11:1143255. [PMID: 36949887 PMCID: PMC10025388 DOI: 10.3389/fbioe.2023.1143255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
The insect cell-baculovirus expression vector system (IC-BEVS) has been widely used to produce recombinant protein at high titers, including complex virus-like particles (VPLs). However, cell-to-cell variability upon infection is yet one of the least understood phenomena in virology, and little is known about its impact on production of therapeutic proteins. This study aimed at dissecting insect cell population heterogeneity during production of influenza VLPs in IC-BEVS using single-cell RNA-seq (scRNA-seq). High Five cell population was shown to be heterogeneous even before infection, with cell cycle being one of the factors contributing for this variation. In addition, infected insect cells were clustered according to the timing and level of baculovirus genes expression, with each cluster reporting similar influenza VLPs transgenes (i.e., hemagglutinin and M1) transcript counts. Trajectory analysis enabled to track infection progression throughout pseudotime. Specific pathways such as translation machinery, protein folding, sorting and degradation, endocytosis and energy metabolism were identified as being those which vary the most during insect cell infection and production of Influenza VLPs. Overall, this study lays the ground for the application of scRNA-seq in IC-BEVS processes to isolate relevant biological mechanisms during recombinant protein expression towards its further optimization.
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Affiliation(s)
- Marco Silvano
- iBET-Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Nikolaus Virgolini
- iBET-Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ricardo Correia
- iBET-Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Colin Clarke
- NIBRT-National Institute for Bioprocessing Research and Training, Dublin, Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - Inês A. Isidro
- iBET-Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Paula M. Alves
- iBET-Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - António Roldão
- iBET-Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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17
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Kannoly S, Oken G, Shadan J, Musheyev D, Singh K, Singh A, Dennehy JJ. Single-Cell Approach Reveals Intercellular Heterogeneity in Phage-Producing Capacities. Microbiol Spectr 2023; 11:e0266321. [PMID: 36541779 PMCID: PMC9927085 DOI: 10.1128/spectrum.02663-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Bacteriophage burst size is the average number of phage virions released from infected bacterial cells, and its magnitude depends on the duration of an intracellular progeny accumulation phase. Burst size is often measured at the population level, not the single-cell level, and consequently, statistical moments are not commonly available. In this study, we estimated the bacteriophage lambda (λ) single-cell burst size mean and variance following different intracellular accumulation period durations by employing Escherichia coli lysogens bearing lysis-deficient λ prophages. Single lysogens can be isolated and chemically lysed at desired times following prophage induction to quantify progeny intracellular accumulation within individual cells. Our data showed that λ phage burst size initially increased exponentially with increased lysis time (i.e., period between induction and chemical lysis) and then saturated at longer lysis times. We also demonstrated that cell-to-cell variation, or "noise," in lysis timing did not contribute significantly to burst size noise. The burst size noise remained constant with increasing mean burst size. The most likely explanation for the experimentally observed constant burst size noise was that cell-to-cell differences in burst size originated from intercellular heterogeneity in cellular capacities to produce phages. The mean burst size measured at different lysis times was positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicated that there are other factors in addition to cell size that determine this cellular capacity. IMPORTANCE Phages produce offspring by hijacking a cell's replicative machinery. Previously, it was noted that the variation in the number of phages produced by single infected cells far exceeded cell size variation. It was hypothesized that this variation is a consequence of variation in the timing of host cell lysis. Here, we show that cell-to-cell variation in lysis timing does not significantly contribute to the burst size variation. We suggest that the constant burst size variation across different host lysis times results from cell-to-cell differences in capacity to produce phages. We found that the mean burst size measured at different lysis times was positively correlated to cell volume, which may determine the cellular phage production capacity. However, experiments controlling for cell size indicated that there are other factors in addition to cell size that determine this cellular capacity.
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Affiliation(s)
- Sherin Kannoly
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Gabriella Oken
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Jonathan Shadan
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - David Musheyev
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Kevin Singh
- Biology Department, Queens College of The City University of New York, New York, New York, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, USA
| | - John J. Dennehy
- Biology Department, Queens College of The City University of New York, New York, New York, USA
- The Graduate Center of The City University of New York, New York, New York, USA
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18
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Zhang N, Kandalai S, Zhou X, Hossain F, Zheng Q. Applying multi-omics toward tumor microbiome research. IMETA 2023; 2:e73. [PMID: 38868335 PMCID: PMC10989946 DOI: 10.1002/imt2.73] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/30/2022] [Accepted: 11/28/2022] [Indexed: 06/14/2024]
Abstract
Rather than a "short-term tenant," the tumor microbiome has been shown to play a vital role as a "permanent resident," affecting carcinogenesis, cancer development, metastasis, and cancer therapies. As the tumor microbiome has great potential to become a target for the early diagnosis and treatment of cancer, recent research on the relevance of the tumor microbiota has attracted a wide range of attention from various scientific fields, resulting in remarkable progress that benefits from the development of interdisciplinary technologies. However, there are still a great variety of challenges in this emerging area, such as the low biomass of intratumoral bacteria and unculturable character of some microbial species. Due to the complexity of tumor microbiome research (e.g., the heterogeneity of tumor microenvironment), new methods with high spatial and temporal resolution are urgently needed. Among these developing methods, multi-omics technologies (combinations of genomics, transcriptomics, proteomics, and metabolomics) are powerful approaches that can facilitate the understanding of the tumor microbiome on different levels of the central dogma. Therefore, multi-omics (especially single-cell omics) will make enormous impacts on the future studies of the interplay between microbes and tumor microenvironment. In this review, we have systematically summarized the advances in multi-omics and their existing and potential applications in tumor microbiome research, thus providing an omics toolbox for investigators to reference in the future.
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Affiliation(s)
- Nan Zhang
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Shruthi Kandalai
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Xiaozhuang Zhou
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Farzana Hossain
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Qingfei Zheng
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
- Department of Biological Chemistry and Pharmacology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
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19
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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] [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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20
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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] [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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21
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Volle R, Murer L, Petkidis A, Andriasyan V, Savi A, Bircher C, Meili N, Fischer L, Sequeira DP, Mark DK, Gomez-Gonzalez A, Greber UF. Methylene blue, Mycophenolic acid, Posaconazole, and Niclosamide inhibit SARS-CoV-2 Omicron variant BA.1 infection of human airway epithelial organoids. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100158. [PMID: 35935678 PMCID: PMC9338451 DOI: 10.1016/j.crmicr.2022.100158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sublineages of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) Omicron variants continue to amass mutations in the spike (S) glycoprotein, which leads to immune evasion and rapid spread of the virus across the human population. Here we demonstrate the susceptibility of the Omicron variant BA.1 (B.1.1.529.1) to four repurposable drugs, Methylene blue (MB), Mycophenolic acid (MPA), Posaconazole (POS), and Niclosamide (Niclo) in post-exposure treatments of primary human airway cell cultures. MB, MPA, POS, and Niclo are known to block infection of human nasal and bronchial airway epithelial explant cultures (HAEEC) with the Wuhan strain, and four variants of concern (VoC), Alpha (B.1.1.7), Beta (B.1.351), Gamma (B.1.1.28), Delta (B.1.617.2) (Weiss et al., 2021, Murer et al., 2022). Our results here not only reinforce the broad anti-coronavirus effects of MB, MPA, POS and Niclo, but also demonstrate that the Omicron variant BA.1 (B.1.1.529.1) sheds infectious virus from HAEEC over at least 15 d, and maintains both intracellular and extracellular viral genomic RNA without overt toxicity, suggesting viral persistence. The data emphasize the potential of repurposable drugs against COVID-19.
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Affiliation(s)
- Romain Volle
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Luca Murer
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Anthony Petkidis
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Life Science Zürich Graduate School, ETH and University of Zurich, 8057 Zurich, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Alessandro Savi
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Life Science Zürich Graduate School, ETH and University of Zurich, 8057 Zurich, Switzerland
| | - Cornelia Bircher
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Life Science Zürich Graduate School, ETH and University of Zurich, 8057 Zurich, Switzerland
| | - Nicole Meili
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lucy Fischer
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Daniela Policarpo Sequeira
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Life Science Zürich Graduate School, ETH and University of Zurich, 8057 Zurich, Switzerland
| | - Daniela Katharina Mark
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Alfonso Gomez-Gonzalez
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Life Science Zürich Graduate School, ETH and University of Zurich, 8057 Zurich, Switzerland
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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22
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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] [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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23
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Abstract
Microfluidics has enabled a new era of cellular and molecular assays due to the small length scales, parallelization, and the modularity of various analysis and actuation functions. Droplet microfluidics, in particular, has been instrumental in providing new tools for biology with its ability to quickly and reproducibly generate drops that act as individual reactors. A notable beneficiary of this technology has been single-cell RNA sequencing, which has revealed new heterogeneities and interactions for the fundamental unit of life. However, viruses far surpass the diversity of cellular life, affect the dynamics of all ecosystems, and are a chronic source of global health crises. Despite their impact on the world, high-throughput and high-resolution viral profiling has been difficult, with conventional methods being limited to population-level averaging, large sample volumes, and few cultivable hosts. Consequently, most viruses have not been identified and studied. Droplet microfluidics holds the potential to address many of these limitations and offers new levels of sensitivity and throughput for virology. This Feature highlights recent efforts that have applied droplet microfluidics to the detection and study of viruses, including for diagnostics, virus-host interactions, and cell-independent virus assays. In combination with traditional virology methods, droplet microfluidics should prove a potent tool toward achieving a better understanding of the most abundant biological species on Earth.
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Affiliation(s)
- Wenyang Jing
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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24
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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. CURRENT RESEARCH IN VIROLOGICAL SCIENCE 2022; 3:100019. [PMID: 35072124 PMCID: PMC8760634 DOI: 10.1016/j.crviro.2022.100019] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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25
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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: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [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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26
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Greber UF. Two years into COVID-19 - Lessons in SARS-CoV-2 and a perspective from papers in FEBS Letters. FEBS Lett 2021; 595:2847-2853. [PMID: 34787897 PMCID: PMC8652506 DOI: 10.1002/1873-3468.14226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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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