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Heinz JL, Hinke DM, Maimaitili M, Wang J, Sabli IKD, Thomsen M, Farahani E, Ren F, Hu L, Zillinger T, Grahn A, von Hofsten J, Verjans GMGM, Paludan SR, Viejo-Borbolla A, Sancho-Shimizu V, Mogensen TH. Varicella zoster virus-induced autophagy in human neuronal and hematopoietic cells exerts antiviral activity. J Med Virol 2024; 96:e29690. [PMID: 38804180 DOI: 10.1002/jmv.29690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
Autophagy is a degradational pathway with pivotal roles in cellular homeostasis and survival, including protection of neurons in the central nervous system (CNS). The significance of autophagy as antiviral defense mechanism is recognized and some viruses hijack and modulate this process to their advantage in certain cell types. Here, we present data demonstrating that the human neurotropic herpesvirus varicella zoster virus (VZV) induces autophagy in human SH-SY5Y neuronal cells, in which the pathway exerts antiviral activity. Productively VZV-infected SH-SY5Y cells showed increased LC3-I-LC3-II conversion as well as co-localization of the viral glycoprotein E and the autophagy receptor p62. The activation of autophagy was dependent on a functional viral genome. Interestingly, inducers of autophagy reduced viral transcription, whereas inhibition of autophagy increased viral transcript expression. Finally, the genotype of patients with severe ocular and brain VZV infection were analyzed to identify potential autophagy-associated inborn errors of immunity. Two patients expressing genetic variants in the autophagy genes ULK1 and MAP1LC3B2, respectively, were identified. Notably, cells of both patients showed reduced autophagy, alongside enhanced viral replication and death of VZV-infected cells. In conclusion, these results demonstrate a neuro-protective role for autophagy in the context of VZV infection and suggest that failure to mount an autophagy response is a potential predisposing factor for development of severe VZV disease.
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Affiliation(s)
- Johanna L Heinz
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Daniëla M Hinke
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | | | - Jiayi Wang
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Ira K D Sabli
- Dept of Paediatric Infectious Diseases & Virology, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Michelle Thomsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Ensieh Farahani
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Fanghui Ren
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Lili Hu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Thomas Zillinger
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Institute of Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University Hospital Bonn, Bonn, Germany
| | - Anna Grahn
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Joanna von Hofsten
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Ophthalmology, Halland Hospital Halmstad, Halmstad, Sweden
| | - Georges M G M Verjans
- Department of Viroscience, HerpeslabNL, Erasmus University MC, Rotterdam, The Netherlands
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Abel Viejo-Borbolla
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence-Resolving Infection Susceptibility (RESIST, EXC 2155), Hannover Medical School, Hannover, Germany
| | - Vanessa Sancho-Shimizu
- Dept of Paediatric Infectious Diseases & Virology, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
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2
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Rozman B, Nachshon A, Levi Samia R, Lavi M, Schwartz M, Stern-Ginossar N. Temporal dynamics of HCMV gene expression in lytic and latent infections. Cell Rep 2022; 39:110653. [PMID: 35417700 PMCID: PMC9035752 DOI: 10.1016/j.celrep.2022.110653] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/19/2022] [Accepted: 03/18/2022] [Indexed: 01/10/2023] Open
Abstract
During productive human cytomegalovirus (HCMV) infection, viral genes are expressed in a coordinated cascade that conventionally relies on the dependencies of viral genes on protein synthesis and viral DNA replication. By contrast, the transcriptional landscape of HCMV latency is poorly understood. Here, we examine viral gene expression dynamics during the establishment of both productive and latent HCMV infections. We redefine HCMV gene expression kinetics during productive infection and reveal that viral gene regulation does not represent a simple sequential cascade; many viral genes are regulated by multiple independent modules. Using our improved gene expression classification combined with transcriptome-wide measurements of the effects of a wide array of epigenetic inhibitors on viral gene expression during latency, we show that a defining feature of latency is the unique repression of immediate-early (IE) genes. Altogether, we recharacterize HCMV gene expression kinetics and reveal governing principles of lytic and latent gene expression. Redefining HCMV gene expression cascade during productive infection Many viral genes are regulated by multiple independent modules Diverse inhibitors induce broad viral gene expression in monocytes In monocytes, immediate-early (IE) genes are repressed compared to all other HCMV genes
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Affiliation(s)
- Batsheva Rozman
- Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Roi Levi Samia
- Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Michael Lavi
- Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel.
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Duffy EE, Schofield JA, Simon MD. Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1513. [PMID: 30370679 DOI: 10.1002/wrna.1513] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022]
Abstract
Cellular RNA levels are the result of a juggling act between RNA transcription, processing, and degradation. By tuning one or more of these parameters, cells can rapidly alter the available pool of transcripts in response to stimuli. While RNA sequencing (RNA-seq) is a vital method to quantify RNA levels genome-wide, it is unable to capture the dynamics of different RNA populations at steady-state or distinguish between different mechanisms that induce changes to the steady-state (i.e., altered rate of transcription vs. degradation). The dynamics of different RNA populations can be studied by targeted incorporation of noncanonical nucleosides. 4-Thiouridine (s4 U) is a commonly used and versatile RNA metabolic label that allows the study of many properties of RNA metabolism from synthesis to degradation. Numerous experimental strategies have been developed that leverage the power of s4 U to label newly transcribed RNA in whole cells, followed by enrichment with activated disulfides or chemistry to induce C mutations at sites of s4 U during sequencing. This review presents existing methods to study RNA population dynamics genome-wide using s4 U metabolic labeling, as well as a discussion of considerations and challenges when designing s4 U metabolic labeling experiments. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Jeremy A Schofield
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
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Metabolic labeling and recovery of nascent RNA to accurately quantify mRNA stability. Methods 2017; 120:39-48. [PMID: 28219744 DOI: 10.1016/j.ymeth.2017.02.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 12/26/2022] Open
Abstract
Changes in the rate of mRNA decay are closely coordinated with transcriptional changes and together these events have profound effects on gene expression during development and disease. Traditional approaches to assess mRNA decay have relied on inhibition of transcription, which can alter mRNA decay rates and confound interpretation. More recently, metabolic labeling combined with chemical modification and fractionation of labeled RNAs has allowed the isolation of nascent transcripts and the subsequent calculation of mRNA decay rates. This approach has been widely adopted for measuring mRNA half-lives on a global scale, but has proven challenging to use for analysis of single genes. We present a series of normalization and quality assurance steps to be used in combination with 4-thiouridine pulse labeling of cultured eukaryotic cells. Importantly, we demonstrate how the relative amount of 4sU-labeled nascent RNA influences accurate quantification. The approach described facilitates reproducible measurement of individual mRNA half-lives using 4-thiouridine and could be adapted for use with other nucleoside analogs.
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Occupancy of RNA Polymerase II Phosphorylated on Serine 5 (RNAP S5P) and RNAP S2P on Varicella-Zoster Virus Genes 9, 51, and 66 Is Independent of Transcript Abundance and Polymerase Location within the Gene. J Virol 2015; 90:1231-43. [PMID: 26559844 DOI: 10.1128/jvi.02617-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/05/2015] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Regulation of gene transcription in varicella-zoster virus (VZV), a ubiquitous human neurotropic alphaherpesvirus, requires coordinated binding of multiple host and virus proteins onto specific regions of the virus genome. Chromatin immunoprecipitation (ChIP) is widely used to determine the location of specific proteins along a genomic region. Since the size range of sheared virus DNA fragments governs the limit of accurate protein localization, particularly for compact herpesvirus genomes, we used a quantitative PCR (qPCR)-based assay to determine the efficiency of VZV DNA shearing before ChIP, after which the assay was used to determine the relationship between transcript abundance and the occupancy of phosphorylated RNA polymerase II (RNAP) on the gene promoter, body, and terminus of VZV genes 9, 51, and 66. The abundance of VZV gene 9, 51, and 66 transcripts in VZV-infected human fetal lung fibroblasts was determined by reverse transcription-linked quantitative PCR. Our results showed that the C-terminal domain of RNAP is hyperphosphorylated at serine 5 (S5(P)) on VZV genes 9, 51, and 66 independently of transcript abundance and the location within the virus gene at both 1 and 3 days postinfection (dpi). In contrast, phosphorylated serine 2 (S2(P))-modified RNAP was not detected at any virus gene location at 3 dpi and was detected at levels only slightly above background levels at 1 dpi. IMPORTANCE Regulation of herpesvirus gene transcription is an elaborate choreography between proteins and DNA that is revealed by chromatin immunoprecipitation (ChIP). We used a quantitative PCR-based assay to determine fragment size after DNA shearing, a critical parameter in ChIP assays, and exposed a basic difference in the mechanism of transcription between mammalian cells and VZV. We found that hyperphosphorylation at serine 5 of the C-terminal domain of RNAP along the lengths of VZV genes (the promoter, body, and transcription termination site) was independent of mRNA abundance. In contrast, little to no enrichment of serine 3 phosphorylation of RNAP was detected at these virus gene regions. This is distinct from the findings for RNAP at highly regulated host genes, where RNAP S5(P) occupancy decreased and S2(P) levels increased as the polymerase transited through the gene. Overall, these results suggest that RNAP associates with human and virus transcriptional units through different mechanisms.
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Baird NL, Bowlin JL, Yu X, Jonjić S, Haas J, Cohrs RJ, Gilden D. Varicella zoster virus DNA does not accumulate in infected human neurons. Virology 2014; 458-459:1-3. [PMID: 24928033 DOI: 10.1016/j.virol.2014.04.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 03/31/2014] [Accepted: 04/07/2014] [Indexed: 01/19/2023]
Abstract
Varicella zoster virus (VZV) is an exclusively human neurotropic alphaherpesvirus. It is unclear why human neurons infected in vitro with VZV at low multiplicity of infection do not exhibit a cytopathic effect (CPE) even though all VZV genes are transcribed, VZV proteins from all kinetic classes are translated and minimal infectious virus is produced. Here, we show that the lack of VZV-induced CPE correlates with the low abundance of viral DNA.
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Affiliation(s)
- Nicholas L Baird
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jacqueline L Bowlin
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xiaoli Yu
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Stipan Jonjić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia; Center for Proteomics, Department of Histology and Embryology, University of Rijeka, Rijeka, Croatia
| | - Jürgen Haas
- Max von Pettenkofer Institut, Ludwig-Maximilians Universität München, München, Germany; Division of Pathway Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Randall J Cohrs
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO, USA; Department of Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Don Gilden
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO, USA; Department of Microbiology, University of Colorado School of Medicine, Aurora, CO, USA.
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Human anti-varicella-zoster virus (VZV) recombinant monoclonal antibody produced after Zostavax immunization recognizes the gH/gL complex and neutralizes VZV infection. J Virol 2012; 87:415-21. [PMID: 23077312 DOI: 10.1128/jvi.02561-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Varicella-zoster virus (VZV) is a ubiquitous, highly cell-associated, and exclusively human neurotropic alphaherpesvirus. VZV infection is initiated by membrane fusion, an event dependent in part on VZV glycoproteins gH and gL. Consistent with its location on the virus envelope, the gH/gL complex is a target of neutralizing antibodies produced after virus infection. One week after immunizing a 59-year-old VZV-seropositive man with Zostavax, we sorted his circulating blood plasma blasts and amplified expressed immunoglobulin variable domain sequences by single-cell PCR. Sequence analysis identified two plasma blast clones, one of which was used to construct a recombinant monoclonal antibody (rec-RC IgG). The rec-RC IgG colocalized with VZV gE on the membranes of VZV-infected cells and neutralized VZV infection in tissue culture. Mass spectrometric analysis of proteins immunoprecipitated by rec-RC IgG identified both VZV gH and gL. Transfection experiments showed that rec-RC IgG recognized a VZV gH/gL protein complex but not individual gH or gL proteins. Overall, our recombinant monoclonal anti-VZV antibody effectively neutralizes VZV and recognizes a conformational epitope within the VZV gH/L protein complex. An unlimited supply of this antibody provides the opportunity to analyze membrane fusion events that follow virus attachment and to identify multiple epitopes on VZV-specific proteins.
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Kinchington PR, Goins WF. Varicella zoster virus-induced pain and post-herpetic neuralgia in the human host and in rodent animal models. J Neurovirol 2011; 17:590-9. [PMID: 22205584 PMCID: PMC3946975 DOI: 10.1007/s13365-011-0069-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/30/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
Abstract
Pain and post-herpetic neuralgia (PHN) are common and highly distressing complications of herpes zoster that remain a significant public health concern and in need of improved therapies. Zoster results from reactivation of the herpesvirus varicella zoster virus (VZV) from a neuronal latent state established at the primary infection (varicella). PHN occurs in some one fifth to one third of zoster cases with severity, incidence, and duration of pain increasing with rising patient age. While VZV reactivation and the ensuing ganglionic damage trigger the pain response, the mechanisms underlying protracted PHN are not understood, and the lack of an animal model of herpes zoster (reactivation) makes this issue more challenging. A recent preclinical rodent model has developed that opens up the potential to allow the exploration of the underlying mechanisms and treatments for VZV-induced pain. Rats inoculated with live cell-associated human VZV into the hind paw reliably demonstrate thermal hyperalgesia and mechanical allodynia for extended periods and then spontaneously recover. Dorsal root ganglia express a limited VZV gene subset, including the IE62 regulatory protein, and upregulate expression of markers suggesting a neuropathic pain state. The model has been used to investigate treatment modalities and aspects of pain signaling and is under investigation by the authors to delineate VZV genetics involved in the induction of pain. This article compares human zoster-associated pain and PHN to the pain indicators in the rat and poses important questions that, if answered, could be the basis for new treatments.
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Affiliation(s)
- Paul R Kinchington
- Department of Ophthalmology, University of Pittsburgh, 1020 EEI Building, 203 Lothrop Street, Pittsburgh, PA 15213, USA.
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