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Badrinath A, Bhatta S, Kloc A. Persistent viral infections and their role in heart disease. Front Microbiol 2022; 13:1030440. [PMID: 36504781 PMCID: PMC9730422 DOI: 10.3389/fmicb.2022.1030440] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2022] Open
Abstract
Viral infections are the culprit of many diseases, including inflammation of the heart muscle, known as myocarditis. Acute myocarditis cases have been described in scientific literature, and viruses, such as parvovirus B19, coxsackievirus B3, or more recently, SARS-CoV-2, were the direct cause of cardiac inflammation. If not treated, myocarditis could progress to dilated cardiomyopathy, which permanently impairs the heart and limits a person's lifespan. Accumulated evidence suggests that certain viruses may persist in cardiac tissue after the initial infection, which could open up the door to reactivation under favorable conditions. Whether this chronic infection contributes to, or initiates, cardiac damage over time, remains a pressing issue in the field of virus-induced heart pathology, and it is directly tied to patients' treatment. Previously, large case studies found that a few viruses: parvovirus B19, coxsackievirus, adenovirus, human herpesvirus 6, cytomegalovirus and Epstein-Barr virus, are most commonly found in human endomyocardial biopsy samples derived from patients experiencing cardiac inflammation, or dilated cardiomyopathy. SARS-CoV-2 infection has also been shown to have cardiovascular consequences. This review examines the role of viral persistence in cardiac inflammation and heart disease, and discusses its implications for patients' outcomes.
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Peischard S, Möller M, Disse P, Ho HT, Verkerk AO, Strutz-Seebohm N, Budde T, Meuth SG, Schweizer PA, Morris S, Mücher L, Eisner V, Thomas D, Klingel K, Busch K, Seebohm G. Virus-induced inhibition of cardiac pacemaker channel HCN4 triggers bradycardia in human-induced stem cell system. Cell Mol Life Sci 2022; 79:440. [PMID: 35864219 PMCID: PMC9304080 DOI: 10.1007/s00018-022-04435-7] [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] [Received: 10/08/2021] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 12/02/2022]
Abstract
The enterovirus Coxsackievirus B3 (CVB3) is known to be a major source for the development of cardiac dysfunctions like viral myocarditis (VMC) and dilatative cardiomyopathy (DCM), but also results in bradycardia and fatal cardiac arrest. Besides clinical reports on bradycardia and sudden cardiac death, very little is known about the influence of CVB3 on the activity of human cardiac pacemaker cells. Here, we address this issue using the first human induced pluripotent stem cell (hiPSC)-derived pacemaker-like cells, in which the expression of a transgenic non-infectious variant of CVB3 can be controlled dose- and time-dependently. We found that CVB3 drastically changed hyperpolarization-activated cyclic nucleotide-gated channel 4 (HCN4) distribution and function in hiPSC-derived pacemaker-like tissue. In addition, using HCN4 cell expression systems, we found that HCN4 currents were decreased with altered voltage dependency of activation when CVB3 was expressed. Increased autophagosome formation and autophagosomal HCN4 insertion was observed in hiPSC-derived pacemaker-like cells under CVB3 expression as well. Individual effects of single, non-structural CVB3 proteins were analyzed and demonstrated that CVB3 proteins 2C and 3A had the most robust effect on HCN4 activity. Treatment of cells with the Rab7 inhibitor CID 106770 or the CVB3-3A inhibitor GW5074 led to the recovery of the cytoplasmatic HCN4 accumulation into a healthy appearing phenotype, indicating that malfunctioning Rab7-directed autophagosome transport is involved in the disturbed, cytoplasmatic HCN4 accumulation in CVB3-expressing human pacemaker-like cells. Summarizing, the enterovirus CVB3 inhibits human cardiac pacemaker function by reducing the pacemaker channel plasma membrane density, an effect that can be corrected by pharmacological intervention of endocytic vesicle trafficking.
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Affiliation(s)
- Stefan Peischard
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, 48149, Münster, Germany
| | - Melina Möller
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, 48149, Münster, Germany
| | - Paul Disse
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, 48149, Münster, Germany.,GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Huyen Tran Ho
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, 48149, Münster, Germany
| | - Arie O Verkerk
- Department of Medical Biology, Amsterdam University Medical Centers, University of Amsterdam, 1105, Amsterdam, The Netherlands
| | - Nathalie Strutz-Seebohm
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, 48149, Münster, Germany.,GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Thomas Budde
- GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany.,Institute of Physiology I, Westfälische-Wilhems Universität Münster, 48149, Münster, Germany
| | - Sven G Meuth
- GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany.,Department of Neurology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Patrick A Schweizer
- Department of Cardiology, Medical University Hospital Heidelberg, 69120, Heidelberg, Germany.,HCR (Heidelberg Center for Heart Rhythm Disorders), University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, University of Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Silke Morris
- Institute for Integrative Cell Biology and Physiology, Department of Biology, University of Münster, 48149, Münster, Germany
| | - Lena Mücher
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, 48149, Münster, Germany
| | - Verónica Eisner
- Department of Cellular and Molecular Biology, School of Biological Sciences, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
| | - Dierk Thomas
- Department of Cardiology, Medical University Hospital Heidelberg, 69120, Heidelberg, Germany.,HCR (Heidelberg Center for Heart Rhythm Disorders), University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, University of Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Karin Klingel
- Cardiopathology, Institute for Pathology and Neuropathology, University Hospital of Tuebingen, 72076, Tübingen, Germany
| | - Karin Busch
- Institute for Integrative Cell Biology and Physiology, Department of Biology, University of Münster, 48149, Münster, Germany
| | - Guiscard Seebohm
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, 48149, Münster, Germany. .,GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Münster, Germany.
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3
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Persistent Enterovirus Infection: Little Deletions, Long Infections. Vaccines (Basel) 2022; 10:vaccines10050770. [PMID: 35632526 PMCID: PMC9143164 DOI: 10.3390/vaccines10050770] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Enteroviruses have now been shown to persist in cell cultures and in vivo by a novel mechanism involving the deletion of varying amounts of the 5′ terminal genomic region termed domain I (also known as the cloverleaf). Molecular clones of coxsackievirus B3 (CVB3) genomes with 5′ terminal deletions (TD) of varying length allow the study of these mutant populations, which are able to replicate in the complete absence of wildtype virus genomes. The study of TD enteroviruses has revealed numerous significant differences from canonical enteroviral biology. The deletions appear and become the dominant population when an enterovirus replicates in quiescent cell populations, but can also occur if one of the cis-acting replication elements of the genome (CRE-2C) is artificially mutated in the element’s stem and loop structures. This review discusses how the TD genomes arise, how they interact with the host, and their effects on host biology.
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Honkimaa A, Kimura B, Sioofy-Khojine AB, Lin J, Laiho J, Oikarinen S, Hyöty H. Genetic Adaptation of Coxsackievirus B1 during Persistent Infection in Pancreatic Cells. Microorganisms 2020; 8:microorganisms8111790. [PMID: 33203081 PMCID: PMC7697981 DOI: 10.3390/microorganisms8111790] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022] Open
Abstract
Coxsackie B (CVB) viruses have been associated with type 1 diabetes. We have recently observed that CVB1 was linked to the initiation of the autoimmune process leading to type 1 diabetes in Finnish children. Viral persistency in the pancreas is currently considered as one possible mechanism. In the current study persistent infection was established in pancreatic ductal and beta cell lines (PANC-1 and 1.1B4) using four different CVB1 strains, including the prototype strain and three clinical isolates. We sequenced 5′ untranslated region (UTR) and regions coding for structural and non-structural proteins and the second single open reading frame (ORF) protein of all persisting CVB1 strains using next generation sequencing to identify mutations that are common for all of these strains. One mutation, K257R in VP1, was found from all persisting CVB1 strains. The mutations were mainly accumulated in viral structural proteins, especially at BC, DE, EF loops and C-terminus of viral capsid protein 1 (VP1), the puff region of VP2, the knob region of VP3 and infection-enhancing epitope of VP4. This showed that the capsid region of the viruses sustains various changes during persistency some of which could be hallmark(s) of persistency.
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Affiliation(s)
- Anni Honkimaa
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
- Correspondence:
| | - Bryn Kimura
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
| | - Amir-Babak Sioofy-Khojine
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
| | - Jake Lin
- Finnish Institute of Molecular Medicine (FIMM), University of Helsinki, 00290 Helsinki, Finland;
| | - Jutta Laiho
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (B.K.); (A.B.S.-K.); (J.L.); (S.O.); (H.H.)
- Fimlab Laboratories, Pirkanmaa Hospital District, 33520 Tampere, Finland
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Watkins CL, Kempf BJ, Beaucourt S, Barton DJ, Peersen OB. Picornaviral polymerase domain exchanges reveal a modular basis for distinct biochemical activities of viral RNA-dependent RNA polymerases. J Biol Chem 2020; 295:10624-10637. [PMID: 32493771 PMCID: PMC7397104 DOI: 10.1074/jbc.ra120.013906] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/28/2020] [Indexed: 01/23/2023] Open
Abstract
Picornaviral RNA-dependent RNA polymerases (RdRPs) have low replication fidelity that is essential for viral fitness and evolution. Their global fold consists of the classical "cupped right hand" structure with palm, fingers, and thumb domains, and these RdRPs also possess a unique contact between the fingers and thumb domains. This interaction restricts movements of the fingers, and RdRPs use a subtle conformational change within the palm domain to close their active sites for catalysis. We have previously shown that this core RdRP structure and mechanism provide a platform for polymerases to fine-tune replication rates and fidelity to optimize virus fitness. Here, we further elucidated the structural basis for differences in replication rates and fidelity among different viruses by generating chimeric RdRPs from poliovirus and coxsackievirus B3. We designed these chimeric polymerases by exchanging the fingers, pinky finger, or thumb domains. The results of biochemical, rapid-quench, and stopped-flow assays revealed that differences in biochemical activity map to individual modular domains of this polymerase. We found that the pinky finger subdomain is a major regulator of initiation and that the palm domain is the major determinant of catalytic rate and nucleotide discrimination. We further noted that thumb domain interactions with product RNA regulate translocation and that the palm and thumb domains coordinately control elongation complex stability. Several RdRP chimeras supported the growth of infectious poliovirus, providing insights into enterovirus species-specific protein-protein interactions required for virus replication.
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Affiliation(s)
- Colleen L Watkins
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Brian J Kempf
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - David J Barton
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Olve B Peersen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
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6
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Oikarinen M, Bertolet L, Toniolo A, Oikarinen S, Laiho JE, Pugliese A, Lloyd RE, Hyöty H. Differential Detection of Encapsidated versus Unencapsidated Enterovirus RNA in Samples Containing Pancreatic Enzymes-Relevance for Diabetes Studies. Viruses 2020; 12:v12070747. [PMID: 32664501 PMCID: PMC7411921 DOI: 10.3390/v12070747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 01/09/2023] Open
Abstract
Using immunohistochemistry, enterovirus capsid proteins were demonstrated in pancreatic islets of patients with type 1 diabetes. Virus proteins are mainly located in beta cells, supporting the hypothesis that enterovirus infections may contribute to the pathogenesis of type 1 diabetes. In samples of pancreatic tissue, enterovirus RNA was also detected, but in extremely small quantities and in a smaller proportion of cases compared to the enteroviral protein. Difficulties in detecting viral RNA could be due to the very small number of infected cells, the possible activity of PCR inhibitors, and the presence—during persistent infection—of the viral genome in unencapsidated forms. The aim of this study was twofold: (a) to examine if enzymes or other compounds in pancreatic tissue could affect the molecular detection of encapsidated vs. unencapsidated enterovirus forms, and (b) to compare the sensitivity of RT-PCR methods used in different laboratories. Dilutions of encapsidated and unencapsidated virus were spiked into human pancreas homogenate and analyzed by RT-PCR. Incubation of pancreatic homogenate on wet ice for 20 h did not influence the detection of encapsidated virus. In contrast, a 15-min incubation on wet ice dramatically reduced detection of unencapsidated forms of virus. PCR inhibitors could not be found in pancreatic extract. The results show that components in the pancreas homogenate may selectively affect the detection of unencapsidated forms of enterovirus. This may lead to difficulties in diagnosing persisting enterovirus infection in the pancreas of patients with type 1 diabetes.
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Affiliation(s)
- Maarit Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (S.O.); (J.E.L.); (H.H.)
- Correspondence: ; Tel.: +358-50-3186338
| | - Lori Bertolet
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (L.B.); (R.E.L.)
| | - Antonio Toniolo
- Global Virus Network, University of Insubria, 21100 Varese, Italy;
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (S.O.); (J.E.L.); (H.H.)
| | - Jutta E. Laiho
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (S.O.); (J.E.L.); (H.H.)
| | - Alberto Pugliese
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
| | - Richard E. Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (L.B.); (R.E.L.)
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (S.O.); (J.E.L.); (H.H.)
- Fimlab Laboratories, Pirkanmaa Hospital District, 33520 Tampere, Finland
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7
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Woodman A, Lee KM, Janissen R, Gong YN, Dekker NH, Shih SR, Cameron CE. Predicting Intraserotypic Recombination in Enterovirus 71. J Virol 2019; 93:e02057-18. [PMID: 30487277 PMCID: PMC6364027 DOI: 10.1128/jvi.02057-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 01/07/2023] Open
Abstract
Enteroviruses are well known for their ability to cause neurological damage and paralysis. The model enterovirus is poliovirus (PV), the causative agent of poliomyelitis, a condition characterized by acute flaccid paralysis. A related virus, enterovirus 71 (EV-A71), causes similar clinical outcomes in recurrent outbreaks throughout Asia. Retrospective phylogenetic analysis has shown that recombination between circulating strains of EV-A71 produces the outbreak-associated strains which exhibit increased virulence and/or transmissibility. While studies on the mechanism(s) of recombination in PV are ongoing in several laboratories, little is known about factors that influence recombination in EV-A71. We have developed a cell-based assay to study recombination of EV-A71 based upon previously reported assays for poliovirus recombination. Our results show that (i) EV-A71 strain type and RNA sequence diversity impacts recombination frequency in a predictable manner that mimics the observations found in nature; (ii) recombination is primarily a replicative process mediated by the RNA-dependent RNA polymerase; (iii) a mutation shown to reduce recombination in PV (L420A) similarly reduces EV-A71 recombination, suggesting conservation in mechanism(s); and (iv) sequencing of intraserotypic recombinant genomes indicates that template switching occurs by a mechanism that may require some sequence homology at the recombination junction and that the triggers for template switching may be sequence independent. The development of this recombination assay will permit further investigation on the interplay between replication, recombination and disease.IMPORTANCE Recombination is a mechanism that contributes to genetic diversity. We describe the first assay to study EV-A71 recombination. Results from this assay mimic what is observed in nature and can be used by others to predict future recombination events within the enterovirus species A group. In addition, our results highlight the central role played by the viral RNA-dependent RNA polymerase (RdRp) in the recombination process. Further, our results show that changes to a conserved residue in the RdRp from different species groups have a similar impact on viable recombinant virus yields, which is indicative of conservation in mechanism.
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Affiliation(s)
- Andrew Woodman
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety, and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
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Kloc A, Rai DK, Rieder E. The Roles of Picornavirus Untranslated Regions in Infection and Innate Immunity. Front Microbiol 2018; 9:485. [PMID: 29616004 PMCID: PMC5870040 DOI: 10.3389/fmicb.2018.00485] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 02/28/2018] [Indexed: 11/17/2022] Open
Abstract
Viral genomes have evolved to maximize their potential of overcoming host defense mechanisms and to induce a variety of disease syndromes. Structurally, a genome of a virus consists of coding and noncoding regions, and both have been shown to contribute to initiation and progression of disease. Accumulated work in picornaviruses has stressed out the importance of the noncoding RNAs, or untranslated 5′- and 3′-regions (UTRs), in both replication and translation of viral genomes. Unsurprisingly, defects in these processes have been reported to cause viral attenuation and affect viral pathogenicity. However, substantial evidence suggests that these untranslated RNAs may influence the outcome of the host innate immune response. This review discusses the involvement of 5′- and 3′-terminus UTRs in induction and regulation of host immunity and its consequences for viral life cycle and virulence.
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Affiliation(s)
- Anna Kloc
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY, United States
| | - Devendra K Rai
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY, United States
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY, United States
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Abstract
Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements. This conservatism stems from genetic robustness or mutational tolerance, which is largely due to the functional degeneracy of many protein and RNA elements as well as to negative selection. Another relevant mechanism is the capacity to restore fitness after genetic damages, also based on replicative infidelity. Conversely, error-prone replication is a major tool that ensures viral evolvability. The potential for changes in debilitated genomes is much higher in small populations, because in the absence of stronger competitors low-fit genomes have a choice of various trajectories to wander along fitness landscapes. Thus, low-fit populations are inherently unstable, and it may be said that to run ahead it is useful to stumble. In this report, focusing on picornaviruses and also considering data from other RNA viruses, we review the biological relevance and mechanisms of various alterations of viral RNA genomes as well as pathways and mechanisms of rehabilitation after loss of fitness. The relationships among mutational robustness, resilience, and evolvability of viral RNA genomes are discussed.
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Immunological and pathological consequences of coxsackievirus RNA persistence in the heart. Virology 2017; 512:104-112. [PMID: 28950225 DOI: 10.1016/j.virol.2017.09.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 12/14/2022]
Abstract
Type B coxsackieviruses (CVB) can cause myocarditis and dilated cardiomyopathy (DCM), a potentially-fatal sequela that has been correlated to the persistence of viral RNA. Herein, we demonstrate that cardiac RNA persistence can be established even after an inapparent primary infection. Using an inducible Cre/lox mouse model, we ask: (i) Does persistent CVB3 RNA cause ongoing immune activation? (ii) If T1IFN signaling into cardiomyocytes is ablated after RNA persistence is established, is there any change in the abundance of persistent CVB3 RNA and/or does cytopathic infectious virus re-emerge? (iii) Does this loss of T1IFN responsiveness by cardiomyocytes lead to the recurrence/exacerbation of myocarditis? Our findings suggest that persistent enteroviral RNAs probably do not contribute to ongoing myocardial disease, and are more likely to be the fading remnants of a recent, possibly sub-clinical, primary infection which may have set in motion the process that ultimately ends in DCM.
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11
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Abstract
PURPOSE OF REVIEW Epigenetics is defined as mitotically heritable changes in gene expression that do not directly alter the DNA sequence. By implication, such epigenetic changes are non-genetically determined, although they can be affected by inherited genetic variation. Extensive evidence indicates that autoimmune diseases including type 1 diabetes are determined by the interaction of genetic and non-genetic factors. Much is known of the genetic causes of these diseases, but the non-genetic effects are less clear-cut. Further, it remains unclear how they interact to cause the destructive autoimmune process. This review identifies the key issues in the genetic/non-genetic interaction, examining the most recent evidence of the role of non-genetic effects in the disease process, including the impact of epigenetic effects on key pathways. RECENT FINDINGS Recent research indicates that these pathways likely involve immune effector cells both of the innate and adaptive immune response. Specifically, there is evidence of cell type-specific enrichment in altered DNA methylation, changes which were temporally stable and enriched at gene regulatory elements. Epigenomics remains in its infancy, and we anticipate further studies will define how the interaction of genetic and non-genetic effects induces tissue-specific destruction and enhances our ability to predict, and possibly even modify that process.
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Affiliation(s)
| | - Mary N. Dang
- Queen Mary University of London, Mile End Rd, London, E1 4NS UK
| | - R. David Leslie
- Queen Mary University of London, Mile End Rd, London, E1 4NS UK
- The Blizard Institute, London, UK
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12
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Functional Consequences of RNA 5'-Terminal Deletions on Coxsackievirus B3 RNA Replication and Ribonucleoprotein Complex Formation. J Virol 2017; 91:JVI.00423-17. [PMID: 28539455 DOI: 10.1128/jvi.00423-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/17/2017] [Indexed: 12/11/2022] Open
Abstract
Group B coxsackieviruses are responsible for chronic cardiac infections. However, the molecular mechanisms by which the virus can persist in the human heart long after the signs of acute myocarditis have abated are still not completely understood. Recently, coxsackievirus B3 strains with 5'-terminal deletions in genomic RNAs were isolated from a patient suffering from idiopathic dilated cardiomyopathy, suggesting that such mutant viruses may be the forms responsible for persistent infection. These deletions lacked portions of 5' stem-loop I, which is an RNA secondary structure required for viral RNA replication. In this study, we assessed the consequences of the genomic deletions observed in vivo for coxsackievirus B3 biology. Using cell extracts from HeLa cells, as well as transfection of luciferase replicons in two types of cardiomyocytes, we demonstrated that coxsackievirus RNAs harboring 5' deletions ranging from 7 to 49 nucleotides in length can be translated nearly as efficiently as those of wild-type virus. However, these 5' deletions greatly reduced the synthesis of viral RNA in vitro, which was detected only for the 7- and 21-nucleotide deletions. Since 5' stem-loop I RNA forms a ribonucleoprotein complex with cellular and viral proteins involved in viral RNA replication, we investigated the binding of the host cell protein PCBP2, as well as viral protein 3CDpro, to deleted positive-strand RNAs corresponding to the 5' end. We found that binding of these proteins was conserved but that ribonucleoprotein complex formation required higher PCBP2 and 3CDpro concentrations, depending on the size of the deletion. Overall, this study confirmed the characteristics of persistent CVB3 infection observed in heart tissues and provided a possible explanation for the low level of RNA replication observed for the 5'-deleted viral genomes-a less stable ribonucleoprotein complex formed with proteins involved in viral RNA replication.IMPORTANCE Dilated cardiomyopathy is the most common indication for heart transplantation worldwide, and coxsackie B viruses are detected in about one-third of idiopathic dilated cardiomyopathies. Terminal deletions at the 5' end of the viral genome involving an RNA secondary structure required for RNA replication have been recently reported as a possible mechanism of virus persistence in the human heart. These mutations are likely to disrupt the correct folding of an RNA secondary structure required for viral RNA replication. In this report, we demonstrate that transfected RNAs harboring 5'-terminal sequence deletions are able to direct the synthesis of viral proteins, but not genomic RNAs, in human and murine cardiomyocytes. Moreover, we show that the binding of cellular and viral replication factors to viral RNA is conserved despite genomic deletions but that the impaired RNA synthesis associated with terminally deleted viruses could be due to destabilization of the ribonucleoprotein complexes formed.
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Revealing enterovirus infection in chronic human disorders: An integrated diagnostic approach. Sci Rep 2017; 7:5013. [PMID: 28694527 PMCID: PMC5504018 DOI: 10.1038/s41598-017-04993-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 05/09/2017] [Indexed: 01/10/2023] Open
Abstract
Enteroviruses (EVs) causing persisting infection are characterized by minimal replication and genetic changes. Typing of these agents may complement disease assessment and shed light on pathogenesis. Here we report an integrated approach for EV detection in human samples that is based on pre-enrichment of virus in cell culture before search for the viral genome and viral antigens. Cases of post-polio syndrome, type 1 diabetes, and chronic cardiomyopathy were investigated. As tissue-based approaches require invasive procedures, information was mainly gleaned from virus in blood. Molecular assays targeting conserved genome regions of all EV types (5'UTR, 2 C, 3Dpol) were employed. As compared to direct assays of plasma or leukocytes, the EV detection rate was significantly enhanced by co-culture of leukocytes with cell lines prior to molecular and immunologic tests. Results of RT-PCR and sequencing were confirmed by staining cell cultures with a panel of EV-specific antibodies. Sequence and phylogenetic analysis showed that EVs of the C species (polioviruses) were associated with the post-polio syndrome, while members of the B species were found in type 1 diabetes and cardiomyopathy. The procedure may be used for investigating the possible association of different EVs with a variety of chronic neurologic, endocrine, and cardiac disorders.
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Jaramillo L, Smithee S, Tracy S, Chapman NM. Domain I of the 5' non-translated genomic region in coxsackievirus B3 RNA is not required for productive replication. Virology 2016; 496:127-130. [PMID: 27289561 DOI: 10.1016/j.virol.2016.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/23/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
Abstract
Domain I is a cloverleaf-like secondary structure at the 5' termini of all enterovirus genomes, comprising part of a cis-acting replication element essential for efficient enteroviral replication. 5' genomic terminal deletions up to as much as 55% of domain I can occur without lethality following coxsackie B virus infections. We report here that the entire CVB structural domain I can be deleted without lethality.
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Affiliation(s)
- L Jaramillo
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA; Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198-5830, USA
| | - S Smithee
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA; Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - S Tracy
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - N M Chapman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA.
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Abstract
The incidence of type 1 diabetes has risen considerably in the past 30 years due to changes in the environment that have been only partially identified. In this Series paper, we critically discuss candidate triggers of islet autoimmunity and factors thought to promote progression from autoimmunity to overt type 1 diabetes. We revisit previously proposed hypotheses to explain the growth in the incidence of type 1 diabetes in light of current data. Finally, we suggest a unified model in which immune tolerance to β cells can be broken by several environmental exposures that induce generation of hybrid peptides acting as neoautoantigens.
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Affiliation(s)
- Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Johnny Ludvigsson
- Division of Pediatrics, Department of Clinical and Experimental Medicine, Medical Faculty, Linköping University and Linköping University Hospital, Linköping, Sweden.
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Vázquez-Calvo Á, Caridi F, González-Magaldi M, Saiz JC, Sobrino F, Martín-Acebes MA. The Amino Acid Substitution Q65H in the 2C Protein of Swine Vesicular Disease Virus Confers Resistance to Golgi Disrupting Drugs. Front Microbiol 2016; 7:612. [PMID: 27199941 PMCID: PMC4846857 DOI: 10.3389/fmicb.2016.00612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/13/2016] [Indexed: 11/13/2022] Open
Abstract
Swine vesicular disease virus (SVDV) is a porcine pathogen and a member of the species Enterovirus B within the Picornaviridae family. Brefeldin A (BFA) is an inhibitor of guanine nucleotide exchange factors of Arf proteins that induces Golgi complex disassembly and alters the cellular secretory pathway. Since BFA has been shown to inhibit the RNA replication of different enteroviruses, including SVDV, we have analyzed the effect of BFA and of golgicide A (GCA), another Golgi disrupting drug, on SVDV multiplication. BFA and GCA similarly inhibited SVDV production. To investigate the molecular basis of the antiviral effect of BFA, SVDV mutants with increased resistance to BFA were isolated. A single amino acid substitution, Q65H, in the non-structural protein 2C was found to be responsible for increased resistance to BFA. These results provide new insight into the relationship of enteroviruses with the components of the secretory pathway and on the role of SVDV 2C protein in this process.
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Affiliation(s)
- Ángela Vázquez-Calvo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM)Madrid, Spain; Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Madrid, Spain
| | - Flavia Caridi
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM) Madrid, Spain
| | | | - Juan-Carlos Saiz
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Madrid, Spain
| | | | - Miguel A Martín-Acebes
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM)Madrid, Spain; Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Madrid, Spain
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Smithee S, Tracy S, Chapman NM. Reversion to wildtype of a mutated and nonfunctional coxsackievirus B3CRE(2C). Virus Res 2016; 220:136-49. [PMID: 27130630 DOI: 10.1016/j.virusres.2016.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/15/2016] [Accepted: 04/18/2016] [Indexed: 11/25/2022]
Abstract
The cis-acting replication element (CRE) in the 2C protein coding region [CRE(2C)] of enteroviruses (EV) facilitates the addition of two uridine residues (uridylylation) onto the virus-encoded protein VPg in order for it to serve as the RNA replication primer. We demonstrated that coxsackievirus B3 (CVB3) is replication competent in the absence of a native (uridylylating) CRE(2C) and also demonstrated that lack of a functional CRE(2C) led to generation of 5' terminal genomic deletions in the CVB3 CRE-knock-out (CVB3-CKO) population. We asked whether reversion of the mutated CRE(2C) occurred, thus permitting sustained replication, and when were 5' terminal deletions generated during replication. Virions were isolated from HeLa cells previously electroporated with infectious CVB3-CKO T7 transcribed RNA or from hearts and spleens of mice after transfection with CVB3-CKO RNA. Viral RNA was isolated in order to amplify the CRE(2C) coding region and the genomic 5' terminal sequences. Sequence analysis revealed reversion of the CVB3-CKO sequence to wildtype occurs by 8 days post-electroporation of HeLa cells and by 20days post-transfection in mice. However, 5' terminal deletions evolve prior to these times. Reversion of the CRE(2C) mutations to wildtype despite loss of the genomic 5' termini is consistent with the hypothesis that an intact CRE(2C) is inherently vital to EV replication even when it is not enabling efficient positive strand initiation.
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Affiliation(s)
- Shane Smithee
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA; Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30033, USA
| | - Steven Tracy
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nora M Chapman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA.
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