1
|
Mohanty P, Panda P, Acharya RK, Pande B, Bhaskar LVKS, Verma HK. Emerging perspectives on RNA virus-mediated infections: from pathogenesis to therapeutic interventions. World J Virol 2023; 12:242-255. [PMID: 38187500 PMCID: PMC10768389 DOI: 10.5501/wjv.v12.i5.242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/07/2023] [Accepted: 11/29/2023] [Indexed: 12/25/2023] Open
Abstract
RNA viruses continue to pose significant threats to global public health, necessitating a profound understanding of their pathogenic mechanisms and the development of effective therapeutic interventions. This manuscript provides a comprehensive overview of emerging perspectives on RNA virus-mediated infections, spanning from the intricate intricacies of viral pathogenesis to the forefront of innovative therapeutic strategies. A critical exploration of antiviral drugs sets the stage, highlighting the diverse classes of compounds that target various stages of the viral life cycle, underscoring the ongoing efforts to combat viral infections. Central to this discussion is the exploration of RNA-based therapeutics, with a spotlight on messenger RNA (mRNA)-based approaches that have revolutionized the landscape of antiviral interventions. Furthermore, the manuscript delves into the intricate world of delivery systems, exploring inno-vative technologies designed to enhance the efficiency and safety of mRNA vaccines. By analyzing the challenges and advancements in delivery mechanisms, this review offers a roadmap for future research and development in this critical area. Beyond conventional infectious diseases, the document explores the expanding applications of mRNA vaccines, including their promising roles in cancer immunotherapy and personalized medicine approaches. This manuscript serves as a valuable resource for researchers, clinicians, and policymakers alike, offering a nuanced perspective on RNA virus pathogenesis and the cutting-edge therapeutic interventions. By synthesizing the latest advancements and challenges, this review contributes significantly to the ongoing discourse in the field, driving the development of novel strategies to combat RNA virus-mediated infections effectively.
Collapse
Affiliation(s)
- Pratik Mohanty
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Poojarani Panda
- Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Rakesh Kumar Acharya
- Department of Zoology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Bilaspur 495009, Chhattisgarh, India
| | - Babita Pande
- Department of Physiology, All India Institute of Medical Science, Raipur 492001, chhattisgarh, India
| | - LVKS Bhaskar
- Department of Zoology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Bilaspur 495009, Chhattisgarh, India
| | - Henu Kumar Verma
- Lung Health and Immunity, Helmholtz Zentrum Munich, Munich 85764, Bayren, Germany
| |
Collapse
|
2
|
Aoyagi H, Iijima H, Gaber ES, Zaitsu T, Matsuda M, Wakae K, Watashi K, Suzuki R, Masaki T, Kahn J, Saito T, El-Kassas M, Shimada N, Kato K, Enomoto M, Hayashi K, Tsubota A, Mimata A, Sakamaki Y, Ichinose S, Muramatsu M, Wake K, Wakita T, Aizaki H. Hepatocellular organellar abnormalities following elimination of hepatitis C virus. Liver Int 2023; 43:1677-1690. [PMID: 37312620 DOI: 10.1111/liv.15624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/14/2023] [Accepted: 05/14/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS The future development of hepatocellular carcinoma (HCC) in patients after sustained virologic response (SVR) is an important issue. The purposes of this study were to investigate pathological alterations in organelle of the liver of SVR patients and to characterize organelle abnormalities that may be related to carcinogenesis after SVR. METHODS The ultrastructure of liver biopsy specimens from patients with chronic hepatitis C (CHC) and SVR were compared to cell and mouse models and assessed semi-quantitatively using transmission electron microscopy. RESULTS Hepatocytes in patients with CHC showed abnormalities in the nucleus, mitochondria, endoplasmic reticulum, lipid droplet, and pericellular fibrosis, comparable to those seen in hepatitis C virus (HCV)-infected mice and cells. DAA treatment significantly reduced organelle abnormalities such as the nucleus, mitochondria, and lipid droplet in the hepatocytes of patients and mice after SVR, and cured cells, but it did not change dilated/degranulated endoplasmic reticulum and pericellular fibrosis in patients and mice after SVR. Further, samples from patients with a post-SVR period of >1 year had significantly larger numbers of abnormalities in the mitochondria and endoplasmic reticulum than those of <1 year. A possible cause of organelle abnormalities in patients after SVR could be oxidative stress of the endoplasmic reticulum and mitochondria associated with abnormalities of the vascular system due to fibrosis. Interestingly, abnormal endoplasmic reticulum was associated with patients with HCC for >1 year after SVR. CONCLUSIONS These results indicate that patients with SVR exhibit a persistent disease state and require long-term follow-up to detect early signs of carcinogenesis.
Collapse
Affiliation(s)
- Haruyo Aoyagi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroko Iijima
- Department of Internal Medicine, Division of Hepatobiliary and Pancreatic Disease, Hyogo College of Medicine, Hyogo, Japan
| | - Eman S Gaber
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takuma Zaitsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mami Matsuda
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kosho Wakae
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takahiro Masaki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Jeffrey Kahn
- Department of Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Takeshi Saito
- Department of Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Mohamed El-Kassas
- Endemic Medicine Department, Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Noritomo Shimada
- Division of Gastroenterology and Hepatology, Ootakanomori Hospital, Chiba, Japan
| | - Keizo Kato
- Division of Gastroenterology and Hepatology, Shinmatsudo Central General Hospital, Chiba, Japan
| | - Masaru Enomoto
- Department of Hepatology, Osaka Metropolitan University, Osaka, Japan
| | - Kazuhiko Hayashi
- Division of Gastroenterology and Hepatology, Meijo Hospital, Nagoya, Japan
| | - Akihito Tsubota
- Core Research Facilities, Research Center for Medical Science, The Jikei University School of Medicine, Tokyo, Japan
| | - Ayako Mimata
- Research Core, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuriko Sakamaki
- Research Core, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shizuko Ichinose
- Department of Plastic, Reconstructive and Aesthetic Surgery, Nippon Medical School, Tokyo, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenjiro Wake
- Liver Research Unit, Minophagen Pharmaceutical Co., Ltd., Tokyo, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Aizaki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
3
|
Islam KU, Anwar S, Patel AA, Mirdad MT, Mirdad MT, Azmi MI, Ahmad T, Fatima Z, Iqbal J. Global Lipidome Profiling Revealed Multifaceted Role of Lipid Species in Hepatitis C Virus Replication, Assembly, and Host Antiviral Response. Viruses 2023; 15:v15020464. [PMID: 36851679 PMCID: PMC9965260 DOI: 10.3390/v15020464] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Hepatitis C virus (HCV) is a major human pathogen that requires a better understanding of its interaction with host cells. There is a close association of HCV life cycle with host lipid metabolism. Lipid droplets (LDs) have been found to be crucial organelles that support HCV replication and virion assembly. In addition to their role in replication, LDs also have protein-mediated antiviral properties that are activated during HCV infection. Studies have shown that HCV replicates well in cholesterol and sphingolipid-rich membranes, but the ways in which HCV alters host cell lipid dynamics are not yet known. In this study, we performed a kinetic study to check the enrichment of LDs at different time points of HCV infection. Based on the LD enrichment results, we selected early and later time points of HCV infection for global lipidomic study. Early infection represents the window period for HCV sensing and host immune response while later infection represents the establishment of viral RNA replication, virion assembly, and egress. We identified the dynamic profile of lipid species at early and later time points of HCV infection by global lipidomic study using mass spectrometry. At early HCV infection, phosphatidylinositol phospholipids (PIPs), lysophosphatidic acid (LPA), triacyl glycerols (TAG), phosphatidylcholine (PC), and trihexosylceramides (Hex3Cer) were observed to be enriched. Similarly, free fatty acids (FFA), phosphatidylethanolamine (PE), N-acylphosphatidylethanolamines (NAPE), and tri acylglycerols were enriched at later time points of HCV infection. Lipids enriched at early time of infection may have role in HCV sensing, viral attachment, and immune response as LPA and PIPs are important for immune response and viral attachment, respectively. Moreover, lipid species observed at later infection may contribute to HCV replication and virion assembly as PE, FFA, and triacylglycerols are known for the similar function. In conclusion, we identified lipid species that exhibited dynamic profile across early and later time points of HCV infection compared to mock cells, which could be therapeutically relevant in the design of more specific and effective anti-viral therapies.
Collapse
Affiliation(s)
- Khursheed Ul Islam
- Multidisciplinary Center for Advanced Research and Studies, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Saleem Anwar
- Multidisciplinary Center for Advanced Research and Studies, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ayyub A. Patel
- Department of Clinical Biochemistry, College of Medicine, King Khalid University, Abha 62529, Saudi Arabia
| | | | | | - Md Iqbal Azmi
- Multidisciplinary Center for Advanced Research and Studies, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Tanveer Ahmad
- Multidisciplinary Center for Advanced Research and Studies, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Zeeshan Fatima
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia
- Amity Institute of Biotechnology, Amity University Haryana, Manesar, Gurugram 122413, India
- Correspondence: (Z.F.); (J.I.)
| | - Jawed Iqbal
- Multidisciplinary Center for Advanced Research and Studies, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
- Correspondence: (Z.F.); (J.I.)
| |
Collapse
|
4
|
Mechanisms and Consequences of Genetic Variation in Hepatitis C Virus (HCV). Curr Top Microbiol Immunol 2023; 439:237-264. [PMID: 36592248 DOI: 10.1007/978-3-031-15640-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chronic infection with hepatitis C virus (HCV) is an important contributor to the global incidence of liver diseases, including liver cirrhosis and hepatocellular carcinoma. Although common for single-stranded RNA viruses, HCV displays a remarkable high level of genetic diversity, produced primarily by the error-prone viral polymerase and host immune pressure. The high genetic heterogeneity of HCV has led to the evolution of several distinct genotypes and subtypes, with important consequences for pathogenesis, and clinical outcomes. Genetic variability constitutes an evasion mechanism against immune suppression, allowing the virus to evolve epitope escape mutants that avoid immune recognition. Thus, heterogeneity and variability of the HCV genome represent a great hindrance for the development of vaccines against HCV. In addition, the high genetic plasticity of HCV allows the virus to rapidly develop antiviral resistance mutations, leading to treatment failure and potentially representing a major hindrance for the cure of chronic HCV patients. In this chapter, we will present the central role that genetic diversity has in the viral life cycle and epidemiology of HCV. Incorporation errors and recombination, both the result of HCV polymerase activity, represent the main mechanisms of HCV evolution. The molecular details of both mechanisms have been only partially clarified and will be presented in the following sections. Finally, we will discuss the major consequences of HCV genetic diversity, namely its capacity to rapidly evolve antiviral and immunological escape variants that represent an important limitation for clearance of acute HCV, for treatment of chronic hepatitis C and for broadly protective vaccines.
Collapse
|
5
|
Ventura-López C, Cervantes-Luevano K, Aguirre-Sánchez JS, Flores-Caballero JC, Alvarez-Delgado C, Bernaldez-Sarabia J, Sánchez-Campos N, Lugo-Sánchez LA, Rodríguez-Vázquez IC, Sander-Padilla JG, Romero-Antonio Y, Arguedas-Núñez MM, González-Canudas J, Licea-Navarro AF. Treatment with metformin glycinate reduces SARS-CoV-2 viral load: An in vitro model and randomized, double-blind, Phase IIb clinical trial. Biomed Pharmacother 2022; 152:113223. [PMID: 35709650 PMCID: PMC9159967 DOI: 10.1016/j.biopha.2022.113223] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/24/2022] Open
Abstract
The health crisis caused by the new coronavirus SARS-CoV-2 highlights the need to identify new treatment strategies for this viral infection. During the past year, over 400 coronavirus disease (COVID-19) treatment patents have been registered; nevertheless, the presence of new virus variants has triggered more severe disease presentations and reduced treatment effectiveness, highlighting the need for new treatment options for the COVID-19. This study evaluates the Metformin Glycinate (MG) effect on the SARS-CoV-2 in vitro and in vivo viral load. The in vitro study was conducted in a model of Vero E6 cells, while the in vivo study was an adaptive, two-armed, randomized, prospective, longitudinal, double-blind, multicentric, and phase IIb clinical trial. Our in vitro results revealed that MG effectively inhibits viral replication after 48 h of exposure to the drug, with no cytotoxic effect in doses up to 100 µM. The effect of the MG was also tested against three variants of interest (alpha, delta, and epsilon), showing increased survival rates in cells treated with MG. These results are aligned with our clinical data, which indicates that MG treatment reduces SARS-CoV2-infected patients´ viral load in just 3.3 days and supplementary oxygen requirements compared with the control group. We expect our results can guide efforts to position MG as a therapeutic option for COVID-19 patients.
Collapse
Affiliation(s)
- Claudia Ventura-López
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, BC 22860, Mexico.
| | - Karla Cervantes-Luevano
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, BC 22860, Mexico.
| | | | | | - Carolina Alvarez-Delgado
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, BC 22860, Mexico.
| | - Johanna Bernaldez-Sarabia
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, BC 22860, Mexico.
| | - Noemí Sánchez-Campos
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, BC 22860, Mexico.
| | | | | | | | | | | | | | - Alexei F Licea-Navarro
- Departamento de Innovación Biomédica, CICESE, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, BC 22860, Mexico.
| |
Collapse
|
6
|
Li J, Boix E. Host Defence RNases as Antiviral Agents against Enveloped Single Stranded RNA Viruses. Virulence 2021; 12:444-469. [PMID: 33660566 PMCID: PMC7939569 DOI: 10.1080/21505594.2021.1871823] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/26/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023] Open
Abstract
Owing to the recent outbreak of Coronavirus Disease of 2019 (COVID-19), it is urgent to develop effective and safe drugs to treat the present pandemic and prevent other viral infections that might come in the future. Proteins from our own innate immune system can serve as ideal sources of novel drug candidates thanks to their safety and immune regulation versatility. Some host defense RNases equipped with antiviral activity have been reported over time. Here, we try to summarize the currently available information on human RNases that can target viral pathogens, with special focus on enveloped single-stranded RNA (ssRNA) viruses. Overall, host RNases can fight viruses by a combined multifaceted strategy, including the enzymatic target of the viral genome, recognition of virus unique patterns, immune modulation, control of stress granule formation, and induction of autophagy/apoptosis pathways. The review also includes a detailed description of representative enveloped ssRNA viruses and their strategies to interact with the host and evade immune recognition. For comparative purposes, we also provide an exhaustive revision of the currently approved or experimental antiviral drugs. Finally, we sum up the current perspectives of drug development to achieve successful eradication of viral infections.
Collapse
Affiliation(s)
- Jiarui Li
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
| | - Ester Boix
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
| |
Collapse
|
7
|
Li HC, Yang CH, Lo SY. Hepatitis C Viral Replication Complex. Viruses 2021; 13:v13030520. [PMID: 33809897 PMCID: PMC8004249 DOI: 10.3390/v13030520] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
The life cycle of the hepatitis C virus (HCV) can be divided into several stages, including viral entry, protein translation, RNA replication, viral assembly, and release. HCV genomic RNA replication occurs in the replication organelles (RO) and is tightly linked to ER membrane alterations containing replication complexes (proteins NS3 to NS5B). The amplification of HCV genomic RNA could be regulated by the RO biogenesis, the viral RNA structure (i.e., cis-acting replication elements), and both viral and cellular proteins. Studies on HCV replication have led to the development of direct-acting antivirals (DAAs) targeting the replication complex. This review article summarizes the viral and cellular factors involved in regulating HCV genomic RNA replication and the DAAs that inhibit HCV replication.
Collapse
Affiliation(s)
- Hui-Chun Li
- Department of Biochemistry, Tzu Chi University, Hualien 97004, Taiwan;
| | - Chee-Hing Yang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan;
| | - Shih-Yen Lo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 97004, Taiwan;
- Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien 97004, Taiwan
- Correspondence: ; Tel.: +886-3-8565301 (ext. 2322)
| |
Collapse
|
8
|
Sphingomyelin Is Essential for the Structure and Function of the Double-Membrane Vesicles in Hepatitis C Virus RNA Replication Factories. J Virol 2020; 94:JVI.01080-20. [PMID: 32938759 DOI: 10.1128/jvi.01080-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/05/2020] [Indexed: 02/07/2023] Open
Abstract
Some plus-stranded RNA viruses generate double-membrane vesicles (DMVs), one type of the membrane replication factories, as replication sites. Little is known about the lipid components involved in the biogenesis of these vesicles. Sphingomyelin (SM) is required for hepatitis C virus (HCV) replication, but the mechanism of SM involvement remains poorly understood. SM biosynthesis starts in the endoplasmic reticulum (ER) and gives rise to ceramide, which is transported from the ER to the Golgi by the action of ceramide transfer protein (CERT), where it can be converted to SM. In this study, inhibition of SM biosynthesis, either by using small-molecule inhibitors or by knockout (KO) of CERT, suppressed HCV replication in a genotype-independent manner. This reduction in HCV replication was rescued by exogenous SM or ectopic expression of the CERT protein, but not by ectopic expression of nonfunctional CERT mutants. Observing low numbers of DMVs in stable replicon cells treated with a SM biosynthesis inhibitor or in CERT-KO cells transfected with either HCV replicon or with constructs that drive HCV protein production in a replication-independent system indicated the significant importance of SM to DMVs. The degradation of SM of the in vitro-isolated DMVs affected their morphology and increased the vulnerability of HCV RNA and proteins to RNase and protease treatment, respectively. Poliovirus, known to induce DMVs, showed decreased replication in CERT-KO cells, while dengue virus, known to induce invaginated vesicles, did not. In conclusion, these findings indicated that SM is an essential constituent of DMVs generated by some plus-stranded RNA viruses.IMPORTANCE Previous reports assumed that sphingomyelin (SM) is essential for HCV replication, but the mechanism was unclear. In this study, we showed for the first time that SM and ceramide transfer protein (CERT), which is in the SM biosynthesis pathway, are essential for the biosynthesis of double-membrane vesicles (DMVs), the sites of viral replication. Low numbers of DMVs were observed in CERT-KO cells transfected with replicon RNA or with constructs that drive HCV protein production in a replication-independent system. HCV replication was rescued by ectopic expression of the CERT protein, but not by CERT mutants, that abolishes the binding of CERT to vesicle-associated membrane protein-associated protein (VAP) or phosphatidylinositol 4-phosphate (PI4P), indicating new roles for VAP and PI4P in HCV replication. The biosynthesis of DMVs has great importance to replication by a variety of plus-stranded RNA viruses. Understanding of this process is expected to facilitate the development of diagnosis and antivirus.
Collapse
|
9
|
Alzahrani N, Wu MJ, Shanmugam S, Yi M. Delayed by Design: Role of Suboptimal Signal Peptidase Processing of Viral Structural Protein Precursors in Flaviviridae Virus Assembly. Viruses 2020; 12:v12101090. [PMID: 32993149 PMCID: PMC7601889 DOI: 10.3390/v12101090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/04/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
The Flaviviridae virus family is classified into four different genera, including flavivirus, hepacivirus, pegivirus, and pestivirus, which cause significant morbidity and mortality in humans and other mammals, including ruminants and pigs. These are enveloped, single-stranded RNA viruses sharing a similar genome organization and replication scheme with certain unique features that differentiate them. All viruses in this family express a single polyprotein that encodes structural and nonstructural proteins at the N- and C-terminal regions, respectively. In general, the host signal peptidase cleaves the structural protein junction sites, while virus-encoded proteases process the nonstructural polyprotein region. It is known that signal peptidase processing is a rapid, co-translational event. Interestingly, certain signal peptidase processing site(s) in different Flaviviridae viral structural protein precursors display suboptimal cleavage kinetics. This review focuses on the recent progress regarding the Flaviviridae virus genus-specific mechanisms to downregulate signal peptidase-mediated processing at particular viral polyprotein junction sites and the role of delayed processing at these sites in infectious virus particle assembly.
Collapse
|
10
|
Balgoma D, Gil-de-Gómez L, Montero O. Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update. Metabolites 2020; 10:E356. [PMID: 32878290 PMCID: PMC7569815 DOI: 10.3390/metabo10090356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022] Open
Abstract
The pathogenic mechanisms underlying the Biology and Biochemistry of viral infections are known to depend on the lipid metabolism of infected cells. From a lipidomics viewpoint, there are a variety of mechanisms involving virus infection that encompass virus entry, the disturbance of host cell lipid metabolism, and the role played by diverse lipids in regard to the infection effectiveness. All these aspects have currently been tackled separately as independent issues and focused on the function of proteins. Here, we review the role of cholesterol and other lipids in ssRNA+ infection.
Collapse
Affiliation(s)
- David Balgoma
- Analytical Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University, Husarg. 3, 75123 Uppsala, Sweden;
| | - Luis Gil-de-Gómez
- Center of Childhood Cancer Center, Children’s Hospital of Philadelphia, Colket Translational Research Center, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA;
| | - Olimpio Montero
- Spanish National Research Council (CSIC), Boecillo’s Technological Park Bureau, Av. Francisco Vallés 8, 47151 Boecillo, Spain
| |
Collapse
|
11
|
Tabata K, Neufeldt CJ, Bartenschlager R. Hepatitis C Virus Replication. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a037093. [PMID: 31570388 DOI: 10.1101/cshperspect.a037093] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Replication and amplification of the viral genome is a key process for all viruses. For hepatitis C virus (HCV), a positive-strand RNA virus, amplification of the viral genome requires the synthesis of a negative-sense RNA template, which is in turn used for the production of new genomic RNA. This process is governed by numerous proteins, both host and viral, as well as distinct lipids and specific RNA elements within the positive- and negative-strand RNAs. Moreover, this process requires specific changes to host cell ultrastructure to create microenvironments conducive to viral replication. This review will focus on describing the processes and factors involved in facilitating or regulating HCV genome replication.
Collapse
Affiliation(s)
- Keisuke Tabata
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany
| | - Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany.,Division of Virus-Associated Carcinogenesis, German Cancer Research Center, 69120 Heidelberg, Germany.,German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| |
Collapse
|
12
|
Sharma G, Tripathi SK, Das S. lncRNA HULC facilitates efficient loading of HCV-core protein onto lipid droplets and subsequent virus-particle release. Cell Microbiol 2019; 21:e13086. [PMID: 31290220 DOI: 10.1111/cmi.13086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 06/29/2019] [Accepted: 07/07/2019] [Indexed: 12/11/2022]
Abstract
The cellular lipid pool plays a central role in hepatitis C virus (HCV) life cycle, from establishing infection to virus propagation. Here, we show that a liver abundant long noncoding RNA, highly upregulated in liver carcinoma (HULC), is upregulated during HCV infection and manipulates the lipid pool to favour virus life cycle. Interestingly, HULC was found to be crucial for the increase in number of lipid droplets in infected cells. This effect was attributed to the role of HULC in lipid biogenesis. Further, we demonstrated that HULC knockdown decreases the association of HCV-core protein with lipid droplets. This exhibited a direct consequence on the release of HCV particles. The role of HULC in HCV-particle release was further substantiated by additional knockdown and mutation experiments. Additionally, we found that increased level of HULC in HCV-infected cells was a result of Retinoid X Receptor Alpha (RXRA)-mediated transcription, which seemed to be aided by HCV-core protein. Taken together, the results identify a distinct role of long noncoding RNA HULC in lipid dynamics during HCV infection, which provides new insights into the complex process of HCV propagation and pathogenesis.
Collapse
Affiliation(s)
- Geetika Sharma
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sachin Kumar Tripathi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,National Institute of Biomedical Genomics, Kalyani, India
| |
Collapse
|
13
|
Hernández S, Díaz A, Loyola A, Villanueva RA. Recombinant HCV NS3 and NS5B enzymes exhibit multiple posttranslational modifications for potential regulation. Virus Genes 2019; 55:227-232. [PMID: 30694421 DOI: 10.1007/s11262-019-01638-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/17/2019] [Indexed: 11/25/2022]
Abstract
Posttranslational modification (PTM) of proteins is critical to modulate protein function and to improve the functional diversity of polypeptides. In this report, we have analyzed the PTM of both hepatitis C virus NS3 and NS5B enzyme proteins, upon their individual expression in insect cells under the baculovirus expression system. Using mass spectrometry, we present evidence that these recombinant proteins exhibit diverse covalent modifications on certain amino acid side chains, such as phosphorylation, ubiquitination, and acetylation. Although the functional implications of these PTM must be further addressed, these data may prove useful toward the understanding of the complex regulation of these key viral enzymes and to uncover novel potential targets for antiviral design.
Collapse
Affiliation(s)
- Sergio Hernández
- Fundación Ciencia &, Vida, Avda. Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile.,Architecture et Fonction des Macromolécules Biologiques, CNRS UMR7257, Department of Medicinal Chemistry, Aix Marseille Universite, Marseille, France
| | - Ariel Díaz
- Fundación Ciencia &, Vida, Avda. Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile
| | - Alejandra Loyola
- Fundación Ciencia &, Vida, Avda. Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile
| | | |
Collapse
|
14
|
Abstract
Super-resolution microscopy (SRM) can provide a window on the nanoscale events of virus replication. Here we describe a protocol for imaging hepatitis C virus-infected cells using localization SRM. We provide details on sample preparation, immunostaining, data collection, and super-resolution image reconstruction. We have made all efforts to generalize the protocol to make it accessible to all budding super-resolution microscopists.
Collapse
|
15
|
Genomic-Scale Interaction Involving Complementary Sequences in the Hepatitis C Virus 5'UTR Domain IIa and the RNA-Dependent RNA Polymerase Coding Region Promotes Efficient Virus Replication. Viruses 2018; 11:v11010017. [PMID: 30597844 PMCID: PMC6357077 DOI: 10.3390/v11010017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/22/2018] [Accepted: 12/23/2018] [Indexed: 12/31/2022] Open
Abstract
The hepatitis C virus (HCV) genome contains structured elements thought to play important regulatory roles in viral RNA translation and replication processes. We used in vitro RNA binding assays to map interactions involving the HCV 5′UTR and distal sequences in NS5B to examine their impact on viral RNA replication. The data revealed that 5′UTR nucleotides (nt) 95–110 in the internal ribosome entry site (IRES) domain IIa and matching nt sequence 8528–8543 located in the RNA-dependent RNA polymerase coding region NS5B, form a high-affinity RNA-RNA complex in vitro. This duplex is composed of both wobble and Watson-Crick base-pairings, with the latter shown to be essential to the formation of the high-affinity duplex. HCV genomic RNA constructs containing mutations in domain IIa nt 95–110 or within the genomic RNA location comprising nt 8528–8543 displayed, on average, 5-fold less intracellular HCV RNA and 6-fold less infectious progeny virus. HCV genomic constructs containing complementary mutations for IRES domain IIa nt 95–110 and NS5B nt 8528–8543 restored intracellular HCV RNA and progeny virus titers to levels obtained for parental virus RNA. We conclude that this long-range duplex interaction between the IRES domain IIa and NS5B nt 8528–8543 is essential for optimal virus replication.
Collapse
|
16
|
Sharma G, Raheja H, Das S. Hepatitis C virus: Enslavement of host factors. IUBMB Life 2018; 70:41-49. [PMID: 29281185 DOI: 10.1002/iub.1702] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus (HCV) has infected over 170 million people world-wide. This infection causes severe liver damage that can progress to hepatocellular carcinoma leading to death of the infected patients. Development of a cell culture model system for the study of HCV infection in the recent past has helped the researchers world-wide to understand the biology of this virus. Studies over the past decade have revealed the tricks played by the virus to sustain itself, for as long as 40 years, in the host setup without being eliminated by the immune system. Today we understand that the host organelles and different cellular proteins are affected during HCV infection. This cytoplasmic virus has all the cellular organelles at its disposal to successfully replicate, from ribosomes and intracellular membranous structures to the nucleus. It modulates these organelles at both the structural and the functional levels. The vast knowledge about the viral genome and viral proteins has also helped in the development of drugs against the virus. Despite the achieved success rate to cure the infected patients, we struggle to eliminate the cases of recurrence and the non-responders. Such cases might emerge owing to the property of the viral genome to accumulate mutations during its succeeding replication cycles which favours its survival. The current situation calls an urgent need for alternate therapeutic strategies to counter this major problem of human health. © 2017 IUBMB Life, 70(1):41-49, 2018.
Collapse
Affiliation(s)
- Geetika Sharma
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Harsha Raheja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| |
Collapse
|
17
|
Blanchard E, Roingeard P. The Hepatitis C Virus-Induced Membranous Web in Liver Tissue. Cells 2018; 7:cells7110191. [PMID: 30388825 PMCID: PMC6262270 DOI: 10.3390/cells7110191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/24/2018] [Accepted: 10/31/2018] [Indexed: 01/01/2023] Open
Abstract
Host cell membrane rearrangements induced by the hepatitis C virus (HCV) have been exclusively studied in vitro. These studies have shown that HCV induces double-membrane vesicles (DMVs), which probably serve to separate replication sites from the cytoplasmic sensors of the innate immune response. We report for the first time the observation of HCV-induced membrane rearrangements in liver biopsy specimens from patients chronically infected with HCV. Unlike observations performed in vitro, the membranous web detected in liver tissue seems essentially made of clusters of single-membrane vesicles derived from the endoplasmic reticulum and close to lipid droplets. This suggests that the DMVs could be a hallmark of laboratory-adapted HCV strains, possibly due to their ability to achieve a high level of replication. Alternatively, the concealment of viral RNA in DMVs may be part of innate immune response mechanisms particularly developed in hepatoma cell lines cultured in vitro. In any case, this constitutes the first report showing the differences in the membranous web established by HCV in vitro and in vivo.
Collapse
Affiliation(s)
- Emmanuelle Blanchard
- INSERM U1259, Université de Tours & CHRU de Tours, 37032 Tours, France.
- Plateforme IBISA de Microscopie Electronique, Université de Tours & CHRU de Tours, 37032 Tours, France.
| | - Philippe Roingeard
- INSERM U1259, Université de Tours & CHRU de Tours, 37032 Tours, France.
- Plateforme IBISA de Microscopie Electronique, Université de Tours & CHRU de Tours, 37032 Tours, France.
| |
Collapse
|
18
|
A role for domain I of the hepatitis C virus NS5A protein in virus assembly. PLoS Pathog 2018; 14:e1006834. [PMID: 29352312 PMCID: PMC5792032 DOI: 10.1371/journal.ppat.1006834] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/31/2018] [Accepted: 12/19/2017] [Indexed: 12/12/2022] Open
Abstract
The NS5A protein of hepatitis C virus (HCV) plays roles in both virus genome replication and assembly. NS5A comprises three domains, of these domain I is believed to be involved exclusively in genome replication. In contrast, domains II and III are required for the production of infectious virus particles and are largely dispensable for genome replication. Domain I is highly conserved between HCV and related hepaciviruses, and is highly structured, exhibiting different dimeric conformations. To investigate the functions of domain I in more detail, we conducted a mutagenic study of 12 absolutely conserved and surface-exposed residues within the context of a JFH-1-derived sub-genomic replicon and infectious virus. Whilst most of these abrogated genome replication, three mutants (P35A, V67A and P145A) retained the ability to replicate but showed defects in virus assembly. P35A exhibited a modest reduction in infectivity, however V67A and P145A produced no infectious virus. Using a combination of density gradient fractionation, biochemical analysis and high resolution confocal microscopy we demonstrate that V67A and P145A disrupted the localisation of NS5A to lipid droplets. In addition, the localisation and size of lipid droplets in cells infected with these two mutants were perturbed compared to wildtype HCV. Biophysical analysis revealed that V67A and P145A abrogated the ability of purified domain I to dimerize and resulted in an increased affinity of binding to HCV 3’UTR RNA. Taken together, we propose that domain I of NS5A plays multiple roles in assembly, binding nascent genomic RNA and transporting it to lipid droplets where it is transferred to Core. Domain I also contributes to a change in lipid droplet morphology, increasing their size. This study reveals novel functions of NS5A domain I in assembly of infectious HCV and provides new perspectives on the virus lifecycle. Hepatitis C virus infects 170 million people worldwide, causing long term liver disease. Recently new therapies comprising direct-acting antivirals (DAAs), small molecule inhibitors of virus proteins, have revolutionised treatment for infected patients. Despite this, we have a limited understanding of how the virus replicates in infected liver cells. Here we identify a previously uncharacterised function of the NS5A protein–a target for one class of DAAs. NS5A is comprised of three domains–we show that the first of these (domain I) plays a role in the production of new, infectious virus particles. Previously it was thought that domain I was only involved in replicating the virus genome. Mutations in domain I perturb dimer formation, enhanced binding to the 3’ end of the virus RNA genome and prevented NS5A from interacting with lipid droplets, cellular lipid storage organelles that are required for assembly of new viruses. We propose that domain I of NS5A plays multiple roles in virus assembly. As domain I is the putative target for one class of DAAs, our observations may have implications for the as yet undefined mode of action of these compounds.
Collapse
|
19
|
Abstract
The Aichi RNA virus remodels host membranes by conscripting two host proteins, PI4KIIIβ (to generate PI4P in the remodeled vesicle) and ACBD3 (that tightly binds PI4KIIIβ), and localizing them on target membranes via Aichi protein 3A. In this issue of Structure, McPhail et al. (2017) reveal structural glimpses of the interfaces involved in this protein threesome using HDX-MS.
Collapse
Affiliation(s)
- Mary F Roberts
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA.
| |
Collapse
|
20
|
Jiang XH, Xie YT, Cai YP, Ren J, Ma T. Effects of hepatitis C virus core protein and nonstructural protein 4B on the Wnt/β-catenin pathway. BMC Microbiol 2017; 17:124. [PMID: 28545480 PMCID: PMC5445264 DOI: 10.1186/s12866-017-1032-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/15/2017] [Indexed: 12/21/2022] Open
Abstract
Background Hepatitis C virus (HCV) core protein and nonstructural protein 4B (NS4B) are potentially oncogenic. Aberrant activation of the Wnt/β-catenin signaling pathway is closely associated with hepatocarcinogenesis. We investigated the effects of HCV type 1b core protein and NS4B on Wnt/β-catenin signaling in various liver cells, and explored the molecular mechanism underlying HCV-related hepatocarcinogenesis. Results Compared with the empty vector control, HCV core protein and NS4B demonstrated the following characteristics in the Huh7 cells: significantly enhanced β-catenin/Tcf-dependent transcriptional activity (F = 40.87, P < 0.01); increased nuclear translocation of β-catenin (F = 165.26, P < 0.01); upregulated nuclear β-catenin, cytoplasmic β-catenin, Wnt1, c-myc, and cyclin D1 protein expression (P < 0.01); and promoted proliferation of Huh7 cells (P < 0.01 or P < 0.05). Neither protein enhanced β-catenin/Tcf-dependent transcriptional activity in the LO2 cells (F = 0.65, P > 0.05), but they did significantly enhance Wnt3a-induced β-catenin/Tcf-dependent transcriptional activity (F = 64.25, P < 0.01), and promoted the nuclear translocation of β-catenin (F = 66.54, P < 0.01) and the Wnt3a-induced proliferation of LO2 cells (P < 0.01 or P < 0.05). Moreover, activation of the Wnt/β-catenin signaling pathway was greater with the core protein than with NS4B (P < 0.01 or P < 0.05). Conclusions HCV core protein and NS4B directly activate the Wnt/β-catenin signaling pathway in Huh7 cells and LO2 cells induced by Wnt3a. These data suggest that HCV core protein and NS4B contribute to HCV-associated hepatocellular carcinogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1032-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xiao-Hua Jiang
- Department of Infectious Diseases, the First Affiliated Hospital of the University of South China, Hengyang, 421001, China
| | - Yu-Tao Xie
- Department of Infectious Diseases, Xiangya Hospital of Central South University, Changsha, 410087, China.
| | - Ya-Ping Cai
- Department of Epidemiology and Health Statistics, the University of South China, Hengyang, 421001, China
| | - Jing Ren
- Department of Infectious Diseases, the First Affiliated Hospital of the University of South China, Hengyang, 421001, China
| | - Tao Ma
- Department of Infectious Diseases, the First Affiliated Hospital of the University of South China, Hengyang, 421001, China
| |
Collapse
|