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Sallam M, Khalil R. Contemporary Insights into Hepatitis C Virus: A Comprehensive Review. Microorganisms 2024; 12:1035. [PMID: 38930417 PMCID: PMC11205832 DOI: 10.3390/microorganisms12061035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
Hepatitis C virus (HCV) remains a significant global health challenge. Approximately 50 million people were living with chronic hepatitis C based on the World Health Organization as of 2024, contributing extensively to global morbidity and mortality. The advent and approval of several direct-acting antiviral (DAA) regimens significantly improved HCV treatment, offering potentially high rates of cure for chronic hepatitis C. However, the promising aim of eventual HCV eradication remains challenging. Key challenges include the variability in DAA access across different regions, slightly variable response rates to DAAs across diverse patient populations and HCV genotypes/subtypes, and the emergence of resistance-associated substitutions (RASs), potentially conferring resistance to DAAs. Therefore, periodic reassessment of current HCV knowledge is needed. An up-to-date review on HCV is also necessitated based on the observed shifts in HCV epidemiological trends, continuous development and approval of therapeutic strategies, and changes in public health policies. Thus, the current comprehensive review aimed to integrate the latest knowledge on the epidemiology, pathophysiology, diagnostic approaches, treatment options and preventive strategies for HCV, with a particular focus on the current challenges associated with RASs and ongoing efforts in vaccine development. This review sought to provide healthcare professionals, researchers, and policymakers with the necessary insights to address the HCV burden more effectively. We aimed to highlight the progress made in managing and preventing HCV infection and to highlight the persistent barriers challenging the prevention of HCV infection. The overarching goal was to align with global health objectives towards reducing the burden of chronic hepatitis, aiming for its eventual elimination as a public health threat by 2030.
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Affiliation(s)
- Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
| | - Roaa Khalil
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
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2
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Koonin EV. Circular RNAs from linear viral RNA genomes: A distinct dimension in the virus world. Proc Natl Acad Sci U S A 2024; 121:e2401335121. [PMID: 38349885 PMCID: PMC10895248 DOI: 10.1073/pnas.2401335121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD20894
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3
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Cao QM, Boonchuen P, Chen TC, Lei S, Somboonwiwat K, Sarnow P. Virus-derived circular RNAs populate hepatitis C virus-infected cells. Proc Natl Acad Sci U S A 2024; 121:e2313002121. [PMID: 38319965 PMCID: PMC10873615 DOI: 10.1073/pnas.2313002121] [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: 07/28/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
It is known that pre-mRNAs in eukaryotic cells can be processed to circular RNAs by a backsplicing mechanism. Circular RNAs have great stability and can sequester proteins or small RNAs to exert functions on cellular pathways. Because viruses often exploit host pathways, we explored whether the RNA genome of the cytoplasmic hepatitis C virus is processed to yield virus-derived circRNAs (vcircRNAs). Computational analyses of RNA-seq experiments predicted that the viral RNA genome is fragmented to generate hundreds of vcircRNAs. More than a dozen of them were experimentally verified by rolling-circle amplification. VcircRNAs that contained the viral internal ribosome entry site were found to be translated into proteins that displayed proviral functions. Furthermore, two highly abundant, nontranslated vcircRNAs were shown to enhance viral RNA abundance. These findings argue that novel vcircRNA molecules modulate viral amplification in cells infected by a cytoplasmic RNA virus.
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Affiliation(s)
- Qian M. Cao
- Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA94305
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Mueang Nakhon Ratchasima30000, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Tzu-Chun Chen
- Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA94305
| | - Shaohua Lei
- Center of Excellence for Leukemia Studies, Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN38105
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN38105
| | - Kunlaya Somboonwiwat
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Peter Sarnow
- Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA94305
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4
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Porpiglia E, Mai T, Kraft P, Holbrook CA, de Morree A, Gonzalez VD, Hilgendorf KI, Frésard L, Trejo A, Bhimaraju S, Jackson PK, Fantl WJ, Blau HM. Elevated CD47 is a hallmark of dysfunctional aged muscle stem cells that can be targeted to augment regeneration. Cell Stem Cell 2022; 29:1653-1668.e8. [PMID: 36384141 PMCID: PMC9746883 DOI: 10.1016/j.stem.2022.10.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/04/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022]
Abstract
In aging, skeletal muscle strength and regenerative capacity decline, due in part to functional impairment of muscle stem cells (MuSCs), yet the underlying mechanisms remain elusive. Here, we capitalize on mass cytometry to identify high CD47 expression as a hallmark of dysfunctional MuSCs (CD47hi) with impaired regenerative capacity that predominate with aging. The prevalent CD47hi MuSC subset suppresses the residual functional CD47lo MuSC subset through a paracrine signaling loop, leading to impaired proliferation. We uncover that elevated CD47 levels on aged MuSCs result from increased U1 snRNA expression, which disrupts alternative polyadenylation. The deficit in aged MuSC function in regeneration can be overcome either by morpholino-mediated blockade of CD47 alternative polyadenylation or antibody blockade of thrombospondin-1/CD47 signaling, leading to improved regeneration in aged mice, with therapeutic implications. Our findings highlight a previously unrecognized age-dependent alteration in CD47 levels and function in MuSCs, which underlies reduced muscle repair in aging.
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Affiliation(s)
- Ermelinda Porpiglia
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedicine, Aarhus University, Aarhus C 8000, Denmark.
| | - Thach Mai
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peggy Kraft
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Colin A Holbrook
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Antoine de Morree
- Department of Biomedicine, Aarhus University, Aarhus C 8000, Denmark; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Veronica D Gonzalez
- Nolan Laboratory, Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keren I Hilgendorf
- Jackson Laboratory, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laure Frésard
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Angelica Trejo
- Nolan Laboratory, Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Sriram Bhimaraju
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter K Jackson
- Jackson Laboratory, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wendy J Fantl
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Jones ST, Cagno V, Janeček M, Ortiz D, Gasilova N, Piret J, Gasbarri M, Constant DA, Han Y, Vuković L, Král P, Kaiser L, Huang S, Constant S, Kirkegaard K, Boivin G, Stellacci F, Tapparel C. Modified cyclodextrins as broad-spectrum antivirals. SCIENCE ADVANCES 2020; 6:eaax9318. [PMID: 32064341 PMCID: PMC6989148 DOI: 10.1126/sciadv.aax9318] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/22/2019] [Indexed: 05/18/2023]
Abstract
Viral infections kill millions of people and new antivirals are needed. Nontoxic drugs that irreversibly inhibit viruses (virucidal) are postulated to be ideal. Unfortunately, all virucidal molecules described to date are cytotoxic. We recently developed nontoxic, broad-spectrum virucidal gold nanoparticles. Here, we develop further the concept and describe cyclodextrins, modified with mercaptoundecane sulfonic acids, to mimic heparan sulfates and to provide the key nontoxic virucidal action. We show that the resulting macromolecules are broad-spectrum, biocompatible, and virucidal at micromolar concentrations in vitro against many viruses [including herpes simplex virus (HSV), respiratory syncytial virus (RSV), dengue virus, and Zika virus]. They are effective ex vivo against both laboratory and clinical strains of RSV and HSV-2 in respiratory and vaginal tissue culture models, respectively. Additionally, they are effective when administrated in mice before intravaginal HSV-2 inoculation. Lastly, they pass a mutation resistance test that the currently available anti-HSV drug (acyclovir) fails.
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Affiliation(s)
- Samuel T. Jones
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Department of Materials, University of Manchester, Manchester M13 9PL, UK
| | - Valeria Cagno
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Matej Janeček
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Daniel Ortiz
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Natalia Gasilova
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Jocelyne Piret
- CHU of Québec-Laval University, Québec City, Québec, Canada
| | - Matteo Gasbarri
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - David A. Constant
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yanxiao Han
- Department of Chemistry, University of Illinois, Chicago, IL 60607, USA
| | - Lela Vuković
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX 79966, USA
| | - Petr Král
- Department of Chemistry, University of Illinois, Chicago, IL 60607, USA
- Department of Physics, and Department of Biopharmaceutical Sciences, University of Illinois, Chicago, IL 60612, USA
| | - Laurent Kaiser
- Division of Infectious diseases, University Hospitals of Geneva, Geneva, Switzerland
| | | | | | - Karla Kirkegaard
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Guy Boivin
- CHU of Québec-Laval University, Québec City, Québec, Canada
| | - Francesco Stellacci
- Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Department of Bionengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Corresponding author. (C.T.); (F.S.)
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
- Corresponding author. (C.T.); (F.S.)
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Abernathy E, Mateo R, Majzoub K, van Buuren N, Bird SW, Carette JE, Kirkegaard K. Differential and convergent utilization of autophagy components by positive-strand RNA viruses. PLoS Biol 2019; 17:e2006926. [PMID: 30608919 PMCID: PMC6334974 DOI: 10.1371/journal.pbio.2006926] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 01/16/2019] [Accepted: 12/06/2018] [Indexed: 12/15/2022] Open
Abstract
Many viruses interface with the autophagy pathway, a highly conserved process for recycling cellular components. For three viral infections in which autophagy constituents are proviral (poliovirus, dengue, and Zika), we developed a panel of knockouts (KOs) of autophagy-related genes to test which components of the canonical pathway are utilized. We discovered that each virus uses a distinct set of initiation components; however, all three viruses utilize autophagy-related gene 9 (ATG9), a lipid scavenging protein, and LC3 (light-chain 3), which is involved in membrane curvature. These results show that viruses use noncanonical routes for membrane sculpting and LC3 recruitment. By measuring viral RNA abundance, we also found that poliovirus utilizes these autophagy components for intracellular growth, while dengue and Zika virus only use autophagy components for post-RNA replication processes. Comparing how RNA viruses manipulate the autophagy pathway reveals new noncanonical autophagy routes, explains the exacerbation of disease by starvation, and uncovers common targets for antiviral drugs. Viruses often co-opt host cellular processes to replicate their genomes and spread to other cells. Many of these cellular pathways provide good targets for antiviral drugs, as they are less likely to develop resistance since they are encoded in the host and not the fast-evolving viral genome. The autophagy pathway is an important stress response pathway that allows cells to recycle cellular components for energy conservation by sequestering cytoplasmic molecules and organelles in double-membraned vesicles (DMVs) and by degrading the contents into reusable elements. Many RNA viruses induce this pathway to provide membrane surfaces for replication and as a source of vesicles for maturation and exit from cells. We developed a panel of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) knockout (KO) human cells lacking individual components of the autophagy pathway to assess what aspects of the pathway diverse RNA viruses utilized. We discovered that poliovirus, dengue virus, and Zika virus all use different initiation components of the autophagy pathway but similar downstream components. Additionally, we found that poliovirus uses autophagy components for genome replication, while dengue and Zika viruses use autophagy components for postreplication processes. Ultimately, we uncovered potential drug targets for multiple RNA viruses.
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Affiliation(s)
- Emma Abernathy
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Roberto Mateo
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Karim Majzoub
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- INSERM U1110, Institute of Viral and Liver Diseases, University of Strasbourg, Strasbourg, France
| | - Nick van Buuren
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sara W. Bird
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jan E. Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Karla Kirkegaard
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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van Buuren N, Kirkegaard K. Detection and Differentiation of Multiple Viral RNAs Using Branched DNA FISH Coupled to Confocal Microscopy and Flow Cytometry. Bio Protoc 2018; 8:e3058. [PMID: 30505886 DOI: 10.21769/bioprotoc.3058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Due to the exceptionally high mutation rates of RNA-dependent RNA polymerases, infectious RNA viruses generate extensive sequence diversity, leading to some of the lowest barriers to the development of antiviral drug resistance in the microbial world. We have previously discovered that higher barriers to the development of drug resistance can be achieved through dominant suppression of drug-resistant viruses by their drug-susceptible parents. We have explored the existence of dominant drug targets in poliovirus, dengue virus and hepatitis C virus (HCV). The low replication capacity of HCV required the development of novel strategies for identifying cells co-infected with drug-susceptible and drug-resistant strains. To monitor co-infected cell populations, we generated codon-altered versions of the JFH1 strain of HCV. Then, we could differentiate the codon-altered and wild-type strains using a novel type of RNA fluorescent in situ hybridization (FISH) coupled with flow cytometry or confocal microscopy. Both of these techniques can be used in conjunction with standard antibody-protein detection methods. Here, we describe a detailed protocol for both RNA FISH flow cytometry and confocal microscopy.
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Affiliation(s)
- Nicholas van Buuren
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Karla Kirkegaard
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
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