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Alghubayshi A, Wijesinghe D, Alwadaani D, Algahtani FH, Abohelaika S, Alzahrani M, Al Saeed HH, Al Zayed A, Alshammari S, Alhendi Y, Alsomaie B, Alsaleh A, Alshabeeb MA. Unraveling the Complex Genomic Interplay of Sickle Cell Disease Among the Saudi Population: A Case-Control GWAS Analysis. Int J Mol Sci 2025; 26:2817. [PMID: 40141459 PMCID: PMC11942740 DOI: 10.3390/ijms26062817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 03/09/2025] [Accepted: 03/13/2025] [Indexed: 03/28/2025] Open
Abstract
Sickle cell disease (SCD) is a severe inherited blood disorder characterized by abnormal hemoglobin (HbS) that leads to varying degrees of severity, including chronic hemolysis, episodic vaso-occlusion, and damage to multiple organs, causing significant morbidity and mortality. While SCD is a monogenic disease, its complications are influenced by polygenic factors. SCD prevalence is notably high in regions including the Middle East, with Saudi Arabia reporting significant cases, particularly in the Eastern Province. Most genetic factors associated with SCD outcomes have been identified in populations predominantly from Africa or of African ancestry. This study aims to identify genetic variants that characterize Saudi SCD patients with the potential to influence disease outcomes in this population. A multicenter case-control genome-wide association study (GWAS) was conducted involving 350 adult Saudi SCD patients and 202 healthy controls. Participants were genotyped using the Affymetrix Axiom array, covering 683,030 markers. Rigorous quality control measures were applied to ensure data integrity. Fisher's exact was used to identify genetic variants with a significant difference in allele frequency (p < 5 × 10-8). Functional annotations and regulatory functions of variants were determined using the Ensembl Variant Effect Predictor (VEP) and RegulomeDB databases. The GWAS identified numerous significant genetic variants characterizing SCD cases in the Saudi population. These variants, distributed across multiple chromosomes, were found in genes with known functional consequences. A substantial proportion of the markers were detected in the olfactory receptor cluster, TRIM family, and HBB locus genes. Many of the identified genes were reported in previous studies showing significant associations with various SCD outcomes, including hemoglobin regulation, inflammation, immune response, and vascular function. The findings highlight the genetic complexity underlying SCD and its clinical manifestations. The identified variants suggest potential molecular biomarkers and therapeutic targets, enhancing our understanding of the molecular basis of SCD in the Saudi population. This is the first genetic analysis characterizing SCD patients compared to healthy individuals, uncovering genetic markers that could serve as diagnostic biomarkers and therapeutic targets. Given the known molecular mechanisms of the detected genetic loci, these provide a foundation for precision medicine in SCD management, highlighting the need for further studies to validate these results and explore their clinical implications.
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Affiliation(s)
- Ali Alghubayshi
- Department of Clinical Pharmacy, College of Pharmacy, University of Ha’il, Ha’il 55473, Saudi Arabia;
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.W.); (S.A.)
| | - Dayanjan Wijesinghe
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.W.); (S.A.)
| | - Deemah Alwadaani
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia;
- King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia; (M.A.); (Y.A.); (B.A.); (A.A.)
| | - Farjah H. Algahtani
- Hematology/Oncology Center, King Saud University Medical City (KSUMC), Riyadh 11411, Saudi Arabia;
| | - Salah Abohelaika
- Research Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia;
- Pharmacy Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia
| | - Mohsen Alzahrani
- King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia; (M.A.); (Y.A.); (B.A.); (A.A.)
- King Fahad Hospital, Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
| | - Hussain H. Al Saeed
- Hematology Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia; (H.H.A.S.); (A.A.Z.)
| | - Abdullah Al Zayed
- Hematology Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia; (H.H.A.S.); (A.A.Z.)
| | - Suad Alshammari
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.W.); (S.A.)
- Department of Clinical Pharmacy, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Yaseen Alhendi
- King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia; (M.A.); (Y.A.); (B.A.); (A.A.)
- Saudi Biobank Center, King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia
| | - Barrak Alsomaie
- King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia; (M.A.); (Y.A.); (B.A.); (A.A.)
- Operations Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia
| | - Abdulmonem Alsaleh
- King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia; (M.A.); (Y.A.); (B.A.); (A.A.)
- Blood and Cancer Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia
| | - Mohammad A. Alshabeeb
- King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia; (M.A.); (Y.A.); (B.A.); (A.A.)
- Pharmaceutical Analysis Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia
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Ma Y, Mao Y, Luo S, Zuo W, Gao P, Ying B. Development and characterization of a miRNA-responsive circular RNA expression system with cell type specificity. MOLECULAR THERAPY. NUCLEIC ACIDS 2025; 36:102450. [PMID: 39967851 PMCID: PMC11834102 DOI: 10.1016/j.omtn.2025.102450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 01/10/2025] [Indexed: 02/20/2025]
Abstract
Although microRNAs (miRNAs) binding to messenger RNAs (mRNAs) generally results in mRNA degradation and reduced protein expression, their interaction with the internal ribosome entry sites (IRES) of certain RNA viruses enhances viral amplification and expression. In this study, we utilized the natural hepatitis C cirus (HCV) 5' UTR region, which contains miR-122 binding sites, as the IRES of circular RNA (circRNAs) constructs. These circRNAs allowed inducible expression of downstream genes with high specificity in response to both exogenous and endogenous miR-122. Substituting the miR-122 binding sites with those for other miRNAs also resulted in the translational activation of circRNAs by their respective miRNAs in transfected cells. Furthermore, mouse models administered intravenously with lipid nanoparticle-formulated circRNAs containing miRNA binding sites (circRNA-LNP) exhibited higher expression in targeted tissues compared to those with mutated binding sites. Our research introduces a novel strategy for tissue-specific regulation of circRNA expression, potentially broadening the therapeutic applications of circRNAs and paving the way for more precise and effective treatments in gene therapy.
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Affiliation(s)
- Yu Ma
- Suzhou Abogen Biosciences Company, Suzhou 215123, China
| | - Yuqiao Mao
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Shirui Luo
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Wenjie Zuo
- Suzhou Abogen Biosciences Company, Suzhou 215123, China
| | - Peng Gao
- Suzhou Abogen Biosciences Company, Suzhou 215123, China
| | - Bo Ying
- Suzhou Abogen Biosciences Company, Suzhou 215123, China
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3
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Żychowska J, Ćmil M, Skórka P, Olejnik-Wojciechowska J, Plewa P, Bakinowska E, Kiełbowski K, Pawlik A. The Role of Epigenetic Mechanisms in the Pathogenesis of Hepatitis C Infection. Biomolecules 2024; 14:986. [PMID: 39199374 PMCID: PMC11352264 DOI: 10.3390/biom14080986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 09/01/2024] Open
Abstract
Hepatitis C virus (HCV) is a hepatotropic virus that can be transmitted through unsafe medical procedures, such as injections, transfusions, and dental treatment. The infection may be self-limiting or manifest as a chronic form that induces liver fibrosis, cirrhosis, or progression into hepatocellular carcinoma (HCC). Epigenetic mechanisms are major regulators of gene expression. These mechanisms involve DNA methylation, histone modifications, and the activity of non-coding RNAs, which can enhance or suppress gene expression. Abnormal activity or the dysregulated expression of epigenetic molecules plays an important role in the pathogenesis of various pathological disorders, including inflammatory diseases and malignancies. In this review, we summarise the current evidence on epigenetic mechanisms involved in HCV infection and progression to HCC.
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Affiliation(s)
- Justyna Żychowska
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
| | - Maciej Ćmil
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
| | - Patryk Skórka
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
| | | | - Paulina Plewa
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland;
| | - Estera Bakinowska
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
| | - Kajetan Kiełbowski
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, 70-111 Szczecin, Poland; (J.Ż.); (M.Ć.); (P.S.); (E.B.); (K.K.)
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Cousineau SE, Camargo C, Sagan SM. Poly(rC)-Binding Protein 2 Does Not Directly Participate in HCV Translation or Replication, but Rather Modulates Genome Packaging. Viruses 2024; 16:1220. [PMID: 39205194 PMCID: PMC11359930 DOI: 10.3390/v16081220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
The hepatitis C virus (HCV) co-opts many cellular factors-including proteins and microRNAs-to complete its life cycle. A cellular RNA-binding protein, poly(rC)-binding protein 2 (PCBP2), was previously shown to bind to the hepatitis C virus (HCV) genome; however, its precise role in the viral life cycle remained unclear. Herein, using the HCV cell culture (HCVcc) system and assays that isolate each step of the viral life cycle, we found that PCBP2 does not have a direct role in viral entry, translation, genome stability, or HCV RNA replication. Rather, our data suggest that PCBP2 depletion only impacts viral RNAs that can undergo genome packaging. Taken together, our data suggest that endogenous PCBP2 modulates the early steps of genome packaging, and therefore only has an indirect effect on viral translation and RNA replication, likely by increasing the translating/replicating pool of viral RNAs to the detriment of virion assembly.
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Affiliation(s)
- Sophie E. Cousineau
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Carolina Camargo
- Department of Microbiology & Immunology, University of British Columbia, 2350 Health Science Mall, Room 4.520, Vancouver, BC V6T 1Z3, Canada
| | - Selena M. Sagan
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4, Canada
- Department of Microbiology & Immunology, University of British Columbia, 2350 Health Science Mall, Room 4.520, Vancouver, BC V6T 1Z3, Canada
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Yao J, Zhu Y, Zhang G, Zhou X, Shang H, Li L, Xu T. Action mechanisms and characteristics of miRNAs to regulate virus replication. Virology 2024; 590:109966. [PMID: 38100983 DOI: 10.1016/j.virol.2023.109966] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
MicroRNAs (miRNAs) have the potential to be explored as antiviral products. It is known that miRNAs have different kinds of target mRNAs and different target sites in mRNAs, and that the action-modes of miRNAs at different target sites may be different. But there is no evidence demonstrating the significance of the differences for the regulation of viruses by miRNAs, which might be crucial for the exploration of miRNA-based antiviral products. Here the experimental studies about the antiviral effects of miRNAs, with validated target mRNAs and target sites in the mRNAs, were systematically collected, based on which the mechanisms whereby miRNAs regulated virus replication were systematically reviewed. And miRNAs' down-regulation rates on target mRNAs and antiviral rates were compared among the miRNAs with different target sites, to analyze the characteristics of action-modes of miRNAs at different target sites during virus replication.
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Affiliation(s)
- Jia Yao
- Jiangxi University of Chinese Medicine, 1688 Mei Ling Avenue, Nanchang, 330004, PR China.
| | - Yating Zhu
- Jiangxi University of Chinese Medicine, 1688 Mei Ling Avenue, Nanchang, 330004, PR China.
| | - Genrong Zhang
- Jiangxi University of Chinese Medicine, 1688 Mei Ling Avenue, Nanchang, 330004, PR China.
| | - Xianfeng Zhou
- Jiangxi University of Chinese Medicine, 1688 Mei Ling Avenue, Nanchang, 330004, PR China.
| | - Hongcai Shang
- Jiangxi University of Chinese Medicine, 1688 Mei Ling Avenue, Nanchang, 330004, PR China; Shang Hongcai, Key Laboratory of Chinese Internal Medicine of MOE and Beijing University of Chinese Medicine, 11 Eastern Section of the North Third Ring Road, Chaoyang District, Beijing, 100029, PR China.
| | - Longxue Li
- Jiangxi University of Chinese Medicine, 1688 Mei Ling Avenue, Nanchang, 330004, PR China.
| | - Tielong Xu
- Jiangxi University of Chinese Medicine, 1688 Mei Ling Avenue, Nanchang, 330004, PR China.
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6
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Yin R, Lu H, Cao Y, Zhang J, Liu G, Guo Q, Kai X, Zhao J, Wei Y. The Mechanisms of miRNAs on Target Regulation and their Recent Advances in Atherosclerosis. Curr Med Chem 2024; 31:5779-5804. [PMID: 37807413 DOI: 10.2174/0109298673253678230920054220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/25/2023] [Accepted: 08/18/2023] [Indexed: 10/10/2023]
Abstract
miRNAs are crucial regulators in a variety of physiological and pathological processes, while their regulation mechanisms were usually described as negatively regulating gene expression by targeting the 3'-untranslated region(3'-UTR) of target gene miRNAs through seed sequence in tremendous studies. However, recent evidence indicated the existence of non-canonical mechanisms mediated by binding other molecules besides mRNAs. Additionally, accumulating evidence showed that functions of intracellular and intercellular miRNAs exhibited spatiotemporal patterns. Considering that detailed knowledge of the miRNA regulating mechanism is essential for understanding the roles and further clinical applications associated with their dysfunction and dysregulation, which is complicated and not fully clarified. Based on that, we summarized the recently reported regulation mechanisms of miRNAs, including recognitions, patterns of actions, and chemical modifications. And we also highlight the novel findings of miRNAs in atherosclerosis progression researches to provide new insights for non-coding RNA-based therapy in intractable diseases.
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Affiliation(s)
- Runting Yin
- School of Pharmacy, Jiangsu University, No. 301, Xuefu Road, Zhenjiang, 212000, China
| | - Hongyu Lu
- School of Pharmacy, Jiangsu University, No. 301, Xuefu Road, Zhenjiang, 212000, China
| | - Yixin Cao
- Department of Medical Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Jia Zhang
- School of Pharmacy, Jiangsu University, No. 301, Xuefu Road, Zhenjiang, 212000, China
| | - Geng Liu
- School of Pharmacy, Jiangsu University, No. 301, Xuefu Road, Zhenjiang, 212000, China
| | - Qian Guo
- School of Pharmacy, Jiangsu University, No. 301, Xuefu Road, Zhenjiang, 212000, China
| | - Xinyu Kai
- School of Pharmacy, Jiangsu University, No. 301, Xuefu Road, Zhenjiang, 212000, China
| | - Jiemin Zhao
- School of Pharmacy, Jiangsu University, No. 301, Xuefu Road, Zhenjiang, 212000, China
| | - Yuan Wei
- School of Pharmacy, Jiangsu University, No. 301, Xuefu Road, Zhenjiang, 212000, China
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Kimura M, Kothari S, Gohir W, Camargo JF, Husain S. MicroRNAs in infectious diseases: potential diagnostic biomarkers and therapeutic targets. Clin Microbiol Rev 2023; 36:e0001523. [PMID: 37909789 PMCID: PMC10732047 DOI: 10.1128/cmr.00015-23] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
MicroRNAs (miRNAs) are conserved, short, non-coding RNAs that play a crucial role in the post-transcriptional regulation of gene expression. They have been implicated in the pathogenesis of cancer and neurological, cardiovascular, and autoimmune diseases. Several recent studies have suggested that miRNAs are key players in regulating the differentiation, maturation, and activation of immune cells, thereby influencing the host immune response to infection. The resultant upregulation or downregulation of miRNAs from infection influences the protein expression of genes responsible for the immune response and can determine the risk of disease progression. Recently, miRNAs have been explored as diagnostic biomarkers and therapeutic targets in various infectious diseases. This review summarizes our current understanding of the role of miRNAs during viral, fungal, bacterial, and parasitic infections from a clinical perspective, including critical functional mechanisms and implications for their potential use as biomarkers and therapeutic targets.
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Affiliation(s)
- Muneyoshi Kimura
- Transplant Infectious Diseases, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Sagar Kothari
- Transplant Infectious Diseases, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Wajiha Gohir
- Transplant Infectious Diseases, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Jose F. Camargo
- Department of Medicine, Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Shahid Husain
- Transplant Infectious Diseases, Ajmera Transplant Program, University Health Network, Toronto, Ontario, Canada
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8
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Scott S, Li Y, Bermek O, Griffith JD, Lemon SM, Choi K. Binding of microRNA-122 to the hepatitis C virus 5' untranslated region modifies interactions with poly(C) binding protein 2 and the NS5B viral polymerase. Nucleic Acids Res 2023; 51:12397-12413. [PMID: 37941151 PMCID: PMC10711565 DOI: 10.1093/nar/gkad1000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023] Open
Abstract
Hepatitis C virus (HCV) requires two cellular factors, microRNA-122 (miR-122) and poly(C) binding protein 2 (PCBP2), for optimal replication. These host factors compete for binding to the 5' end of the single-stranded RNA genome to regulate the viral replication cycle. To understand how they interact with the RNA, we measured binding affinities of both factors for an RNA probe representing the 5' 45 nucleotides of the HCV genome (HCV45). Isothermal titration calorimetry revealed two, unequal miR-122 binding sites in HCV45, high-affinity (S1) and low-affinity (S2), differing roughly 100-fold in binding affinity. PCBP2 binds a site overlapping S2 with affinity similar to miR-122 binding to S2. PCBP2 circularizes the genome by also binding to the 3' UTR, bridging the 5' and 3' ends of the genome. By competing with PCBP2 for binding at S2, miR-122 disrupts PCBP2-mediated genome circularization. We show that the viral RNA-dependent RNA polymerase, NS5B, also binds to HCV45, and that the binding affinity of NS5B is increased in the presence of miR-122, suggesting miR-122 promotes recruitment of the polymerase. We propose that competition between miR-122 and PCBP2 for HCV45 functions as a translation-to-replication switch, determining whether the RNA genome templates protein synthesis or RNA replication.
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Affiliation(s)
- Seth Scott
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - You Li
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
| | - Oya Bermek
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
| | - Stanley M Lemon
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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9
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Kosek DM, Banijamali E, Becker W, Petzold K, Andersson E. Efficient 3'-pairing renders microRNA targeting less sensitive to mRNA seed accessibility. Nucleic Acids Res 2023; 51:11162-11177. [PMID: 37819016 PMCID: PMC10639062 DOI: 10.1093/nar/gkad795] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate gene expression by binding to specific sites in mRNAs. Site recognition is primarily mediated by the seed region (nucleotides g2-g8 in the miRNA), but pairing beyond the seed (3'-pairing) is important for some miRNA:target interactions. Here, we use SHAPE, luciferase reporter assays and transcriptomics analyses to study the combined effect of 3'-pairing and secondary structures in mRNAs on repression efficiency. Using the interaction between miR-34a and its SIRT1 binding site as a model, we provide structural and functional evidence that 3'-pairing can compensate for low seed-binding site accessibility, enabling repression of sites that would otherwise be ineffective. We show that miRNA 3'-pairing regions can productively base-pair with nucleotides far upstream of the seed-binding site and that both hairpins and unstructured bulges within the target site are tolerated. We use SHAPE to show that sequences that overcome inaccessible seed-binding sites by strong 3'-pairing adopt the predicted structures and corroborate the model using luciferase assays and high-throughput modelling of 8177 3'-UTR targets for six miRNAs. Finally, we demonstrate that PHB2, a target of miR-141, is an inaccessible target rescued by efficient 3'-pairing. We propose that these results could refine predictions of effective target sites.
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Affiliation(s)
- David M Kosek
- Department of Cell and Molecular Biology, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177Stockholm, Sweden
| | - Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177Stockholm, Sweden
| | - Walter Becker
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177Stockholm, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Centre D9:3, Husargatan 3, 752 37 Uppsala, Sweden
| | - Emma R Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177Stockholm, Sweden
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10
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Al-Gazally ME, Khan R, Imran M, Ramírez-Coronel AA, Alshahrani SH, Altalbawy FMA, Turki Jalil A, Romero-Parra RM, Zabibah RS, Shahid Iqbal M, Karampoor S, Mirzaei R. The role and mechanism of action of microRNA-122 in cancer: Focusing on the liver. Int Immunopharmacol 2023; 123:110713. [PMID: 37523968 DOI: 10.1016/j.intimp.2023.110713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/08/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
microRNA-122 (miR-122) is a highly conserved microRNA that is predominantly expressed in the liver and plays a critical role in the regulation of liver metabolism. Recent studies have shown that miR-122 is involved in the pathogenesis of various types of cancer, particularly liver cancer. In this sense, The current findings highlighted the potential role of miR-122 in regulating many vital processes in cancer pathophysiology, including apoptosis, signaling pathway, cell metabolism, immune system response, migration, and invasion. These results imply that miR-122, which has been extensively studied for its biological functions and potential therapeutic applications, acts as a tumor suppressor or oncogene in cancer development. We first provide an overview and summary of the physiological function and mode of action of miR-122 in liver cancer. We will examine the various signaling pathways and molecular mechanisms through which miR-122 exerts its effects on cancer cells, including the regulation of oncogenic and tumor suppressor genes, the modulation of cell proliferation and apoptosis, and the regulation of metastasis. Most importantly, we will also discuss the potential diagnostic and therapeutic applications of miR-122 in cancer, including the development of miRNA-based biomarkers for cancer diagnosis and prognosis, and the potential use of miR-122 as a therapeutic target for cancer treatment.
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Affiliation(s)
| | - Ramsha Khan
- MBBS, Nawaz Sharif Medical College, Gujrat, Pakistan
| | - Muhammad Imran
- MBBS, Multan Medical and Dental College, Multan, Pakistan
| | | | | | - Farag M A Altalbawy
- National Institute of Laser Enhanced Sciences (NILES), University of Cairo, Giza 12613, Egypt; Department of Chemistry, University College of Duba, University of Tabuk, Tabuk, Saudi Arabia
| | - Abduladheem Turki Jalil
- Medical Laboratories Techniques Department, Al-Mustaqbal University College, Babylon, Hilla 51001, Iraq
| | | | - Rahman S Zabibah
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Muhammad Shahid Iqbal
- Department of Clinical Pharmacy, College of Pharmacy, Prince Sattam bin Abdulaziz University, 11942 Alkharj, Saudi Arabia
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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11
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Mirzaei R, Karampoor S, Korotkova NL. The emerging role of miRNA-122 in infectious diseases: Mechanisms and potential biomarkers. Pathol Res Pract 2023; 249:154725. [PMID: 37544130 DOI: 10.1016/j.prp.2023.154725] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
microRNAs (miRNAs) are small, non-coding RNA molecules that play crucial regulatory roles in numerous cellular processes. Recent investigations have highlighted the significant involvement of miRNA-122 (miR-122) in the pathogenesis of infectious diseases caused by diverse pathogens, encompassing viral, bacterial, and parasitic infections. In the context of viral infections, miR-122 exerts regulatory control over viral replication by binding to the viral genome and modulating the host's antiviral response. For instance, in hepatitis B virus (HBV) infection, miR-122 restricts viral replication, while HBV, in turn, suppresses miR-122 expression. Conversely, miR-122 interacts with the hepatitis C virus (HCV) genome, facilitating viral replication. Regarding bacterial infections, miR-122 has been found to regulate host immune responses by influencing inflammatory cytokine production and phagocytosis. In Vibrio anguillarum infections, there is a significant reduction in miR-122 expression, contributing to the pathophysiology of bacterial infections. Toll-like receptor 14 (TLR14) has been identified as a novel target gene of miR-122, affecting inflammatory and immune responses. In the context of parasitic infections, miR-122 plays a crucial role in regulating host lipid metabolism and immune responses. For example, during Leishmania infection, miR-122-containing extracellular vesicles from liver cells are unable to enter infected macrophages, leading to a suppression of the inflammatory response. Furthermore, miR-122 exhibits promise as a potential biomarker for various infectious diseases. Its expression level in body fluids, particularly in serum and plasma, correlates with disease severity and treatment response in patients affected by HCV, HBV, and tuberculosis. This paper also discusses the potential of miR-122 as a biomarker in infectious diseases. In summary, this review provides a comprehensive and insightful overview of the emerging role of miR-122 in infectious diseases, detailing its mechanism of action and potential implications for the development of novel therapeutic strategies.
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Affiliation(s)
- Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Nadezhda Lenoktovna Korotkova
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Russia; Federal State Budgetary Educational Institution of Higher Education "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation (FSBEI HE PRMU MOH Russia), Russia
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12
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Panigrahi M, Palmer MA, Wilson JA. Enhanced Virus Translation Enables miR-122-Independent Hepatitis C Virus Propagation. J Virol 2023:e0085821. [PMID: 37338370 PMCID: PMC10373559 DOI: 10.1128/jvi.00858-21] [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: 06/07/2021] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
The 5' untranslated region (UTR) of the hepatitis C virus (HCV) genome forms RNA structures that regulate virus replication and translation. The region contains an internal ribosomal entry site (IRES) and a 5'-terminal region. Binding of the liver-specific microRNA (miRNA) miR-122 to two binding sites in the 5'-terminal region regulates viral replication, translation, and genome stability and is essential for efficient virus replication, but its precise mechanism of action is still unresolved. A current hypothesis is that miR-122 binding stimulates viral translation by facilitating the viral 5' UTR to form the translationally active HCV IRES RNA structure. While miR-122 is essential for detectable replication of wild-type HCV genomes in cell culture, several viral variants with 5' UTR mutations exhibit low-level replication in the absence of miR-122. We show that HCV mutants capable of replicating independently of miR-122 display an enhanced translation phenotype that correlates with their ability to replicate independently of miR-122. Further, we provide evidence that translation regulation is the major role for miR-122 and show that miR-122-independent HCV replication can be rescued to miR-122-dependent levels by the combined impacts of 5' UTR mutations that stimulate translation and by stabilizing the viral genome by knockdown of host exonucleases and phosphatases that degrade the genome. Finally, we show that HCV mutants capable of replicating independently of miR-122 also replicate independently of other microRNAs generated by the canonical miRNA synthesis pathway. Thus, we provide a model suggesting that translation stimulation and genome stabilization are the primary roles for miR-122 in promoting HCV. IMPORTANCE The unusual and essential role of miR-122 in promoting HCV propagation is incompletely understood. To better understand its role, we have analyzed HCV mutants capable of replicating independently of miR-122. Our data show that the ability of viruses to replicate independently of miR-122 correlates with enhanced virus translation but that genome stabilization is required to restore efficient HCV replication. This suggests that viruses must gain both abilities to escape the need for miR-122 and impacts the possibility that HCV can evolve to replicate outside the liver.
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Affiliation(s)
- Mamata Panigrahi
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Michael A Palmer
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Joyce A Wilson
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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13
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Barnard TR, Landry BN, Wang AB, Sagan SM. Zika virus NS3 and NS5 proteins determine strain-dependent differences in dsRNA accumulation in a host cell type-dependent manner. J Gen Virol 2023; 104. [PMID: 37289497 DOI: 10.1099/jgv.0.001855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
For positive-sense RNA viruses, initiation of viral RNA replication represents a major target of antiviral responses to infection. Despite this, the interplay between viral replication and the innate antiviral response at early steps in the Zika virus (ZIKV) life cycle is not well understood. We have previously identified ZIKV isolates with differing levels of dsRNA accumulation, ZIKVPR (high dsRNA per infected cell) and ZIKVCDN (low dsRNA per infected cell), and we hypothesized that we could use reverse genetics to investigate how host and viral factors contribute to the establishment of viral RNA replication. We found that both the ZIKV NS3 and NS5 proteins as well as host factors were necessary to determine the dsRNA accumulation phenotype. Additionally, we show that dsRNA correlates with viral negative-strand RNA measured by strand-specific RT-qPCR, suggesting that dsRNA is an accurate readout of viral RNA replication. Interestingly, although we did not observe NS3- and NS5-dependent differences in cells with defects in interferon (IFN) production, differences in RNA accumulation precede induction of the IFN response, suggesting that RNA sensing pathways or intrinsic restriction factors may differentially restrict ZIKV in an NS3- and NS5-dependent manner. This work expands our understanding of the interplay of early steps of viral RNA replication and the induction of the innate antiviral response to ZIKV infection.
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Affiliation(s)
- Trisha R Barnard
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Breanna N Landry
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Alex B Wang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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14
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Rheault M, Cousineau SE, Fox DR, Abram QH, Sagan S. Elucidating the distinct contributions of miR-122 in the HCV life cycle reveals insights into virion assembly. Nucleic Acids Res 2023; 51:2447-2463. [PMID: 36807979 PMCID: PMC10018354 DOI: 10.1093/nar/gkad094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/20/2023] [Accepted: 02/18/2023] [Indexed: 02/23/2023] Open
Abstract
Efficient hepatitis C virus (HCV) RNA accumulation is dependent upon interactions with the human liver-specific microRNA, miR-122. MiR-122 has at least three roles in the HCV life cycle: it acts as an RNA chaperone, or 'riboswitch', allowing formation of the viral internal ribosomal entry site; it provides genome stability; and promotes viral translation. However, the relative contribution of each role in HCV RNA accumulation remains unclear. Herein, we used point mutations, mutant miRNAs, and HCV luciferase reporter RNAs to isolate each of the roles and evaluate their contribution to the overall impact of miR-122 in the HCV life cycle. Our results suggest that the riboswitch has a minimal contribution in isolation, while genome stability and translational promotion have similar contributions in the establishment phase of infection. However, in the maintenance phase, translational promotion becomes the dominant role. Additionally, we found that an alternative conformation of the 5' untranslated region, termed SLIIalt, is important for efficient virion assembly. Taken together, we have clarified the overall importance of each of the established roles of miR-122 in the HCV life cycle and provided insight into the regulation of the balance between viral RNAs in the translating/replicating pool and those engaged in virion assembly.
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Affiliation(s)
- Marylin Rheault
- Department of Microbiology & Immunology, McGill University, Montréal, Canada
| | - Sophie E Cousineau
- Department of Microbiology & Immunology, McGill University, Montréal, Canada
| | - Danielle R Fox
- Department of Microbiology & Immunology, McGill University, Montréal, Canada
- Department of Physiology, McGill University, Montréal, Canada
| | - Quinn H Abram
- Department of Biochemistry, McGill University, Montréal, Canada
| | - Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montréal, Canada
- Department of Biochemistry, McGill University, Montréal, Canada
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15
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Passos-Castilho AM, Udhesister STP, Fontaine G, Jeong D, Dickie M, Lund C, Russell R, Kronfli N, on behalf of the Canadian Network on Hepatitis C (CanHepC). The 11th Canadian Symposium on Hepatitis C Virus: 'Getting back on track towards hepatitis C elimination'. CANADIAN LIVER JOURNAL 2023; 6:56-69. [PMID: 36908576 PMCID: PMC9997521 DOI: 10.3138/canlivj-2022-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/20/2022] [Indexed: 11/05/2022]
Abstract
Hepatitis C virus (HCV) affects approximately 204,000 Canadians. Safe and effective direct-acting antiviral therapies have contributed to decreased rates of chronic HCV infection and increased treatment uptake in Canada, but major challenges for HCV elimination remain. The 11th Canadian Symposium on Hepatitis C Virus took place in Ottawa, Ontario on May 13, 2022 as a hybrid conference themed 'Getting back on track towards hepatitis C elimination.' It brought together research scientists, clinicians, community health workers, patient advocates, community members, and public health officials to discuss priorities for HCV elimination in the wake of the COVID-19 pandemic, which had devastating effects on HCV care in Canada, particularly on priority populations. Plenary sessions showcased topical research from prominent international and national researchers, complemented by select abstract presentations. This event was hosted by the Canadian Network on Hepatitis C (CanHepC), with support from the Public Health Agency of Canada and the Canadian Institutes of Health Research and in partnership with the Canadian Liver Meeting. CanHepC has an established record in HCV research and in advocacy activities to address improved diagnosis and treatment, and immediate and long-term needs of those affected by HCV infection. The Symposium addressed the remaining challenges and barriers to HCV elimination in priority populations and principles for meaningful engagement of Indigenous communities and individuals with living and lived experience in HCV research. It emphasized the need for disaggregated data and simplified pathways for creating and monitoring interventions for equitably achieving elimination targets.
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Affiliation(s)
- Ana Maria Passos-Castilho
- Centre for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Sasha Tejna Persaud Udhesister
- Faculté de Médecine, Université de Montréal, Centre de Recherche du Centre hospitalier de l'Université de Montré (CRCHUM), Montréal, Québec, Canada
| | - Guillaume Fontaine
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Dahn Jeong
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melisa Dickie
- Community Health Programming, CATIE, Toronto, Ontario, Canada
| | | | - Rodney Russell
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Nadine Kronfli
- Department of Medicine, Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre, Montreal, Quebec, Canada.,Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
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16
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Subversion of a protein-microRNA signaling pathway by hepatitis C virus. Proc Natl Acad Sci U S A 2023; 120:e2220406120. [PMID: 36649406 PMCID: PMC9942813 DOI: 10.1073/pnas.2220406120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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17
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Emanuelson C, Ankenbruck N, Kumbhare R, Thomas M, Connelly C, Baktash Y, Randall G, Deiters A. Transcriptional Inhibition of MicroRNA miR-122 by Small Molecules Reduces Hepatitis C Virus Replication in Liver Cells. J Med Chem 2022; 65:16338-16352. [PMID: 36449366 PMCID: PMC9942140 DOI: 10.1021/acs.jmedchem.2c01141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
MicroRNAs (miRNAs) are noncoding RNA molecules of 22-24 nucleotides that are estimated to regulate thousands of genes in humans, and their dysregulation has been implicated in many diseases. MicroRNA-122 (miR-122) is the most abundant miRNA in the liver and has been linked to the development of hepatocellular carcinoma and hepatitis C virus (HCV) infection. Its role in these diseases renders miR-122 a potential target for small-molecule therapeutics. Here, we report the discovery of a new sulfonamide class of small-molecule miR-122 inhibitors from a high-throughput screen using a luciferase-based reporter assay. Structure-activity relationship (SAR) studies and secondary assays led to the development of potent and selective miR-122 inhibitors. Preliminary mechanism-of-action studies suggest a role in the promoter-specific transcriptional inhibition of miR-122 expression through direct binding to the liver-enriched transcription factor hepatocyte nuclear factor 4α. Importantly, the developed inhibitors significantly reduce HCV replication in human liver cells.
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Affiliation(s)
- Cole Emanuelson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Rohan Kumbhare
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Meryl Thomas
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Colleen Connelly
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yasmine Baktash
- Department of Microbiology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Glenn Randall
- Department of Microbiology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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18
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Xu T, Li LX, Jia Y, Wu Q, Zhu W, Xu Z, Zheng B, Lu X. One microRNA has the potential to target whole viral mRNAs in a given human coronavirus. Front Microbiol 2022; 13:1035044. [PMID: 36439806 PMCID: PMC9686371 DOI: 10.3389/fmicb.2022.1035044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/24/2022] [Indexed: 09/29/2023] Open
Abstract
MicroRNAs (miRNAs) can repress viral replication by targeting viral messenger RNA (mRNA), which makes them potential antiviral agents. The antiviral effects of miRNAs on infectious viruses have been explored extensively; however, recent studies mainly considered the action modes of miRNAs, neglecting another key factor, the molecular biology of viruses, which may be particularly important in the study of miRNA actions against a given virus. In this paper, the action modes of miRNAs and the molecular biology of viruses are jointly considered for the first time and based on the reported roles of miRNAs on viruses and human coronaviruses (HCoVs) molecular biology, the general and specific interaction modes of miRNAs-HCoVs are systematically reviewed. It was found that HCoVs transcriptome is a nested set of subgenomic mRNAs, sharing the same 5' leader, 3' untranslated region (UTR) and open reading frame (ORF). For a given HCoV, one certain miRNA with a target site in the 5' leader or 3' UTR has the potential to target all viral mRNAs, indicating tremendous antiviral effects against HCoVs. However, for the shared ORFs, some parts are untranslatable attributed to the translation pattern of HCoVs mRNA, and it is unknown whether the base pairing between the untranslated ORFs and miRNAs plays a regulatory effect on the local mRNAs where the untranslated ORFs are located; therefore, the regulatory effects of miRNAs with targets within the shared ORFs are complicated and need to be confirmed. Collectively, miRNAs may bepromising antiviral agents against HCoVs due to their intrinsically nested set of mRNAs, and some gaps are waiting to be filled. In this review, insight is provided into the exploration of miRNAs that can interrupt HCoVs infection.
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Affiliation(s)
- Tielong Xu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Long-xue Li
- Laboratory Animal Science and Technology Center, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yao Jia
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Qingni Wu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Weifeng Zhu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Zhou Xu
- Evidence-Based Medicine Research Center Department, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Bin Zheng
- National Institute of Parasitic Diseases Chinese Center for Disease Control and Prevention, and WHO Collaborating Center for Tropical Diseases, Shanghai, China
| | - Xuexin Lu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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19
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Micro RNAs—The Small Big Players in Hepatitis E Virus Infection: A Comprehensive Review. Biomolecules 2022; 12:biom12111543. [PMID: 36358893 PMCID: PMC9687951 DOI: 10.3390/biom12111543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 12/02/2022] Open
Abstract
The molecular mechanism of hepatitis E virus (HEV) pathology is still unclear. The micro RNAs (miRNAs), of host or viral origin, interfere with virus replication and host environment in order to create an appropriate condition for the production of mature HEV progeny. Understanding the biogenesis and the interference of miRNAs with HEV will help to revile the mechanism of viral pathogenesis.
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20
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Panigrahi M, Palmer MA, Wilson JA. MicroRNA-122 Regulation of HCV Infections: Insights from Studies of miR-122-Independent Replication. Pathogens 2022; 11:1005. [PMID: 36145436 PMCID: PMC9504723 DOI: 10.3390/pathogens11091005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/18/2022] Open
Abstract
Despite the advancement in antiviral therapy, Hepatitis C remains a global health challenge and one of the leading causes of hepatitis related deaths worldwide. Hepatitis C virus, the causative agent, is a positive strand RNA virus that requires a liver specific microRNA called miR-122 for its replication. Unconventional to the canonical role of miRNAs in translation suppression by binding to 3'Untranslated Region (UTR) of messenger RNAs, miR-122 binds to two sites on the 5'UTR of viral genome and promotes viral propagation. In this review, we describe the unique relationship between the liver specific microRNA and HCV, the current knowledge on the mechanisms by which the virus uses miR-122 to promote the virus life cycle, and how miR-122 impacts viral tropism and pathogenesis. We will also discuss the use of anti-miR-122 therapy and its impact on viral evolution of miR-122-independent replication. This review further provides insight into how viruses manipulate host factors at the initial stage of infection to establish a successful infection.
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Affiliation(s)
| | | | - Joyce A. Wilson
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
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21
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Development and Use of a Kinetical and Real-Time Monitoring System to Analyze the Replication of Hepatitis C Virus. Int J Mol Sci 2022; 23:ijms23158711. [PMID: 35955844 PMCID: PMC9368937 DOI: 10.3390/ijms23158711] [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: 06/24/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
In microbiological research, it is important to understand the time course of each step in a pathogen's lifecycle and changes in the host cell environment induced by infection. This study is the first to develop a real-time monitoring system that kinetically detects luminescence reporter activity over time without sampling cells or culture supernatants for analyzing the virus replication. Subgenomic replicon experiments with hepatitis C virus (HCV) showed that transient translation and genome replication can be detected separately, with the first peak of translation observed at 3-4 h and replication beginning around 20 h after viral RNA introduction into cells. From the bioluminescence data set measured every 30 min (48 measurements per day), the initial rates of translation and replication were calculated, and their capacity levels were expressed as the sums of the measured signals in each process, which correspond to the areas on the kinetics graphs. The comparison of various HuH-7-derived cell lines showed that the bioluminescence profile differs among cell lines, suggesting that both translation and replication capacities potentially influence differences in HCV susceptibility. The effects of RNA mutations within the 5' UTR of the replicon on viral translation and replication were further analyzed in the system developed, confirming that mutations to the miR-122 binding sites primarily reduce replication activity rather than translation. The newly developed real-time monitoring system should be applied to the studies of various viruses and contribute to the analysis of transitions and progression of each process of their life cycle.
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22
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Viral Encoded miRNAs in Tumorigenesis: Theranostic Opportunities in Precision Oncology. Microorganisms 2022; 10:microorganisms10071448. [PMID: 35889167 PMCID: PMC9321719 DOI: 10.3390/microorganisms10071448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022] Open
Abstract
About 15% of all human cancers have a viral etiology. Although progress has been made, understanding the viral oncogenesis and associated molecular mechanisms remain complex. The discovery of cellular miRNAs has led to major breakthroughs. Interestingly, viruses have also been discovered to encode their own miRNAs. These viral, small, non-coding miRNAs are also known as viral-miRNAs (v-miRNAs). Although the function of v-miRNAs largely remains to be elucidated, their role in tumorigenesis cannot be ignored. V-miRNAs have also been shown to exploit the cellular machinery to benefit viral replication and survival. Although the discovery of Hepatitis C virus (HCV), and its viral miRNAs, is a work in progress, the existence of HPV-, EBV-, HBV-, MCPyV- and KSHV-encoded miRNA has been documented. V-miRNAs have been shown to target host factors to advance tumorigenesis, evade and suppress the immune system, and deregulate both the cell cycle and the apoptotic machinery. Although the exact mechanisms of v-miRNAs-induced tumorigenesis are still unclear, v-miRNAs are active role-players in tumorigenesis, viral latency and cell transformation. Furthermore, v-miRNAs can function as posttranscriptional gene regulators of both viral and host genes. Thus, it has been proposed that v-miRNAs may serve as diagnostic biomarkers and therapeutic targets for cancers with a viral etiology. Although significant challenges exist in their clinical application, emerging reports demonstrate their potent role in precision medicine. This review will focus on the roles of HPV-, HCV-, EBV-, HBV-, MCPyV-, and KSHV-produced v-miRNAs in tumorigenesis, as effectors in immune evasion, as diagnostic biomarkers and as novel anti-cancer therapeutic targets. Finally, it will discuss the challenges and opportunities associated with v-miRNAs theranostics in precision oncology.
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23
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Breuer J, Barth P, Noe Y, Shalamova L, Goesmann A, Weber F, Rossbach O. What goes around comes around: Artificial circular RNAs bypass cellular antiviral responses. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:623-635. [PMID: 35497503 PMCID: PMC9042720 DOI: 10.1016/j.omtn.2022.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022]
Abstract
Natural circular RNAs have been found to sequester microRNAs and suppress their function. We have used this principle as a molecular tool and produced artificial circular RNA sponges in a cell-free system by in vitro transcription and ligation. Formerly, we were able to inhibit hepatitis C virus propagation by applying a circular RNA decoy strategy against microRNA-122, which is essential for the viral life cycle. In another proof-of-principle study, we used circular RNAs to sequester microRNA-21, an oncogenic and pro-proliferative microRNA. This strategy slowed tumor growth in a 3D cell culture model system, as well as in xenograft mice upon systemic delivery. In the wake of the global use of an in vitro transcribed RNA in coronavirus disease 2019 (COVID-19) vaccines, the question arose whether therapeutic circular RNAs trigger cellular antiviral defense mechanisms when delivered systemically. In this study, we present data on the cellular innate immune response as a consequence of liposome-based transfection of the circular RNA sponges we previously used to inhibit microRNA function. We find that circular RNAs produced by the presented methodology do not trigger the antiviral response and do not activate innate immune-signaling pathways.
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24
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Annual Meeting of the Canadian Association for the Study of the Liver (CASL), the Canadian Network on Hepatitis C (CanHepC), the Canadian Association of Hepatology Nurses (CAHN), and the Canadian NASH Network 2022 Abstracts. CANADIAN LIVER JOURNAL 2022; 5:169-317. [PMID: 35991483 PMCID: PMC9236590 DOI: 10.3138/canlivj.5.2.abst] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 09/17/2023]
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25
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Zhuang H, Fan X, Ji D, Wang Y, Fan J, Li M, Ni D, Lu S, Li X, Chai Z. Elucidation of the conformational dynamics and assembly of Argonaute-RNA complexes by distinct yet coordinated actions of the supplementary microRNA. Comput Struct Biotechnol J 2022; 20:1352-1365. [PMID: 35356544 PMCID: PMC8933676 DOI: 10.1016/j.csbj.2022.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 02/07/2023] Open
Abstract
Argonaute (AGO) proteins, the core of RNA-induced silencing complex, are guided by microRNAs (miRNAs) to recognize target RNA for repression. The miRNA-target RNA recognition forms initially through pairing at the seed region while the additional supplementary pairing can enhance target recognition and compensate for seed mismatch. The extension of miRNA lengths can strengthen the target affinity when pairing both in the seed and supplementary regions. However, the mechanism underlying the effect of the supplementary pairing on the conformational dynamics and the assembly of AGO-RNA complex remains poorly understood. To address this, we performed large-scale molecular dynamics simulations of AGO-RNA complexes with different pairing patterns and miRNA lengths. The results reveal that the additional supplementary pairing can not only strengthen the interaction between miRNA and target RNA, but also induce the increased plasticity of the PAZ domain and enhance the domain connectivity among the PAZ, PIWI, N domains of the AGO protein. The strong community network between these domains tightens the mouth of the supplementary chamber of AGO protein, which prevents the escape of target RNA from the complex and shields it from solvent water attack. Importantly, the inner stronger matching pairs between the miRNA and target RNA can compensate for weaker mismatches at the edge of supplementary region. These findings provide guidance for the design of miRNA mimics and anti-miRNAs for both clinical and experimental use and open the way for further engineering of AGO proteins as a new tool in the field of gene regulation.
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Affiliation(s)
- Haiming Zhuang
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xiaohua Fan
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Dong Ji
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Yuanhao Wang
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jigang Fan
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Mingyu Li
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Duan Ni
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shaoyong Lu
- Department of Pathophysiology, Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai 200438, China
- Department of Hepatic Surgery, Shanghai Geriatric Center, Shanghai 201104, China
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Li Y, Li J, Cao Y, Jiang P, Tang Y, Chen Z, Han K. A visual method for determination of hepatitis C virus RNAs based on a 3D nanocomposite prepared from graphene quantum dots. Anal Chim Acta 2022; 1203:339693. [DOI: 10.1016/j.aca.2022.339693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 02/22/2022] [Accepted: 03/05/2022] [Indexed: 01/17/2023]
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Poly(rC)-Binding Protein 1 Limits Hepatitis C Virus Virion Assembly and Secretion. Viruses 2022; 14:v14020291. [PMID: 35215884 PMCID: PMC8877974 DOI: 10.3390/v14020291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/16/2022] Open
Abstract
The hepatitis C virus (HCV) co-opts numerous cellular elements, including proteins, lipids, and microRNAs, to complete its viral life cycle. The cellular RNA-binding protein, poly(rC)-binding protein 1 (PCBP1), was previously reported to bind to the 5′ untranslated region (UTR) of the HCV genome; however, its importance in the viral life cycle has remained unclear. Herein, we sought to clarify the role of PCBP1 in the HCV life cycle. Using the HCV cell culture (HCVcc) system, we found that knockdown of endogenous PCBP1 resulted in an overall decrease in viral RNA accumulation, yet resulted in an increase in extracellular viral titers. To dissect PCBP1’s specific role in the HCV life cycle, we carried out assays for viral entry, translation, genome stability, RNA replication, as well as virion assembly and secretion. We found that PCBP1 knockdown did not directly affect viral entry, translation, RNA stability, or RNA replication, but resulted in an overall increase in infectious particle secretion. This increase in virion secretion was evident even when viral RNA synthesis was inhibited, and blocking virus secretion could partially restore the viral RNA accumulation decreased by PCBP1 knockdown. We therefore propose a model where endogenous PCBP1 normally limits virion assembly and secretion, which increases viral RNA accumulation in infected cells by preventing the departure of viral genomes packaged into virions. Overall, our findings improve our understanding of how cellular RNA-binding proteins influence viral genomic RNA utilization during the HCV life cycle.
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Spectrum of microRNAs and their target genes in cancer: intervention in diagnosis and therapy. Mol Biol Rep 2022; 49:6827-6846. [PMID: 35031927 DOI: 10.1007/s11033-021-07040-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022]
Abstract
Till date, several groups have studied the mechanism of microRNA (miRNA) biogenesis, processing, stability, silencing, and their dysregulation in cancer. The miRNA coding genes recurrently go through abnormal amplification, deletion, transcription, and epigenetic regulation in cancer. Some miRNAs function as tumor promoters while few others are tumor suppressors based on the transcriptional regulation of target genes. A review of miRNAs and their target genes in a wide range of cancers is attempted in this article, which may help in the development of new diagnostic tools and intervention therapies. The contribution of miRNAs for drug sensitivity or resistance in cancer therapy and opportunities of miRNAs in cancer prognosis or diagnosis and therapy is also presented in detail.
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Laudenbach BT, Krey K, Emslander Q, Andersen LL, Reim A, Scaturro P, Mundigl S, Dächert C, Manske K, Moser M, Ludwig J, Wohlleber D, Kröger A, Binder M, Pichlmair A. NUDT2 initiates viral RNA degradation by removal of 5'-phosphates. Nat Commun 2021; 12:6918. [PMID: 34824277 PMCID: PMC8616924 DOI: 10.1038/s41467-021-27239-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 11/08/2021] [Indexed: 12/22/2022] Open
Abstract
While viral replication processes are largely understood, comparably little is known on cellular mechanisms degrading viral RNA. Some viral RNAs bear a 5'-triphosphate (PPP-) group that impairs degradation by the canonical 5'-3' degradation pathway. Here we show that the Nudix hydrolase 2 (NUDT2) trims viral PPP-RNA into monophosphorylated (P)-RNA, which serves as a substrate for the 5'-3' exonuclease XRN1. NUDT2 removes 5'-phosphates from PPP-RNA in an RNA sequence- and overhang-independent manner and its ablation in cells increases growth of PPP-RNA viruses, suggesting an involvement in antiviral immunity. NUDT2 is highly homologous to bacterial RNA pyrophosphatase H (RppH), a protein involved in the metabolism of bacterial mRNA, which is 5'-tri- or diphosphorylated. Our results show a conserved function between bacterial RppH and mammalian NUDT2, indicating that the function may have adapted from a protein responsible for RNA turnover in bacteria into a protein involved in the immune defense in mammals.
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Affiliation(s)
- Beatrice T Laudenbach
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried/Munich, Germany
| | - Karsten Krey
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Quirin Emslander
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Line Lykke Andersen
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Alexander Reim
- Department of Proteomics and Signal transduction, Max-Planck Institute of Biochemistry, Martinsried/Munich, Germany
| | - Pietro Scaturro
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
- Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
| | - Sarah Mundigl
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Christopher Dächert
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response" (division F170), German Cancer Research Center, Heidelberg (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Katrin Manske
- Technical University of Munich, School of Medicine, Institute of Molecular Immunology, Munich, Germany
| | - Markus Moser
- Department of Molecular Medicine, Max-Planck Institute of Biochemistry, Martinsried/Munich, Germany
- Technical University of Munich, School of Medicine, Institute of Experimental Hematology, Munich, Germany
| | - Janos Ludwig
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Dirk Wohlleber
- Technical University of Munich, School of Medicine, Institute of Molecular Immunology, Munich, Germany
| | - Andrea Kröger
- Otto von Guericke University Magdeburg, Institute for Medical Microbiology, Magdeburg, Germany
- Helmholtz Centre for Infection Research, Innate Immunity and Infection, Braunschweig, Germany
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response" (division F170), German Cancer Research Center, Heidelberg (DKFZ), Heidelberg, Germany
| | - Andreas Pichlmair
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany.
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried/Munich, Germany.
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany.
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A structured RNA motif locks Argonaute2:miR-122 onto the 5' end of the HCV genome. Nat Commun 2021; 12:6836. [PMID: 34824224 PMCID: PMC8616905 DOI: 10.1038/s41467-021-27177-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/27/2021] [Indexed: 12/03/2022] Open
Abstract
microRNAs (miRNAs) form regulatory networks in metazoans. Viruses engage miRNA networks in numerous ways, with Flaviviridae members exploiting direct interactions of their RNA genomes with host miRNAs. For hepatitis C virus (HCV), binding of liver-abundant miR-122 stabilizes the viral RNA and regulates viral translation. Here, we investigate the structural basis for these activities, taking into consideration that miRNAs function in complex with Argonaute (Ago) proteins. The crystal structure of the Ago2:miR-122:HCV complex reveals a structured RNA motif that traps Ago2 on the viral RNA, masking its 5’ end from enzymatic attack. The trapped Ago2 can recruit host factor PCBP2, implicated in viral translation, while binding of a second Ago2:miR-122 competes with PCBP2, creating a potential molecular switch for translational control. Combined results reveal a viral RNA structure that modulates Ago2:miR-122 dynamics and repurposes host proteins to generate a functional analog of the mRNA cap-binding complex. The RNA genome of the Hepatitis C Virus binds to the liver-specific miR122. Here the authors report the crystal structure of the Ago2:miR122:HCV complex showing that the viral RNA’s structural element traps the Ago2:miR-122 complex on the 5’ end of the viral genome to protect it from degradation.
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Host miRNA and immune cell interactions: relevance in nano-therapeutics for human health. Immunol Res 2021; 70:1-18. [PMID: 34716546 DOI: 10.1007/s12026-021-09247-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022]
Abstract
Around 2200 miRNA (microRNA) genes were found in the human genome. miRNAs are arranged in clusters within the genome and share the same transcriptional regulatory units. It has been revealed that approximately 50% of miRNAs elucidated in the genome are transcribed from non-protein-coding genes, and the leftover miRNAs are present in the introns of coding sequences. We are now approaching a stage in which miRNA diagnostics and therapies can be established confidently, and several commercial efforts are underway to carry these innovations from the bench to the clinic. MiRNAs control many of the significant cellular activities such as production, differentiation, growth, and metabolism. Particularly in the immune system, miRNAs have emerged as a crucial biological component during diseased state and homeostasis. miRNAs have been found to regulate inflammatory responses and autoimmune disorders. Moreover, each miRNA targets multiple genes simultaneously, making miRNAs promising tools as diagnostic biomarkers and as remedial targets. Still, one of the major obstacles in miRNA-based approaches is the achievement of specific and efficient systemic delivery of miRNAs. To overcome these challenges, nanoformulations have been synthesized to protect miRNAs from degradation and enhance cellular uptake. The current review deals with the miRNA-mediated regulation of the recruitment and activation of immune cells, especially in the tumor microenvironment, viral infection, inflammation, and autoimmunity. The nano-based miRNA delivery modes are also discussed here, especially in the context of immune modulation.
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Gokhale NS, Smith JR, Van Gelder RD, Savan R. RNA regulatory mechanisms that control antiviral innate immunity. Immunol Rev 2021; 304:77-96. [PMID: 34405416 DOI: 10.1111/imr.13019] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022]
Abstract
From the initial sensing of viral nucleotides by pattern recognition receptors, through the induction of type I and III interferons (IFN), upregulation of antiviral effector proteins, and resolution of the inflammatory response, each step of innate immune signaling is under tight control. Though innate immunity is often associated with broad regulation at the level of gene transcription, RNA-centric post-transcriptional processes have emerged as critical mechanisms for ensuring a proper antiviral response. Here, we explore the diverse RNA regulatory mechanisms that modulate the innate antiviral immune response, with a focus on RNA sensing by RIG-I-like receptors (RLR), interferon (IFN) and IFN signaling pathways, viral pathogenesis, and host genetic variation that contributes to these processes. We address the post-transcriptional interactions with RNA-binding proteins, non-coding RNAs, transcript elements, and modifications that control mRNA stability, as well as alternative splicing events that modulate the innate immune antiviral response.
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Affiliation(s)
- Nandan S Gokhale
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Julian R Smith
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Rachel D Van Gelder
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Ram Savan
- Department of Immunology, School of Medicine, University of Washington, Seattle, Washington, USA
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miR-122-based therapies select for three distinct resistance mechanisms based on alterations in RNA structure. Proc Natl Acad Sci U S A 2021; 118:2103671118. [PMID: 34385308 PMCID: PMC8379925 DOI: 10.1073/pnas.2103671118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
MicroRNA (miRNA)–based drugs are quickly taking the clinic by storm. Herein, we analyzed resistance-associated variants (RAVs) to the first miRNA inhibitors to make it to the clinic, namely miR-122 inhibitors for chronic hepatitis C virus (HCV) infection. We uncovered three distinct resistance mechanisms based on unique alterations to the structure of the viral RNA. Specifically, RAVs altered the structure of the viral RNA in a manner that promotes riboswitch activity, genome stability, or positive-strand viral RNA synthesis. Our findings support recent models of miR-122–mediated HCV RNA accumulation and provide mechanism(s) of resistance to antiviral therapy. These early insights into the mechanism(s) of resistance to miRNA-based therapies may be of importance as more miRNA-targeted therapies enter into the clinic. Hepatitis C virus (HCV) is a positive-sense RNA virus that interacts with a liver-specific microRNA called miR-122. miR-122 binds to two sites in the 5′ untranslated region of the viral genome and promotes HCV RNA accumulation. This interaction is important for viral RNA accumulation in cell culture, and miR-122 inhibitors have been shown to be effective at reducing viral titers in chronic HCV-infected patients. Herein, we analyzed resistance-associated variants that were isolated in cell culture or from patients who underwent miR-122 inhibitor–based therapy and discovered three distinct resistance mechanisms all based on changes to the structure of the viral RNA. Specifically, resistance-associated variants promoted riboswitch activity, genome stability, or positive-strand viral RNA synthesis, all in the absence of miR-122. Taken together, these findings provide insight into the mechanism(s) of miR-122–mediated viral RNA accumulation and provide mechanisms of antiviral resistance mediated by changes in RNA structure.
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34
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Li HC, Yang CH, Lo SY. Cellular factors involved in the hepatitis C virus life cycle. World J Gastroenterol 2021; 27:4555-4581. [PMID: 34366623 PMCID: PMC8326260 DOI: 10.3748/wjg.v27.i28.4555] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/04/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023] Open
Abstract
The hepatitis C virus (HCV), an obligatory intracellular pathogen, highly depends on its host cells to propagate successfully. The HCV life cycle can be simply divided into several stages including viral entry, protein translation, RNA replication, viral assembly and release. Hundreds of cellular factors involved in the HCV life cycle have been identified over more than thirty years of research. Characterization of these cellular factors has provided extensive insight into HCV replication strategies. Some of these cellular factors are targets for anti-HCV therapies. In this review, we summarize the well-characterized and recently identified cellular factors functioning at each stage of the HCV life cycle.
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Affiliation(s)
- Hui-Chun Li
- Department of Biochemistry, Tzu Chi University, Hualien 970, Taiwan
| | - Chee-Hing Yang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 970, Taiwan
| | - Shih-Yen Lo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 970, Taiwan
- Department of Laboratory Medicine, Buddhist Tzu Chi General Hospital, Hualien 970, Taiwan
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35
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Ohtsuka M, Iwamoto K, Naito A, Imasato M, Hyuga S, Nakahara Y, Mikamori M, Furukawa K, Moon J, Asaoka T, Kishi K, Shamma A, Akamatsu H, Mizushima T, Yamamoto H. Circulating MicroRNAs in Gastrointestinal Cancer. Cancers (Basel) 2021; 13:cancers13133348. [PMID: 34283058 PMCID: PMC8267753 DOI: 10.3390/cancers13133348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary The screening methods and therapeutic strategies for gastrointestinal cancer (GIC) have improved, but mortality in GIC patients remains high. Early detection and precise evaluation of GIC are required to further improve treatment outcomes in GIC patients. MicroRNAs (miRNAs), which do not encode proteins, have attracted attention as biomarkers of various diseases. Since the first report revealing the strong correlation between miRNAs and cancer in 2002, numerous studies have illustrated the changes in the expression and the biological and oncological effects of miRNAs in GIC. Furthermore, miRNAs circulating in the blood are reported to be associated with GIC status. These miRNAs are thought to be useful as noninvasive biomarkers because of their stability in blood. Herein, we discuss the potential of miRNAs as noninvasive biomarkers for each type of GIC on the basis of previous reports and describe perspectives for their future application. Abstract Gastrointestinal cancer (GIC) is a common disease and is considered to be the leading cause of cancer-related death worldwide; thus, new diagnostic and therapeutic strategies for GIC are urgently required. Noncoding RNAs (ncRNAs) are functional RNAs that are transcribed from the genome but do not encode proteins. MicroRNAs (miRNAs) are short ncRNAs that are reported to function as both oncogenes and tumor suppressors. Moreover, several miRNA-based drugs are currently proceeding to clinical trials for various diseases, including cancer. In recent years, the stability of circulating miRNAs in blood has been demonstrated. This is of interest because these miRNAs could be potential noninvasive biomarkers of cancer. In this review, we focus on circulating miRNAs associated with GIC and discuss their potential as novel biomarkers.
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Affiliation(s)
- Masahisa Ohtsuka
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita, Osaka 565-0871, Japan; (A.S.); (H.Y.)
- Correspondence: ; Tel.: +81-6-6771-6051; Fax: +81-6-6771-2838
| | - Kazuya Iwamoto
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Atsushi Naito
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Mitsunobu Imasato
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Satoshi Hyuga
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Yujiro Nakahara
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Manabu Mikamori
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Kenta Furukawa
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Jeongho Moon
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Tadafumi Asaoka
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Kentaro Kishi
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Awad Shamma
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita, Osaka 565-0871, Japan; (A.S.); (H.Y.)
| | - Hiroki Akamatsu
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Tsunekazu Mizushima
- Department of Surgery, Osaka Police Hospital, 10-31 Kitayama-cho, Tennouji-ku, Osaka 543-0035, Japan; (K.I.); (A.N.); (M.I.); (S.H.); (Y.N.); (M.M.); (K.F.); (J.M.); (T.A.); (K.K.); (H.A.); (T.M.)
| | - Hirofumi Yamamoto
- Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka University, Yamadaoka 1-7, Suita, Osaka 565-0871, Japan; (A.S.); (H.Y.)
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Jin S, Zhan J, Zhou Y. Argonaute proteins: structures and their endonuclease activity. Mol Biol Rep 2021; 48:4837-4849. [PMID: 34117606 DOI: 10.1007/s11033-021-06476-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/05/2021] [Indexed: 01/12/2023]
Abstract
Argonaute proteins are highly conserved and widely expressed in almost all organisms. They not only play a critical role in the biogenesis of small RNAs but also defend against invading nucleic acids via small RNA or DNA-mediated gene silencing pathways. One functional mechanism of Argonaute proteins is acting as a nucleic-acid-guided endonuclease, which can cleave targets complementary to DNA or RNA guides. The cleavage then leads to translational silencing directly or indirectly by recruiting additional silencing proteins. Here, we summarized the latest research progress in structural and biological studies of Argonaute proteins and pointed out their potential applications in the field of gene editing.
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Affiliation(s)
- Shujuan Jin
- Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Jian Zhan
- Institute for Glycomics, Griffith University, Brisbane, QLD, Australia
| | - Yaoqi Zhou
- Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
- Institute for Glycomics, Griffith University, Brisbane, QLD, Australia.
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China.
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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: 18] [Impact Index Per Article: 4.5] [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.
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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)
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38
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Zhao W, Yu J, Jiang F, Wang W, Kang L, Cui F. Coordination between terminal variation of the viral genome and insect microRNAs regulates rice stripe virus replication in insect vectors. PLoS Pathog 2021; 17:e1009424. [PMID: 33690727 PMCID: PMC7984632 DOI: 10.1371/journal.ppat.1009424] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/22/2021] [Accepted: 02/25/2021] [Indexed: 12/31/2022] Open
Abstract
Maintenance of a balance between the levels of viral replication and selective pressure from the immune systems of insect vectors is one of the prerequisites for efficient transmission of insect-borne propagative phytoviruses. The mechanism regulating the adaptation of RNA viruses to insect vectors by genomic variation remains unknown. Our previous study demonstrated an extension of the 3’-untranslated terminal region (UTR) of two genomic segments of rice stripe virus (RSV). In the present study, a reverse genetic system for RSV in human cells and an insect vector, the small brown planthopper Laodelphax striatellus, was used to demonstrate that the 3’-terminal extensions suppressed viral replication in vector insects by inhibiting promoter activity due to structural interference with the panhandle structure formed by viral 3’- and 5’-UTRs. The extension sequence in the viral RNA1 segment was targeted by an endogenous insect microRNA, miR-263a, which decreased the inhibitory effect of the extension sequence on viral promoter activity. Surprisingly, the expression of miR-263a was negatively regulated by RSV infection. This elaborate coordination between terminal variation of the viral genome and endogenous insect microRNAs controls RSV replication in planthopper, thus reflecting a distinct strategy of adaptation of phytoviruses to insect vectors. Mutations frequently happen when insect-transmitted RNA viruses circulate between insect vectors and plant or mammalian hosts. However, the significance of these mutations for viral fitness in the two distinct organisms is poorly understood. We discovered that a high proportion of rice stripe virus (RSV) had terminally extended genomes when the virus infected insect vectors. In the present study, we found that the extension sequence suppressed viral replication in insect vectors by impairing a special structure formed by the two ends of the viral genomes. An endogenous insect small RNA was able to bind the extension sequence to relieve the inhibitory effect. However, the expression of this small RNA was reduced in the presence of RSV to ultimately maintain the inhibitory effect of the extension sequence. This elaborate coordination between virus and vector enables a limited level of RSV replication that does not produce serious damage to vectors, thus reflecting a distinct strategy of adaptation of insect-transmitted plant viruses.
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Affiliation(s)
- Wan Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jinting Yu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Feng Jiang
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
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39
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Loureiro D, Tout I, Narguet S, Benazzouz SM, Mansouri A, Asselah T. miRNAs as Potential Biomarkers for Viral Hepatitis B and C. Viruses 2020; 12:E1440. [PMID: 33327640 PMCID: PMC7765125 DOI: 10.3390/v12121440] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Around 257 million people are living with hepatitis B virus (HBV) chronic infection and 71 million with hepatitis C virus (HCV) chronic infection. Both HBV and HCV infections can lead to liver complications such as cirrhosis and hepatocellular carcinoma (HCC). To take care of these chronically infected patients, one strategy is to diagnose the early stage of fibrosis in order to treat them as soon as possible to decrease the risk of HCC development. microRNAs (or miRNAs) are small non-coding RNAs which regulate many cellular processes in metazoans. Their expressions were frequently modulated by up- or down-regulation during fibrosis progression. In the serum of patients with HBV chronic infection (CHB), miR-122 and miR-185 expressions are increased, while miR-29, -143, -21 and miR-223 expressions are decreased during fibrosis progression. In the serum of patients with HCV chronic infection (CHC), miR-143 and miR-223 expressions are increased, while miR-122 expression is decreased during fibrosis progression. This review aims to summarize current knowledge of principal miRNAs modulation involved in fibrosis progression during chronic hepatitis B/C infections. Furthermore, we also discuss the potential use of miRNAs as non-invasive biomarkers to diagnose fibrosis with the intention of prioritizing patients with advanced fibrosis for treatment and surveillance.
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Affiliation(s)
| | | | | | | | | | - Tarik Asselah
- Department of Hepatology, Université de Paris, CRI, INSERM UMR 1149, AP-HP Hôpital Beaujon, 92110 Clichy, France; (D.L.); (I.T.); (S.N.); (S.M.B.); (A.M.)
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40
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Kunden RD, Ghezelbash S, Khan JQ, Wilson JA. Location specific annealing of miR-122 and other small RNAs defines an Hepatitis C Virus 5' UTR regulatory element with distinct impacts on virus translation and genome stability. Nucleic Acids Res 2020; 48:9235-9249. [PMID: 32810257 PMCID: PMC7498337 DOI: 10.1093/nar/gkaa664] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus (HCV) replication requires annealing of a liver specific small-RNA, miR-122 to 2 sites on 5′ untranslated region (UTR). Annealing has been reported to (a) stabilize the genome, (b) stimulate translation and (c) promote the formation of translationally active Internal Ribosome Entry Site (IRES) RNA structure. In this report, we map the RNA element to which small RNA annealing promotes HCV to nucleotides 1–44 and identify the relative impact of small RNA annealing on virus translation promotion and genome stabilization. We mapped the optimal region on the HCV genome to which small RNA annealing promotes virus replication to nucleotides 19–37 and found the efficiency of viral RNA accumulation decreased as annealing moved away from this region. Then, by using a panel of small RNAs that promote replication with varying efficiencies we link the efficiency of lifecycle promotion with translation stimulation. By contrast small RNA annealing stabilized the viral genome even if they did not promote virus replication. Thus, we propose that miR-122 annealing promotes HCV replication by annealing to an RNA element that activates the HCV IRES and stimulates translation, and that miR-122 induced HCV genome stabilization is insufficient alone but enhances virus replication.
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Affiliation(s)
- Rasika D Kunden
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Sarah Ghezelbash
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Juveriya Q Khan
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Joyce A Wilson
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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41
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MicroRNAs: Diverse Mechanisms of Action and Their Potential Applications as Cancer Epi-Therapeutics. Biomolecules 2020; 10:biom10091285. [PMID: 32906681 PMCID: PMC7565521 DOI: 10.3390/biom10091285] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/10/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022] Open
Abstract
Usually, miRNAs function post-transcriptionally, by base-pairing with the 3′UTR of target mRNAs, repressing protein synthesis in the cytoplasm. Furthermore, other regions including gene promoters, as well as coding and 5′UTR regions of mRNAs are able to interact with miRNAs. In recent years, miRNAs have emerged as important regulators of both translational and transcriptional programs. The expression of miRNA genes, similar to protein-coding genes, can be epigenetically regulated, in turn miRNA molecules (named epi-miRs) are able to regulate epigenetic enzymatic machinery. The most recent line of evidence indicates that miRNAs can influence physiological processes, such as embryonic development, cell proliferation, differentiation, and apoptosis as well as pathological processes (e.g., tumorigenesis) through epigenetic mechanisms. Some tumor types show repression of tumor-suppressor epi-miRs resulting in cancer progression and metastasis, hence these molecules have become novel therapeutic targets in the last few years. This review provides information about miRNAs involvement in the various levels of transcription and translation regulation, as well as discusses therapeutic potential of tumor-suppressor epi-miRs used in in vitro and in vivo anti-cancer therapy.
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42
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Baldassarre A, Paolini A, Bruno SP, Felli C, Tozzi AE, Masotti A. Potential use of noncoding RNAs and innovative therapeutic strategies to target the 5'UTR of SARS-CoV-2. Epigenomics 2020; 12:1349-1361. [PMID: 32875809 PMCID: PMC7466951 DOI: 10.2217/epi-2020-0162] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
After the increasing number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections all over the world, researchers and clinicians are struggling to find a vaccine or innovative therapeutic strategies to treat this viral infection. The severe acute respiratory syndrome coronavirus infection that occurred in 2002, Middle East respiratory syndrome (MERS) and other more common infectious diseases such as hepatitis C virus, led to the discovery of many RNA-based drugs. Among them, siRNAs and antisense locked nucleic acids have been demonstrated to have effective antiviral effects both in animal models and humans. Owing to the high genomic homology of SARS-CoV-2 and severe acute respiratory syndrome coronavirus (80–82%) the use of these molecules could be employed successfully also to target this emerging coronavirus. Trying to translate this approach to treat COVID-19, we analyzed the common structural features of viral 5’UTR regions that can be targeted by noncoding RNAs and we also identified miRNAs binding sites suitable for designing RNA-based drugs to be employed successfully against SARS-CoV-2.
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Affiliation(s)
- Antonella Baldassarre
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Alessandro Paolini
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Stefania Paola Bruno
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Cristina Felli
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Alberto Eugenio Tozzi
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
| | - Andrea Masotti
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories; Multifactorial & Complex Phenotype Research Area, V.le di San Paolo 15, Rome 00146, Italy
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Moradi M, Mozafari F, Hosseini S, Rafiee R, Ghasemi F. A concise review on impacts of microRNAs in biology and medicine of hepatitis C virus. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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44
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Kokkonos KG, Fossat N, Nielsen L, Holm C, Hepkema WM, Bukh J, Scheel TKH. Evolutionary selection of pestivirus variants with altered or no microRNA dependency. Nucleic Acids Res 2020; 48:5555-5571. [PMID: 32374844 PMCID: PMC7261151 DOI: 10.1093/nar/gkaa300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/19/2020] [Indexed: 12/15/2022] Open
Abstract
Host microRNA (miRNA) dependency is a hallmark of the human pathogen hepatitis C virus (HCV) and was also described for the related pestiviruses, which are important livestock pathogens. The liver-specific miR-122 binds within the HCV 5′ untranslated region (UTR), whereas the broadly expressed let-7 and miR-17 families bind two sites (S1 and S2, respectively) in the pestiviral 3′ UTR. Here, we dissected the mechanism of miRNA dependency of the pestivirus bovine viral diarrhea virus (BVDV). Argonaute 2 (AGO2) and miR-17 binding were essential for viral replication, whereas let-7 binding was mainly required for full translational efficiency. Furthermore, using seed site randomized genomes and evolutionary selection experiments, we found that tropism could be redirected to different miRNAs. AGO cross-linking and immunoprecipitation (CLIP) experiments and miRNA antagonism demonstrated that these alternative variants bound and depended on the corresponding miRNAs. Interestingly, we also identified miRNA-independent variants that were obtained through acquisition of compensatory mutations near the genomic 3′ terminus. Rescue experiments demonstrated that miRNA binding and 3′ mutagenesis contribute to replication through mutually exclusive mechanisms. Altogether, our findings suggest that pestiviruses, although capable of miRNA-independent replication, took advantage of miRNAs as essential host factors, suggesting a favorable path during evolutionary adaptation.
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Affiliation(s)
- Konstantinos G Kokkonos
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Nicolas Fossat
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Louise Nielsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Christina Holm
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Wytske M Hepkema
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Troels K H Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.,Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
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45
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Abstract
Oligonucleotides can be used to modulate gene expression via a range of processes including RNAi, target degradation by RNase H-mediated cleavage, splicing modulation, non-coding RNA inhibition, gene activation and programmed gene editing. As such, these molecules have potential therapeutic applications for myriad indications, with several oligonucleotide drugs recently gaining approval. However, despite recent technological advances, achieving efficient oligonucleotide delivery, particularly to extrahepatic tissues, remains a major translational limitation. Here, we provide an overview of oligonucleotide-based drug platforms, focusing on key approaches - including chemical modification, bioconjugation and the use of nanocarriers - which aim to address the delivery challenge.
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46
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The Role of the Liver-Specific microRNA, miRNA-122 in the HCV Replication Cycle. Int J Mol Sci 2020; 21:ijms21165677. [PMID: 32784807 PMCID: PMC7460827 DOI: 10.3390/ijms21165677] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023] Open
Abstract
Hepatitis C virus (HCV) replication requires annealing of a liver specific microRNA, miR-122 to 2 sites on 5' untranslated region (UTR). While, microRNAs downregulate gene expression by binding to the 3' untranslated region of the target mRNA, in this case, the microRNA anneals to the 5'UTR of the viral genomes and upregulates the viral lifecycle. In this review, we explore the current understandings of the mechanisms by which miR-122 promotes the HCV lifecycle, and its contributions to pathogenesis. Annealing of miR-122 has been reported to (a) stimulate virus translation by promoting the formation of translationally active internal ribosome entry site (IRES) RNA structure, (b) stabilize the genome, and (c) induce viral genomic RNA replication. MiR-122 modulates lipid metabolism and suppresses tumor formation, and sequestration by HCV may influence virus pathogenesis. We also discuss the possible use of miR-122 as a biomarker for chronic hepatitis and as a therapeutic target. Finally, we discuss roles for miR-122 and other microRNAs in promoting other viruses.
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47
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Ono C, Fukuhara T, Li S, Wang J, Sato A, Izumi T, Fauzyah Y, Yamamoto T, Morioka Y, Dokholyan NV, Standley DM, Matsuura Y. Various miRNAs compensate the role of miR-122 on HCV replication. PLoS Pathog 2020; 16:e1008308. [PMID: 32574204 PMCID: PMC7337399 DOI: 10.1371/journal.ppat.1008308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/06/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
One of the determinants for tissue tropism of hepatitis C virus (HCV) is miR-122, a liver-specific microRNA. Recently, it has been reported that interaction of miR-122 to HCV RNA induces a conformational change of the 5'UTR internal ribosome entry site (IRES) structure to form stem-loop II structure (SLII) and hijack of translating 80S ribosome through the binding of SLIII to 40S subunit, which leads to efficient translation. On the other hand, low levels of HCV-RNA replication have also been detected in some non-hepatic cells; however, the details of extrahepatic replication remain unknown. These observations suggest the possibility that miRNAs other than miR-122 can support efficient replication of HCV-RNA in non-hepatic cells. Here, we identified a number of such miRNAs and show that they could be divided into two groups: those that bind HCV-RNA at two locations (miR-122 binding sites I and II), in a manner similar to miR-122 (miR-122-like), and those that target a single site that bridges sites I and II and masking both G28 and C29 in the 5'UTR (non-miR-122-like). Although the enhancing activity of these non-hepatic miRNAs were lower than those of miR-122, substantial expression was detected in various normal tissues. Furthermore, structural modeling indicated that both miR-122-like and non-miR-122-like miRNAs not only can facilitate the formation of an HCV IRES SLII but also can stabilize IRES 3D structure in order to facilitate binding of SLIII to the ribosome. Together, these results suggest that HCV facilitates miR-122-independent replication in non-hepatic cells through recruitment of miRNAs other than miR-122. And our findings can provide a more detailed mechanism of miR-122-dependent enhancement of HCV-RNA translation by focusing on IRES tertiary structure.
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Affiliation(s)
- Chikako Ono
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takasuke Fukuhara
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Songling Li
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Jian Wang
- Department of Pharmacology, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Asuka Sato
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takuma Izumi
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yuzy Fauzyah
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takuya Yamamoto
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yuhei Morioka
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
- Department of Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania, United States of America
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
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48
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Emma MR, Augello G, Cusimano A, Azzolina A, Montalto G, McCubrey JA, Cervello M. GSK-3 in liver diseases: Friend or foe? BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118743. [PMID: 32417256 DOI: 10.1016/j.bbamcr.2020.118743] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
Liver diseases, including hepatitis due to hepatitis B or C virus infection, non-alcoholic fatty liver disease, and hepatocellular carcinoma pose major challenges for overall health due to limited curative treatment options. Thus, there is an urgent need to develop new therapeutic strategies for the treatment of these diseases. A better understanding of the signaling pathways involved in the pathogenesis of liver diseases can help to improve the efficacy of emerging therapies, mainly based on pharmacological approaches, which influence one or more specific molecules involved in key signal transduction pathways. These emerging therapies are very promising for the prevention and treatment of liver diseases. One promising druggable molecular target is the multifunctional serine/threonine kinase, glycogen synthase kinase 3 (GSK-3). In this review, we discuss conditions in which GSK-3 is implicated in liver diseases. In addition, we explore newly emerging drugs that target GSK-3β, as well as their potential use in and impact on the management of liver diseases.
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Affiliation(s)
- Maria R Emma
- Institute for Biomedical Research and Innovation, National Research Council (CNR), Palermo, Italy
| | - Giuseppa Augello
- Institute for Biomedical Research and Innovation, National Research Council (CNR), Palermo, Italy
| | - Antonella Cusimano
- Institute for Biomedical Research and Innovation, National Research Council (CNR), Palermo, Italy
| | - Antonina Azzolina
- Institute for Biomedical Research and Innovation, National Research Council (CNR), Palermo, Italy
| | - Giuseppe Montalto
- Institute for Biomedical Research and Innovation, National Research Council (CNR), Palermo, Italy; Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Melchiorre Cervello
- Institute for Biomedical Research and Innovation, National Research Council (CNR), Palermo, Italy.
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49
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Fulzele S, Sahay B, Yusufu I, Lee TJ, Sharma A, Kolhe R, Isales CM. COVID-19 Virulence in Aged Patients Might Be Impacted by the Host Cellular MicroRNAs Abundance/Profile. Aging Dis 2020; 11:509-522. [PMID: 32489698 PMCID: PMC7220294 DOI: 10.14336/ad.2020.0428] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/28/2020] [Indexed: 01/08/2023] Open
Abstract
The World health organization (WHO) declared Coronavirus disease 2019 (COVID-19) a global pandemic and a severe public health crisis. Drastic measures to combat COVID-19 are warranted due to its contagiousness and higher mortality rates, specifically in the aged patient population. At the current stage, due to the lack of effective treatment strategies for COVID-19 innovative approaches need to be considered. It is well known that host cellular miRNAs can directly target both viral 3'UTR and coding region of the viral genome to induce the antiviral effect. In this study, we did in silico analysis of human miRNAs targeting SARS (4 isolates) and COVID-19 (29 recent isolates from different regions) genome and correlated our findings with aging and underlying conditions. We found 848 common miRNAs targeting the SARS genome and 873 common microRNAs targeting the COVID-19 genome. Out of a total of 848 miRNAs from SARS, only 558 commonly present in all COVID-19 isolates. Interestingly, 315 miRNAs are unique for COVID-19 isolates and 290 miRNAs unique to SARS. We also noted that out of 29 COVID-19 isolates, 19 isolates have identical miRNA targets. The COVID-19 isolates, Netherland (EPI_ISL_422601), Australia (EPI_ISL_413214), and Wuhan (EPI_ISL_403931) showed six, four, and four unique miRNAs targets, respectively. Furthermore, GO, and KEGG pathway analysis showed that COVID-19 targeting human miRNAs involved in various age-related signaling and diseases. Recent studies also suggested that some of the human miRNAs targeting COVID-19 decreased with aging and underlying conditions. GO and KEGG identified impaired signaling pathway may be due to low abundance miRNA which might be one of the contributing factors for the increasing severity and mortality in aged individuals and with other underlying conditions. Further, in vitro and in vivo studies are needed to validate some of these targets and identify potential therapeutic targets.
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Affiliation(s)
- Sadanand Fulzele
- Department of Medicine, Augusta University, Augusta, GA, USA.
- Center for Healthy Aging, Augusta University, Augusta, GA, USA.
| | - Bikash Sahay
- Department of Infectious Diseases and Immunology, University of Florida, Gainesville, FL, USA.
| | - Ibrahim Yusufu
- Department of Medicine, Augusta University, Augusta, GA, USA.
| | - Tae Jin Lee
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA.
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA 30912, USA.
| | - Ravindra Kolhe
- Departments of Pathology, Augusta University, Augusta, GA 30912, USA
| | - Carlos M Isales
- Department of Medicine, Augusta University, Augusta, GA, USA.
- Center for Healthy Aging, Augusta University, Augusta, GA, USA.
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Hepatitis C Virus Translation Regulation. Int J Mol Sci 2020; 21:ijms21072328. [PMID: 32230899 PMCID: PMC7178104 DOI: 10.3390/ijms21072328] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/12/2022] Open
Abstract
Translation of the hepatitis C virus (HCV) RNA genome is regulated by the internal ribosome entry site (IRES), located in the 5’-untranslated region (5′UTR) and part of the core protein coding sequence, and by the 3′UTR. The 5′UTR has some highly conserved structural regions, while others can assume different conformations. The IRES can bind to the ribosomal 40S subunit with high affinity without any other factors. Nevertheless, IRES activity is modulated by additional cis sequences in the viral genome, including the 3′UTR and the cis-acting replication element (CRE). Canonical translation initiation factors (eIFs) are involved in HCV translation initiation, including eIF3, eIF2, eIF1A, eIF5, and eIF5B. Alternatively, under stress conditions and limited eIF2-Met-tRNAiMet availability, alternative initiation factors such as eIF2D, eIF2A, and eIF5B can substitute for eIF2 to allow HCV translation even when cellular mRNA translation is downregulated. In addition, several IRES trans-acting factors (ITAFs) modulate IRES activity by building large networks of RNA-protein and protein–protein interactions, also connecting 5′- and 3′-ends of the viral RNA. Moreover, some ITAFs can act as RNA chaperones that help to position the viral AUG start codon in the ribosomal 40S subunit entry channel. Finally, the liver-specific microRNA-122 (miR-122) stimulates HCV IRES-dependent translation, most likely by stabilizing a certain structure of the IRES that is required for initiation.
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