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Circulating MicroRNA-122 as a Potential Biomarker for Hepatitis C Virus Induced Hepatocellular Carcinoma. INTERNATIONAL JOURNAL OF CANCER MANAGEMENT 2022. [DOI: 10.5812/ijcm-131221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Background: The microRNA (miRNA) mediated translational repression can cause various diseases in humans. The liver-specific miRNA (microRNA-122 (miR-122)) is primarily involved in tissue tropism during hepatitis C virus (HCV) infection which ultimately leads to hepatocellular carcinoma (HCC). Objectives: This study focuses on evaluating host serum miR-122 as a prognostic marker in HCV-induced hepatocellular carcinoma. Methods: Evaluation of miR-122 expression was carried out by quantitative real time PCR. Results: Positive expression of miR-122 was observed in patients with chronic hepatitis C (CHC) followed by HCC patients compared to healthy controls. A difference in median levels of the miR-122 expression in CHC and HCC patients (P < 0.000) was found in contrast to cirrhosis patients (P = 0.511). The serum miR-122 expression was found threefold higher in liver cirrhosis patients than chronic hepatitis. Further, the area under the receiver operating characteristic curve (AUROC) analysis of miR-122 expression profile can efficiently distinguish CHC patients (AUROC = 0.978, P = 0.000, 95% confidence interval (CI) = 0.958 to 0.998) and HCC from healthy controls (AUROC = 0.971, P = 0.000, 95% CI = 0.944 to 0.997). Moreover, receiver operating characteristic (ROC) curve analysis significantly distinguished between CHC patients from cirrhosis patients (AUROC = 0.955, P = 0.000, 95% CI = 0.925 to 0.986) but not CHC from HCC patients (AUROC = 0.584, P = 0.104, 95% CI = 0.485 to 0.684). This study revealed a substantial correlation of miR-122 with HCV viral load (r = 0.56, P = 0.000), ALT (r = 0.67, P = 0.000) and AST (r = 0.65, P = 0.000) levels. Conclusions: Serum miR-122 can potentially serve as a promising prognostic tool for HCV induced HCC.
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Thakur A, Kumar M. AntiVIRmiR: A repository of host antiviral miRNAs and their expression along with experimentally validated viral miRNAs and their targets. Front Genet 2022; 13:971852. [PMID: 36159991 PMCID: PMC9493126 DOI: 10.3389/fgene.2022.971852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
miRNAs play an essential role in promoting viral infections as well as modulating the antiviral defense. Several miRNA repositories have been developed for different species, e.g., human, mouse, and plant. However, ‘VIRmiRNA’ is the only existing resource for experimentally validated viral miRNAs and their targets. We have developed a ‘AntiVIRmiR’ resource encompassing data on host/virus miRNA expression during viral infection. This resource with 22,741 entries is divided into four sub-databases viz., ‘DEmiRVIR’, ‘AntiVmiR’, ‘VIRmiRNA2’ and ‘VIRmiRTar2’. ‘DEmiRVIR’ has 10,033 differentially expressed host-viral miRNAs for 21 viruses. ‘AntiVmiR’ incorporates 1,642 entries for host miRNAs showing antiviral activity for 34 viruses. Additionally, ‘VIRmiRNA2’ includes 3,340 entries for experimentally validated viral miRNAs from 50 viruses along with 650 viral isomeric sequences for 14 viruses. Further, ‘VIRmiRTar2’ has 7,726 experimentally validated targets for viral miRNAs against 21 viruses. Furthermore, we have also performed network analysis for three sub-databases. Interactions between up/down-regulated human miRNAs and viruses are displayed for ‘AntiVmiR’ as well as ‘DEmiRVIR’. Moreover, ‘VIRmiRTar2’ interactions are shown among different viruses, miRNAs, and their targets. We have provided browse, search, external hyperlinks, data statistics, and useful analysis tools. The database available at https://bioinfo.imtech.res.in/manojk/antivirmir would be beneficial for understanding the host-virus interactions as well as viral pathogenesis.
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Affiliation(s)
- Anamika Thakur
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- *Correspondence: Manoj Kumar,
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Gharib AF, Eed EM, Khalifa AS, Raafat N, Shehab-Eldeen S, Alwakeel HR, Darwiesh E, Essa A. Value of Serum miRNA-96-5p and miRNA-99a-5p as Diagnostic Biomarkers for Hepatocellular Carcinoma. Int J Gen Med 2022; 15:2427-2436. [PMID: 35264879 PMCID: PMC8901257 DOI: 10.2147/ijgm.s354842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/15/2022] [Indexed: 12/23/2022] Open
Abstract
Purpose Circulatory microRNAs (miRNAs) have the potential to be employed as markers for cancer detection and as prognostic tools for disease management. As a result, our goal was to explore the effectiveness of serum miRNA-96-5p and miRNA-99a-5p as diagnostic tools in hepatocellular carcinoma (HCC). Patients and methods Blood samples were collected from 55 patients with HCV-induced HCC, 55 patients with HCV-induced liver cirrhosis, and 55 healthy controls. The expression levels of miRNA-96-5p and miRNA-99a-5p were measured using quantitative RT-PCR. Results miRNA-96-5p expression levels were increased in HCC patient sera, while miRNA-99a-5p levels were reduced. According to ROC curve analysis, using a combination of circulating miRNA-96-5p, miRNA-99a-5-, and alpha-fetoprotein (AFP) improves the accuracy of diagnoses for HCC, with an area under the curve (AUC) of 0.97, compared to AUCs of 0.82, 0.86, and 0.73, respectively, for the individual biomarkers. Furthermore, the present data suggested that higher serum miRNA-96-5p levels were linked to larger tumors and metastasis, whereas lower serum miRNA-99a-5p levels were exclusively linked to HCC metastasis. Conclusion Using miRNA-96-5p and miRNA-99a-5p in combination with AFP increased both sensitivity and specificity for the diagnosis of HCC. Furthermore, serum levels were linked to tumor size and metastasis. These findings suggested that serum miRNA-96-5p and miRNA-99a-5p could be used as non-invasive biomarkers for the diagnosis of HCC.
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Affiliation(s)
- Amal F Gharib
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, 21944, Saudi Arabia
| | - Emad M Eed
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, 21944, Saudi Arabia
| | - Amany S Khalifa
- Clinical Pathology Department, Faculty of Medicine, Menoufia University, Shebin El-Kom, Egypt
| | - Nermin Raafat
- Department of Medical Biochemistry, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Somaia Shehab-Eldeen
- Tropical Medicine Department, Faculty of Medicine, Menoufia University, Shebin El-Kom, Egypt
- Department of Internal Medicine, College of Medicine, King Faisal University, Al-Ahsaa, Saudi Arabia
- Correspondence: Somaia Shehab-Eldeen, Tropical Medicine Department, Faculty of Medicine, Menoufia University, Yassen Abd Al Ghafar Street, Shebin El-Kom, 32511, Egypt, Tel +20 1117251523, Email
| | - Hany R Alwakeel
- Department of Hepatology, National Liver Institute, Menoufia University, Shebin El-Kom, Egypt
| | - Ehab Darwiesh
- Department of Tropical Medicine, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Abdallah Essa
- Tropical Medicine Department, Faculty of Medicine, Menoufia University, Shebin El-Kom, Egypt
- Department of Internal Medicine, College of Medicine, King Faisal University, Al-Ahsaa, Saudi Arabia
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Chung CZ, Balasuriya N, Siddika T, Frederick MI, Heinemann IU. Gld2 activity and RNA specificity is dynamically regulated by phosphorylation and interaction with QKI-7. RNA Biol 2021; 18:397-408. [PMID: 34288801 DOI: 10.1080/15476286.2021.1952540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
In the cell, RNA abundance is dynamically controlled by transcription and decay rates. Posttranscriptional nucleotide addition at the RNA 3' end is a means of regulating mRNA and RNA stability and activity, as well as marking RNAs for degradation. The human nucleotidyltransferase Gld2 polyadenylates mRNAs and monoadenylates microRNAs, leading to an increase in RNA stability. The broad substrate range of Gld2 and its role in controlling RNA stability make the regulation of Gld2 activity itself imperative. Gld2 activity can be regulated by post-translational phosphorylation via the oncogenic kinase Akt1 and other kinases, leading to either increased or almost abolished enzymatic activity, and here we confirm that Akt1 phosphorylates Gld2 in a cellular context. Another means to control Gld2 RNA specificity and activity is the interaction with RNA binding proteins. Known interactors are QKI-7 and CPEB, which recruit Gld2 to specific miRNAs and mRNAs. We investigate the interplay between five phosphorylation sites in the N-terminal domain of Gld2 and three RNA binding proteins. We found that the activity and RNA specificity of Gld2 is dynamically regulated by this network. Binding of QKI-7 or phosphorylation at S62 relieves the autoinhibitory function of the Gld2 N-terminal domain. Binding of QKI-7 to a short peptide sequence within the N-terminal domain can also override the deactivation caused by Akt1 phosphorylation at S116. Our data revealed that Gld2 substrate specificity and activity can be dynamically regulated to match the cellular need of RNA stabilization and turnover.
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Affiliation(s)
- Christina Z Chung
- Department of Biochemistry, Schulich School of Medicine and Dentistry, the University of Western Ontario, London, Canada
| | - Nileeka Balasuriya
- Department of Biochemistry, Schulich School of Medicine and Dentistry, the University of Western Ontario, London, Canada
| | - Tarana Siddika
- Department of Biochemistry, Schulich School of Medicine and Dentistry, the University of Western Ontario, London, Canada
| | - Mallory I Frederick
- Department of Biochemistry, Schulich School of Medicine and Dentistry, the University of Western Ontario, London, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, Schulich School of Medicine and Dentistry, the University of Western Ontario, London, Canada
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HCV Proteins Modulate the Host Cell miRNA Expression Contributing to Hepatitis C Pathogenesis and Hepatocellular Carcinoma Development. Cancers (Basel) 2021; 13:cancers13102485. [PMID: 34069740 PMCID: PMC8161081 DOI: 10.3390/cancers13102485] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary According to the last estimate by the World Health Organization (WHO), more than 71 million individuals have chronic hepatitis C worldwide. The persistence of HCV infection leads to chronic hepatitis, which can evolve into liver cirrhosis and ultimately into hepatocellular carcinoma (HCC). Although the pathogenic mechanisms are not fully understood, it is well established that an interplay between host cell factors, including microRNAs (miRNA), and viral components exist in all the phases of the viral infection and replication. Those interactions establish a complex equilibrium between host cells and HCV and participate in multiple mechanisms characterizing hepatitis C pathogenesis. The present review aims to describe the role of HCV structural and non-structural proteins in the modulation of cellular miRNA during HCV infection and pathogenesis. Abstract Hepatitis C virus (HCV) genome encodes for one long polyprotein that is processed by cellular and viral proteases to generate 10 polypeptides. The viral structural proteins include the core protein, and the envelope glycoproteins E1 and E2, present at the surface of HCV particles. Non-structural (NS) proteins consist of NS1, NS2, NS3, NS4A, NS4B, NS5a, and NS5b and have a variable function in HCV RNA replication and particle assembly. Recent findings evidenced the capacity of HCV virus to modulate host cell factors to create a favorable environment for replication. Indeed, increasing evidence has indicated that the presence of HCV is significantly associated with aberrant miRNA expression in host cells, and HCV structural and non-structural proteins may be responsible for these alterations. In this review, we summarize the recent findings on the role of HCV structural and non-structural proteins in the modulation of host cell miRNAs, with a focus on the molecular mechanisms responsible for the cell re-programming involved in viral replication, immune system escape, as well as the oncogenic process. In this regard, structural and non-structural proteins have been shown to modulate the expression of several onco-miRNAs or tumor suppressor miRNAs.
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Wei XY, Ding J, Tian WG, Yu YC. MicroRNA-122 as a diagnostic biomarker for hepatocellular carcinoma related to hepatitis C virus: a meta-analysis and systematic review. J Int Med Res 2021; 48:300060520941634. [PMID: 32790532 PMCID: PMC7543180 DOI: 10.1177/0300060520941634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Objective MicroRNA-122 (miR-122) has been identified as a biomarker of liver diseases. However, the miR-122 detection accuracy in patients with hepatocellular carcinoma (HCC) associated with hepatitis C virus (HCV) is inconclusive. Methods We conducted a systematic literature search of Web of Science, Cochrane Library, PubMed, and Embase to identify studies related to the diagnostic value of miR-122 in HCV-related HCC. We analyzed the results and validated them using data from the Cancer Genome Atlas (TCGA). Results Six articles were included in this meta-analysis, comprising 354 cases and 420 controls. The pooled specificity, sensitivity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the curve were 0.87, 0.83, 5.1, 0.16, 32, and 0.92, respectively. Additional sub-group analyses showed that results for plasma were more sensitive than those for serum. In addition, miR-122 was better at distinguishing between HCV-associated HCC and healthy people or those with HCV than between those with HCV-associated HCC and HCV-related cirrhosis. Small samples (≤100) had better diagnostic odds ratios than larger samples (>100). Analysis of data from TCGA confirmed that miRNA-122 had a high diagnostic value. Conclusion This meta-analysis demonstrates that miR-122 may be a useful diagnostic biomarker for HCV-associated HCC.
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Affiliation(s)
- Xiao-Yu Wei
- Department of Infectious Diseases, Yongchuan Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Jing Ding
- Department of Infectious Diseases, Yongchuan Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Wen-Guang Tian
- Department of Infectious Diseases, Yongchuan Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Yi-Chuan Yu
- Department of Emergency, Yongchuan Hospital of Chongqing Medical University, Chongqing, P.R. China
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Frederick MI, Heinemann IU. Regulation of RNA stability at the 3' end. Biol Chem 2021; 402:425-431. [PMID: 33938180 PMCID: PMC10884531 DOI: 10.1515/hsz-2020-0325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/04/2020] [Indexed: 01/09/2023]
Abstract
RNA homeostasis is regulated by a multitude of cellular pathways. Although the addition of untemplated adenine residues to the 3' end of mRNAs has long been known to affect RNA stability, newly developed techniques for 3'-end sequencing of RNAs have revealed various unexpected RNA modifications. Among these, uridylation is most recognized for its role in mRNA decay but is also a key regulator of numerous RNA species, including miRNAs and tRNAs, with dual roles in both stability and maturation of miRNAs. Additionally, low levels of untemplated guanidine and cytidine residues have been observed as parts of more complex tailing patterns.
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Affiliation(s)
- Mallory I Frederick
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London ON, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London ON, Canada
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Kim GW, Siddiqui A. The role of N6-methyladenosine modification in the life cycle and disease pathogenesis of hepatitis B and C viruses. Exp Mol Med 2021; 53:339-345. [PMID: 33742132 PMCID: PMC8080661 DOI: 10.1038/s12276-021-00581-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent modification of mammalian cellular RNAs. m6A methylation is linked to epigenetic regulation of several aspects of gene expression, including RNA stability, splicing, nuclear export, RNA folding, and translational activity. m6A modification is reversibly catalyzed by methyltransferases (m6A writers) and demethylases (m6A erasers), and the dynamics of m6A-modified RNA are regulated by m6A-binding proteins (m6A readers). Recently, several studies have shown that m6A methylation sites have been identified in hepatitis B virus (HBV) transcripts and the hepatitis C virus (HCV) RNA genome. Here, we review the role of m6A modification in HBV/HCV replication and its contribution to liver disease pathogenesis. A better understanding of the functions of m6A methylation in the life cycles of HBV and HCV is required to establish the role of these modifications in liver diseases associated with these viral infections.
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Affiliation(s)
- Geon-Woo Kim
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Aleem Siddiqui
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
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The Significance of HCV Viral Load in the Incidence of HCC: a Correlation Between Mir-122 and CCL2. J Gastrointest Cancer 2021; 51:412-417. [PMID: 31385234 DOI: 10.1007/s12029-019-00281-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the fifth most common cancer, the third leading cause of cancer deaths worldwide with over 500,000 people affected. It is a major cause of death in patients with chronic hepatitis C virus (HCV) infection. Overwhelming lines of epidemiological evidence have indicated that persistent infection with HCV is a major risk for the development of HCC. Although a proportion of patients with a chronic hepatitis C virus infection progress to HCC, the peak incidence of HCC associated with HCV infection has not yet occurred. AIM This review aimed to assess the impact of hepatitis C viral load on the development of HCC as a correlation between mir-122 and, the key factor in fibrogenesis, CCL2. CONCLUSION According to the detailed explanation of the role of mir-122 and CCL2 in HCV and HCC and the evidence of the inverse correlation between them, it may be concluded that HCV may affect mir-122 expression level of the hepatocytes with different patterns depending on the viral genotype. Collectively, HCV viral load alone is not sufficient to predict the HCC development and progression. Besides the quantitative evaluation of the HCV, mir-122 and CCL2 determinations should also be taken into consideration.
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Kim GW, Imam H, Khan M, Mir SA, Kim SJ, Yoon SK, Hur W, Siddiqui A. HBV-Induced Increased N6 Methyladenosine Modification of PTEN RNA Affects Innate Immunity and Contributes to HCC. Hepatology 2021; 73:533-547. [PMID: 32394474 PMCID: PMC7655655 DOI: 10.1002/hep.31313] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/10/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Epitranscriptomic modification of RNA has emerged as the most prevalent form of regulation of gene expression that affects development, differentiation, metabolism, viral infections, and most notably cancer. We have previously shown that hepatitis B virus (HBV) transcripts are modified by N6 methyladenosine (m6 A) addition. HBV also affects m6 A modification of several host RNAs, including phosphatase and tensin homolog (PTEN), a well-known tumor suppressor. PTEN plays a critical role in antiviral innate immunity and the development of hepatocellular carcinoma (HCC). Reports have shown that PTEN controlled interferon regulatory factor 3 (IRF-3) nuclear localization by negative phosphorylation of IRF-3 at Ser97, and PTEN reduced carcinogenesis by inhibiting the phosphatidylinositol-3-kinase (PI3K)/AKT pathway. APPROACH AND RESULTS Here, we show that HBV significantly increases the m6 A modification of PTEN RNA, which contributes to its instability with a corresponding decrease in PTEN protein levels. This is reversed in cells in which the expression of m6 A methyltransferases is silenced. PTEN expression directly increases activated IRF-3 nuclear import and subsequent interferon synthesis. In the absence of PTEN, IRF-3 dephosphorylation at the Ser97 site is decreased and interferon synthesis is crippled. In chronic HBV patient biopsy samples, m6 A-modified PTEN mRNA levels were uniformly up-regulated with a concomitant decrease of PTEN mRNA levels. HBV gene expression also activated the PI3K/AKT pathway by regulating PTEN mRNA stability in HCC cell lines. CONCLUSIONS The m6 A epitranscriptomic regulation of PTEN by HBV affects innate immunity by inhibiting IRF-3 nuclear import and the development of HCC by activating the PI3K/AKT pathway. Our studies collectively provide new insights into the mechanisms of HBV-directed immune evasion and HBV-associated hepatocarcinogenesis through m6 A modification of the host PTEN mRNAs.
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Affiliation(s)
- Geon-Woo Kim
- Division of Infectious DiseasesDepartment of MedicineUniversity of California, San DiegoLa JollaCA
| | - Hasan Imam
- Division of Infectious DiseasesDepartment of MedicineUniversity of California, San DiegoLa JollaCA
| | - Mohsin Khan
- Division of Infectious DiseasesDepartment of MedicineUniversity of California, San DiegoLa JollaCA
| | - Saiful Anam Mir
- Division of Infectious DiseasesDepartment of MedicineUniversity of California, San DiegoLa JollaCA
| | - Seong-Jun Kim
- Center for Convergent Research of Emerging Virus InfectionKorea Research Institute of Chemical TechnologyDaejeonSouth Korea
| | - Seung Kew Yoon
- The Catholic University Liver Research CenterCollege of MedicineThe Catholic University of KoreaSeoulSouth Korea.,Division of HepatologyDepartment of Internal MedicineSeoul St. Mary's HospitalCollege of MedicineThe Catholic University of KoreaSeoulSouth Korea
| | - Wonhee Hur
- The Catholic University Liver Research CenterCollege of MedicineThe Catholic University of KoreaSeoulSouth Korea
| | - Aleem Siddiqui
- Division of Infectious DiseasesDepartment of MedicineUniversity of California, San DiegoLa JollaCA
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Kim GW, Imam H, Khan M, Siddiqui A. N6-Methyladenosine modification of hepatitis B and C viral RNAs attenuates host innate immunity via RIG-I signaling. J Biol Chem 2020; 295:13123-13133. [PMID: 32719095 PMCID: PMC7489896 DOI: 10.1074/jbc.ra120.014260] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/20/2020] [Indexed: 12/25/2022] Open
Abstract
N6-Methyladenosine (m6A), the methylation of the adenosine base at the nitrogen 6 position, is the most common epitranscriptomic modification of mRNA that affects a wide variety of biological functions. We have previously reported that hepatitis B viral RNAs are m6A-modified, displaying a dual functional role in the viral life cycle. Here, we show that cellular m6A machinery regulates host innate immunity against hepatitis B and C viral infections by inducing m6A modification of viral transcripts. The depletion of the m6A writer enzymes (METTL3 and METTL14) leads to an increase in viral RNA recognition by retinoic acid-inducible gene I (RIG-I), thereby stimulating type I interferon production. This is reversed in cells in which m6A METTL3 and METTL14 are overexpressed. The m6A modification of viral RNAs renders RIG-I signaling less effective, whereas single nucleotide mutation of m6A consensus motif of viral RNAs enhances RIG-I sensing activity. Importantly, m6A reader proteins (YTHDF2 and YTHDF3) inhibit RIG-I-transduced signaling activated by viral RNAs by occupying m6A-modified RNAs and inhibiting RIG-I recognition. Collectively, our results provide new insights into the mechanism of immune evasion via m6A modification of viral RNAs.
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Affiliation(s)
- Geon-Woo Kim
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Hasan Imam
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Mohsin Khan
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Aleem Siddiqui
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, California, USA.
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Liudkovska V, Dziembowski A. Functions and mechanisms of RNA tailing by metazoan terminal nucleotidyltransferases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1622. [PMID: 33145994 PMCID: PMC7988573 DOI: 10.1002/wrna.1622] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/28/2022]
Abstract
Termini often determine the fate of RNA molecules. In recent years, 3' ends of almost all classes of RNA species have been shown to acquire nontemplated nucleotides that are added by terminal nucleotidyltransferases (TENTs). The best-described role of 3' tailing is the bulk polyadenylation of messenger RNAs in the cell nucleus that is catalyzed by canonical poly(A) polymerases (PAPs). However, many other enzymes that add adenosines, uridines, or even more complex combinations of nucleotides have recently been described. This review focuses on metazoan TENTs, which are either noncanonical PAPs or terminal uridylyltransferases with varying processivity. These enzymes regulate RNA stability and RNA functions and are crucial in early development, gamete production, and somatic tissues. TENTs regulate gene expression at the posttranscriptional level, participate in the maturation of many transcripts, and protect cells against viral invasion and the transposition of repetitive sequences. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Vladyslava Liudkovska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Kumar S, Xie H, Shi H, Gao J, Juhlin CC, Björnhagen V, Höög A, Lee L, Larsson C, Lui W. Merkel cell polyomavirus oncoproteins induce microRNAs that suppress multiple autophagy genes. Int J Cancer 2020; 146:1652-1666. [PMID: 31180579 PMCID: PMC7003823 DOI: 10.1002/ijc.32503] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/09/2019] [Accepted: 05/29/2019] [Indexed: 01/12/2023]
Abstract
Viruses can inhibit host autophagy through multiple mechanisms, and evasion of autophagy plays an important role in immune suppression and viral oncogenesis. Merkel cell polyomavirus (MCPyV) T-antigens are expressed and involved in the pathogenesis of a large proportion of Merkel cell carcinoma (MCC). Yet, how MCPyV induces tumorigenesis is not fully understood. Herein, we show that MCPyV T-antigens induce miR-375, miR-30a-3p and miR-30a-5p expressions, which target multiple key genes involved in autophagy, including ATG7, SQSTM1 (p62) and BECN1. In MCC tumors, low expression of ATG7 and p62 are associated with MCPyV-positive tumors. Ectopic expression of MCPyV small T-antigen and truncated large T-antigen (LT), but not the wild-type LT, resulted in autophagy suppression, suggesting the importance of autophagy evasion in MCPyV-mediated tumorigenesis. Torin-1 treatment induced cell death, which was attenuated by autophagy inhibitor, but not pan-caspase inhibitor, suggesting a potential role of autophagy in promoting cell death in MCC. Conceptually, our study shows that MCPyV oncoproteins suppress autophagy to protect cancer cells from cell death, which contribute to a better understanding of MCPyV-mediated tumorigenesis and potential MCC treatment.
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Affiliation(s)
- Satendra Kumar
- Department of Oncology‐PathologyKarolinska Institutet; Cancer Center Karolinska, Karolinska University HospitalStockholmSweden
| | - Hong Xie
- Department of Oncology‐PathologyKarolinska Institutet; Cancer Center Karolinska, Karolinska University HospitalStockholmSweden
- Tianjin Life Science Research Center and Department of Pathogen BiologySchool of Basic Medical Sciences, Tianjin Medical UniversityTianjinChina
| | - Hao Shi
- Department of Oncology‐PathologyKarolinska Institutet; Cancer Center Karolinska, Karolinska University HospitalStockholmSweden
| | - Jiwei Gao
- Department of Oncology‐PathologyKarolinska Institutet; Cancer Center Karolinska, Karolinska University HospitalStockholmSweden
| | - Carl Christofer Juhlin
- Department of Oncology‐PathologyKarolinska Institutet; Cancer Center Karolinska, Karolinska University HospitalStockholmSweden
- Department of Clinical Pathology and CytologyKarolinska University HospitalStockholmSweden
| | - Viveca Björnhagen
- Department of Reconstructive Plastic SurgeryKarolinska University HospitalStockholmSweden
| | - Anders Höög
- Department of Oncology‐PathologyKarolinska Institutet; Cancer Center Karolinska, Karolinska University HospitalStockholmSweden
- Department of Clinical Pathology and CytologyKarolinska University HospitalStockholmSweden
| | - Linkiat Lee
- Department of Oncology‐PathologyKarolinska Institutet; Cancer Center Karolinska, Karolinska University HospitalStockholmSweden
| | - Catharina Larsson
- Department of Oncology‐PathologyKarolinska Institutet; Cancer Center Karolinska, Karolinska University HospitalStockholmSweden
- Department of Clinical Pathology and CytologyKarolinska University HospitalStockholmSweden
| | - Weng‐Onn Lui
- Department of Oncology‐PathologyKarolinska Institutet; Cancer Center Karolinska, Karolinska University HospitalStockholmSweden
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14
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Cho H, Lee W, Kim GW, Lee SH, Moon JS, Kim M, Kim HS, Oh JW. Regulation of La/SSB-dependent viral gene expression by pre-tRNA 3' trailer-derived tRNA fragments. Nucleic Acids Res 2019; 47:9888-9901. [PMID: 31504775 PMCID: PMC6765225 DOI: 10.1093/nar/gkz732] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 07/29/2019] [Accepted: 08/16/2019] [Indexed: 12/19/2022] Open
Abstract
tRNA-derived RNA fragments (tRFs) have emerged as a new class of functional RNAs implicated in cancer, metabolic and neurological disorders, and viral infection. Yet our understanding of their biogenesis and functions remains limited. In the present study, through analysis of small RNA profile we have identified a distinct set of tRFs derived from pre-tRNA 3′ trailers in the hepatocellular carcinoma cell line Huh7. Among those tRFs, tRF_U3_1, which is a 19-nucleotide-long chr10.tRNA2-Ser(TGA)-derived trailer, was expressed most abundantly in both Huh7 and cancerous liver tissues, being present primarily in the cytoplasm. We show that genetic loss of tRF_U3_1 does not affect cell growth and it is not involved in Ago2-mediated gene silencing. Using La/SSB knockout Huh7 cell lines, we demonstrate that this nuclear-cytoplasmic shuttling protein directly binds to the 3′ U-tail of tRF_U3_1 and other abundantly expressed trailers and plays a critical role in their stable cytoplasmic accumulation. The pre-tRNA trailer-derived tRFs capable of sequestering the limiting amounts of La/SSB in the cytoplasm rendered cells resistant to various RNA viruses, which usurp La/SSB with RNA chaperone activity for their gene expression. Collectively, our results establish the trailer-derived tRF-La/SSB interface, regulating viral gene expression.
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Affiliation(s)
- Hee Cho
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Wooseong Lee
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Geon-Woo Kim
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Seung-Hoon Lee
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Jae-Su Moon
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Minwoo Kim
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Hyun Seok Kim
- Severance Biomedical Science Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Jong-Won Oh
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
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15
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Hojo H, Yashiro Y, Noda Y, Ogami K, Yamagishi R, Okada S, Hoshino SI, Suzuki T. The RNA-binding protein QKI-7 recruits the poly(A) polymerase GLD-2 for 3' adenylation and selective stabilization of microRNA-122. J Biol Chem 2019; 295:390-402. [PMID: 31792053 DOI: 10.1074/jbc.ra119.011617] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
MicroRNA-122 (miR-122) is highly expressed in hepatocytes, where it plays an important role in regulating cholesterol and fatty acid metabolism, and it is also a host factor required for hepatitis C virus replication. miR-122 is selectively stabilized by 3' adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2 (also known as PAPD4 or TENT2). However, it is unclear how GLD-2 specifically stabilizes miR-122. Here, we show that QKI7 KH domain-containing RNA binding (QKI-7), one of three isoforms of the QKI proteins, which are members of the signal transduction and activation of RNA (STAR) family of RNA-binding proteins, is involved in miR-122 stabilization. QKI down-regulation specifically decreased the steady-state level of mature miR-122, but did not affect the pre-miR-122 level. We also found that QKI-7 uses its C-terminal region to interact with GLD-2 and its QUA2 domain to associate with the RNA-induced silencing complex protein Argonaute 2 (Ago2), indicating that the GLD-2-QKI-7 interaction recruits GLD-2 to Ago2. QKI-7 exhibited specific affinity to miR-122 and significantly promoted GLD-2-mediated 3' adenylation of miR-122 in vitro Taken together, our findings indicate that miR-122 binds Ago2-interacting QKI-7, which recruits GLD-2 for 3' adenylation and stabilization of miR-122.
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Affiliation(s)
- Hiroaki Hojo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuka Yashiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuta Noda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Koichi Ogami
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Ryota Yamagishi
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Shunpei Okada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shin-Ichi Hoshino
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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16
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Chung CZ, Balasuriya N, Manni E, Liu X, Li SSC, O’Donoghue P, Heinemann IU. Gld2 activity is regulated by phosphorylation in the N-terminal domain. RNA Biol 2019; 16:1022-1033. [PMID: 31057087 PMCID: PMC6602411 DOI: 10.1080/15476286.2019.1608754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/25/2019] [Accepted: 04/14/2019] [Indexed: 02/06/2023] Open
Abstract
The de-regulation of microRNAs (miRNAs) is associated with multiple human diseases, yet cellular mechanisms governing miRNA abundance remain largely elusive. Human miR-122 is required for Hepatitis C proliferation, and low miR-122 abundance is associated with hepatic cancer. The adenylyltransferase Gld2 catalyses the post-transcriptional addition of a single adenine residue (A + 1) to the 3'-end of miR-122, enhancing its stability. Gld2 activity is inhibited by binding to the Hepatitis C virus core protein during HepC infection, but no other mechanisms of Gld2 regulation are known. We found that Gld2 activity is regulated by site-specific phosphorylation in its disordered N-terminal domain. We identified two phosphorylation sites (S62, S110) where phosphomimetic substitutions increased Gld2 activity and one site (S116) that markedly reduced activity. Using mass spectrometry, we confirmed that HEK 293 cells readily phosphorylate the N-terminus of Gld2. We identified protein kinase A (PKA) and protein kinase B (Akt1) as the kinases that site-specifically phosphorylate Gld2 at S116, abolishing Gld2-mediated nucleotide addition. The data demonstrate a novel phosphorylation-dependent mechanism to regulate Gld2 activity, revealing tumour suppressor miRNAs as a previously unknown target of Akt1-dependent signalling.
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Affiliation(s)
- Christina Z. Chung
- Department of Biochemistry, The University of Western Ontario, London, Canada
| | - Nileeka Balasuriya
- Department of Biochemistry, The University of Western Ontario, London, Canada
| | - Emad Manni
- Department of Biochemistry, The University of Western Ontario, London, Canada
| | - Xuguang Liu
- Department of Biochemistry, The University of Western Ontario, London, Canada
| | - Shawn Shun-Cheng Li
- Department of Biochemistry, The University of Western Ontario, London, Canada
- Department of Oncology and Child Health Research Institute, The University of Western Ontario, London, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Canada
- Department of Chemistry, The University of Western Ontario, London, Canada
| | - Ilka U. Heinemann
- Department of Biochemistry, The University of Western Ontario, London, Canada
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17
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Identifying and characterizing functional 3' nucleotide addition in the miRNA pathway. Methods 2018; 152:23-30. [PMID: 30138674 DOI: 10.1016/j.ymeth.2018.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/02/2018] [Accepted: 08/14/2018] [Indexed: 02/07/2023] Open
Abstract
Over the past decade, modifications to microRNAs (miRNAs) via 3' end nucleotide addition have gone from a deep-sequencing curiosity to experimentally confirmed drivers of a range of regulatory activities. Here we overview the methods that have been deployed by researchers seeking to untangle these diverse functional roles and include characterizing not only the nucleotidyl transferases catalyzing the additions but also the nucleotides being added, and the timing of their addition during the miRNA pathway. These methods and their further development are key to clarifying the diverse and sometimes contradictory functional findings presently attributed to these nucleotide additions.
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18
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Lee W, Lee SH, Kim M, Moon JS, Kim GW, Jung HG, Kim IH, Oh JE, Jung HE, Lee HK, Ku KB, Ahn DG, Kim SJ, Kim KS, Oh JW. Vibrio vulnificus quorum-sensing molecule cyclo(Phe-Pro) inhibits RIG-I-mediated antiviral innate immunity. Nat Commun 2018; 9:1606. [PMID: 29686409 PMCID: PMC5913291 DOI: 10.1038/s41467-018-04075-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 04/03/2018] [Indexed: 02/06/2023] Open
Abstract
The recognition of pathogen-derived ligands by pattern recognition receptors activates the innate immune response, but the potential interaction of quorum-sensing (QS) signaling molecules with host anti-viral defenses remains largely unknown. Here we show that the Vibrio vulnificus QS molecule cyclo(Phe-Pro) (cFP) inhibits interferon (IFN)-β production by interfering with retinoic-acid-inducible gene-I (RIG-I) activation. Binding of cFP to the RIG-I 2CARD domain induces a conformational change in RIG-I, preventing the TRIM25-mediated ubiquitination to abrogate IFN production. cFP enhances susceptibility to hepatitis C virus (HCV), as well as Sendai and influenza viruses, each known to be sensed by RIG-I but did not affect the melanoma-differentiation-associated gene 5 (MDA5)-recognition of norovirus. Our results reveal an inter-kingdom network between bacteria, viruses and host that dysregulates host innate responses via a microbial quorum-sensing molecule modulating the response to viral infection.
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Affiliation(s)
- Wooseong Lee
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Seung-Hoon Lee
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Minwoo Kim
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Jae-Su Moon
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Geon-Woo Kim
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Hae-Gwang Jung
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - In Hwang Kim
- Department of Life Science, Sogang University, Seoul, 04107, Korea
| | - Ji Eun Oh
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Hi Eun Jung
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Heung Kyu Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Keun Bon Ku
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Dae-Gyun Ahn
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Seong-Jun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Kun-Soo Kim
- Department of Life Science, Sogang University, Seoul, 04107, Korea
| | - Jong-Won Oh
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea.
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19
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He CL, Liu M, Tan ZX, Hu YJ, Zhang QY, Kuang XM, Kong WL, Mao Q. Hepatitis C virus core protein-induced miR-93-5p up-regulation inhibits interferon signaling pathway by targeting IFNAR1. World J Gastroenterol 2018; 24:226-236. [PMID: 29375208 PMCID: PMC5768941 DOI: 10.3748/wjg.v24.i2.226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the mechanism by which hepatitis C virus (HCV) core protein-induced miR-93-5p up-regulation regulates the interferon (IFN) signaling pathway.
METHODS HCV-1b core protein was exogenously expressed in Huh7 cells using pcDNA3.1 (+) vector. The expression of miR-93-5p and interferon receptor 1 (IFNAR1) was measured using quantitative reverse transcription-polymerase chain reaction and Western blot. The protein expression and phosphorylation level of STAT1 were evaluated by Western blot. The overexpression and silencing of miR-93-5p and IFNAR1 were performed using miR-93-5p agomir and antagomir, and pcDNA3.1-IFNAR1 and IFNAR1 siRNA, respectively. Luciferase assay was used to identify whether IFNAR1 is a target of miR-93-5p. Cellular experiments were also conducted.
RESULTS Serum miR-93-5p level was increased in patients with HCV-1b infection and decreased to normal level after HCV-1b clearance, but persistently increased in those with pegylated interferon-α resistance, compared with healthy subjects. Serum miR-93-5p expression had an AUC value of 0.8359 in distinguishing patients with pegylated interferon-α resistance from those with pegylated interferon-α sensitivity. HCV-1b core protein increased miR-93-5p expression and induced inactivation of the IFN signaling pathway in Huh7 cells. Furthermore, IFNAR1 was identified as a direct target of miR-93-5p, and IFNAR1 restore could rescue miR-93-5p-reduced STAT1 phosphorylation, suggesting that the miR-93-5p-IFNAR1 axis regulates the IFN signaling pathway.
CONCLUSION HCV-1b core protein-induced miR-93-5p up-regulation inhibits the IFN signaling pathway by directly targeting IFNAR1, and the miR-93-5p-IFNAR1 axis regulates STAT1 phosphorylation. This axis may be a potential therapeutic target for HCV-1b infection.
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Affiliation(s)
- Chang-Long He
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
- Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing 400037, China
| | - Ming Liu
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
- Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing 400037, China
| | - Zhao-Xia Tan
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
- Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing 400037, China
| | - Ya-Jun Hu
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
- Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing 400037, China
| | - Qiao-Yue Zhang
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
- Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing 400037, China
| | - Xue-Mei Kuang
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
- Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing 400037, China
| | - Wei-Long Kong
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
- Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing 400037, China
| | - Qing Mao
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400037, China
- Chongqing Key Laboratory for Research of Infectious Diseases, Chongqing 400037, China
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20
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Yamane D, Selitsky SR, Shimakami T, Li Y, Zhou M, Honda M, Sethupathy P, Lemon SM. Differential hepatitis C virus RNA target site selection and host factor activities of naturally occurring miR-122 3΄ variants. Nucleic Acids Res 2017; 45:4743-4755. [PMID: 28082397 PMCID: PMC5416874 DOI: 10.1093/nar/gkw1332] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 12/22/2016] [Indexed: 01/07/2023] Open
Abstract
In addition to suppressing cellular gene expression, certain miRNAs potently facilitate replication of specific positive-strand RNA viruses. miR-122, a pro-viral hepatitis C virus (HCV) host factor, binds and recruits Ago2 to tandem sites (S1 and S2) near the 5΄ end of the HCV genome, stabilizing it and promoting its synthesis. HCV target site selection follows canonical miRNA rules, but how non-templated 3΄ miR-122 modifications impact this unconventional miRNA action is unknown. High-throughput sequencing revealed that a 22 nt miRNA with 3΄G (‘22–3΄G’) comprised <63% of total miR-122 in human liver, whereas other variants (23–3΄A, 23–3΄U, 21–3΄U) represented 11–17%. All loaded equivalently into Ago2, and when tested individually functioned comparably in suppressing gene expression. In contrast, 23–3΄A and 23–3΄U were more active than 22–3΄G in stabilizing HCV RNA and promoting its replication, whereas 21–3΄U was almost completely inactive. This lack of 21–3΄U HCV host factor activity correlated with reduced recruitment of Ago2 to the HCV S1 site. Additional experiments demonstrated strong preference for guanosine at nt 22 of miR-122. Our findings reveal the importance of non-templated 3΄ miR-122 modifications to its HCV host factor activity, and identify unexpected differences in miRNA requirements for host gene suppression versus RNA virus replication.
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Affiliation(s)
- Daisuke Yamane
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Departments of Medicine and Microbiology & Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292, USA
| | - Sara R Selitsky
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Bioinformatics and Computational Biology Curriculum, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tetsuro Shimakami
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Ishikawa 920-8641, Japan
| | - You Li
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Departments of Medicine and Microbiology & Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292, USA
| | - Mi Zhou
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Bioinformatics and Computational Biology Curriculum, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Masao Honda
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Ishikawa 920-8641, Japan
| | - Praveen Sethupathy
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Bioinformatics and Computational Biology Curriculum, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stanley M Lemon
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Departments of Medicine and Microbiology & Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7292, USA
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