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Rad SMAH, Wannigama DL, Hirankarn N, McLellan AD. The impact of non-synonymous mutations on miRNA binding sites within the SARS-CoV-2 NSP3 and NSP4 genes. Sci Rep 2023; 13:16945. [PMID: 37805621 PMCID: PMC10560223 DOI: 10.1038/s41598-023-44219-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/05/2023] [Indexed: 10/09/2023] Open
Abstract
Non-synonymous mutations in the SARS-CoV-2 spike region affect cell entry, tropism, and immune evasion, while frequent synonymous mutations may modify viral fitness. Host microRNAs, a type of non-coding RNA, play a crucial role in the viral life cycle, influencing viral replication and the host immune response directly or indirectly. Recently, we identified ten miRNAs with a high complementary capacity to target various regions of the SARS-CoV-2 genome. We filtered our candidate miRNAs to those only expressed with documented expression in SARS-CoV-2 target cells, with an additional focus on miRNAs that have been reported in other viral infections. We determined if mutations in the first SARS-CoV-2 variants of concern affected these miRNA binding sites. Out of ten miRNA binding sites, five were negatively impacted by mutations, with three recurrent synonymous mutations present in multiple SARS-CoV-2 lineages with high-frequency NSP3: C3037U and NSP4: G9802U/C9803U. These mutations were predicted to negatively affect the binding ability of miR-197-5p and miR-18b-5p, respectively. In these preliminary findings, using a dual-reporter assay system, we confirmed the ability of these miRNAs in binding to the predicted NSP3 and NSP4 regions and the loss/reduced miRNA bindings due to the recurrent mutations.
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Affiliation(s)
- S M Ali Hosseini Rad
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok, Thailand.
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand.
| | - Dhammika Leshan Wannigama
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Center of Excellence in Antimicrobial Resistance and Stewardship Research, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries, The University of Sheffield, Sheffield, UK
- Pathogen Hunter's Research Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata, 990-2212, Japan
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok, Thailand.
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand.
| | - Alexander D McLellan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
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Ali FE, Abd El-Aziz MK, Sharab EI, Bakr AG. Therapeutic interventions of acute and chronic liver disorders: A comprehensive review. World J Hepatol 2023; 15:19-40. [PMID: 36744165 PMCID: PMC9896501 DOI: 10.4254/wjh.v15.i1.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/17/2022] [Accepted: 12/21/2022] [Indexed: 01/16/2023] Open
Abstract
Liver disorders are one of the most common pathological problems worldwide. It affects more than 1.5 billion worldwide. Many types of hepatic cells have been reported to be involved in the initiation and propagation of both acute and chronic liver diseases, including hepatocytes, Kupffer cells, sinusoidal endothelial cells, and hepatic stellate cells (HSCs). In addition, oxidative stress, cytokines, fibrogenic factors, microRNAs, and autophagy are also involved. Understanding the molecular mechanisms of liver diseases leads to discovering new therapeutic interventions that can be used in clinics. Recently, antioxidant, anti-inflammatory, anti-HSCs therapy, gene therapy, cell therapy, gut microbiota, and nanoparticles have great potential for preventing and treating liver diseases. Here, we explored the recent possible molecular mechanisms involved in the pathogenesis of acute and chronic liver diseases. Besides, we overviewed the recent therapeutic interventions that targeted liver diseases and summarized the recent studies concerning liver disorders therapy.
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Affiliation(s)
- Fares Em Ali
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut 71524, Egypt.
| | | | - Elham I Sharab
- Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut 71524, Egypt
| | - Adel G Bakr
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut 71524, Egypt
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Zhao D, Liu Z, Zhang H. The protective effect of the TUG1/miR‑197/MAPK1 axis on lipopolysaccharide‑induced podocyte injury. Mol Med Rep 2019; 20:49-56. [PMID: 31115515 DOI: 10.3892/mmr.2019.10216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 01/16/2019] [Indexed: 01/02/2023] Open
Abstract
The podocyte, a type of glomerular epithelial cell, is the key constituent of the filtration barrier layer in the kidney. Previous studies have shown that long non‑coding RNA (lncRNA)‑taurine‑upregulated gene 1 (TUG1) served a protective role in diabetes‑induced podocyte damage. The aim of the present study was to investigate the potential role of TUG1 in the progress of podocyte injury induced by lipopolysaccharide (LPS), and explore the underlying mechanisms. The results showed that TUG1 expression was suppressed in LPS‑induced podocytes. Enhanced TUG1 expression by exogenous recombinant vector regulated the expression of podocyte associated proteins [Nephrin, Podocin and CCAAT/enhancer‑binding protein (CHOP)]. A marked decrease was observed in the level the albumin influx in cells transfected with TUG1. Further study indicated that microRNA (miR)‑197 is a potential target of TUG1. The enhanced level of miR‑197 induced by LPS was inhibited in cells transfected with TUG1. The decreased Nephrin and Podocin expression, upregulated CHOP expression and the increased albumin influx were slightly enhanced by miR‑197 mimic transfection, while markedly suppressed by miR‑197 inhibitor transfection in LPS‑induced podocytes. Mitogen‑activated protein kinase (MAPK) protein was predicted as a potential target of miR‑197. The downregulated expression of phosphorylated‑MAPK/MAPK induced by LPS was significantly suppressed by TUG1 transfection in podocytes. In addition to this, autophagy was promoted by TUG1 transfection via the elevation of the Beclin1 and light chain (LC)3 II/LC3 I levels, and suppressing p62 expression. However, the p38 MAPK inhibitor SB203580 reversed the changes that TUG1 induced in the levels of Beclin1, LC3 II/LC3 I and p62. Taken together, these results demonstrated that LPS‑induced podocyte injury could be alleviated by the TUG1/miR‑197/MAPK1 axis.
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Affiliation(s)
- Dong Zhao
- Department of Nephrology, Jining No. 1 People's Hospital, Jining, Shandong 272011, P.R. China
| | - Zheng Liu
- Department of Nephropathy and Diabetes Mellitus, Baoji Central Hospital, Baoji, Shaanxi 721008, P.R. China
| | - Heng Zhang
- Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing 400038, P.R. China
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Serum levels of miRNA in patients with hepatitis B virus-associated acute-on-chronic liver failure. Hepatobiliary Pancreat Dis Int 2018; 17:126-132. [PMID: 29602672 DOI: 10.1016/j.hbpd.2018.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 01/05/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hepatitis B virus (HBV)-associated acute-on-chronic liver failure (HBV-ACLF) is a life-threatening condition and its exact pathophysiology and progression remain unclear. The present study aimed to assess the role of serum miRNAs in the evaluation of HBV-ACLF and to develop a model to predict the outcomes for ACLF. METHODS Serum was collected from 41 chronic hepatitis B and 55 HBV-ACLF patients in addition to 30 chronic asymptomatic HBV carriers as controls. The miRNAs expressions were measured by real-time quantitative PCR (q-PCR). Statistical analyses were conducted to assess the ability of differentially expressed miRNAs and other prognostic factors in identifying ACLF prognosis and to develop a new predictive model. RESULTS Real-time q-PCR indicated that serum miR-146a-5p, miR-122-3p and miR-328-3p levels were significantly upregulated in ACLF patients compared to chronic hepatitis B and chronic asymptomatic HBV carriers patients. In addition, multivariate regression analyses indicated that Na+, INR, gastrointestinal bleeding and miR-122-3p are all independent factors that are reliable and sensitive to the prognosis of HBV-ACLF. Therefore, we developed a new model for the prediction of HBV-ACLF disease state: Y = 0.402 × Na+ - 1.72 × INR - 4.963 × gastrointestinal bleeding (Yes = 0; No = 1)-0.278 × (miR-122-3p) + 50.449. The predictive accuracy of the model was 95.3% and the area under the receiver operating characteristic curve (AUROC) was 0.847. CONCLUSIONS Expression levels of these miRNAs (miR-146a-5p, miR-122-3p and miR-328-3p) positively correlate with the severity of liver inflammation in patients with ACLF and may be useful to predict HBV-ACLF severity.
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