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El-Ashmawy NE, Khedr EG, Darwish RT, Ibrahim AO. Competing endogenous RNAs network and therapeutic implications: New horizons in disease research. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1868:195073. [PMID: 39631541 DOI: 10.1016/j.bbagrm.2024.195073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Revised: 11/17/2024] [Accepted: 11/29/2024] [Indexed: 12/07/2024]
Abstract
Different diseases may arise from the dysregulation of non-coding RNAs (ncRNAs), which regulation is necessary for maintaining cellular homeostasis. ncRNAs are regulated by transcriptional, post-transcriptional, translational and post-translational processes. Post-transcriptional regulation of gene expression is carried out by microRNAs (miRNAs), a class of small ncRNA molecules, which can identify their target sites by a brief nucleotide sequence, known as the miRNA response element (MRE), present on the miRNA seed sequence and the target transcript. This binding between miRNAs and targets can regulate the gene expression through inhibition of translation or degradation of target messenger RNA (mRNA). The transcripts that share MREs can be involved in competition for the central miRNA pool, which could have an indirect impact on each other's regulation. This competition network is called competing endogenous RNAs network (ceRNET). Many ncRNAs, including circular RNA, pseudogene, and long non-coding RNA, as well as mRNA, a coding RNA transcript, make up ceRNET. These components play a crucial role in post-transcriptional regulation and are involved in the diagnosis and treatment of many pathological disorders. The mechanism of ceRNET and its essential components, as well as their therapeutic implications in different diseases such as cancer, diabetes mellitus, neurological, cardiovascular, hepatic and respiratory disorders were covered in this review.
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Affiliation(s)
- Nahla E El-Ashmawy
- Biochemistry Department, Faculty of Pharmacy, Tanta University, 31527, Egypt; Department of Pharmacology and Biochemistry, Faculty of Pharmacy, The British University in Egypt, El Sherouk City, Cairo 11837, Egypt
| | - Eman G Khedr
- Biochemistry Department, Faculty of Pharmacy, Tanta University, 31527, Egypt
| | - Renad T Darwish
- Biochemistry Department, Faculty of Pharmacy, Tanta University, 31527, Egypt
| | - Amera O Ibrahim
- Biochemistry Department, Faculty of Pharmacy, Tanta University, 31527, Egypt.
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2
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Liu J, Zhou B. The dual role of HCV protein expression in communication between host cells presents potential applications in the treatment of liver fibrosis. Ann Hepatol 2024; 30:101747. [PMID: 39615626 DOI: 10.1016/j.aohep.2024.101747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 09/10/2024] [Indexed: 12/09/2024]
Affiliation(s)
- Junxi Liu
- School of Life Science, Tsinghua University, Beijing 100089, China
| | - Boda Zhou
- Department of Cardiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China.
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Yu T, Lu X, Liang Y, Yang L, Yin Y, Chen H. Naringenin alleviates liver fibrosis by triggering autophagy-dependent ferroptosis in hepatic stellate cells. Heliyon 2024; 10:e28865. [PMID: 38576562 PMCID: PMC10990976 DOI: 10.1016/j.heliyon.2024.e28865] [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: 12/29/2023] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Inhibition of activated hepatic stellate cells (HSCs) is a promising approach for treating liver fibrosis, and the ferroptosis has emerged as a pivotal mechanism to achieve this inhibition. The effects of naringenin, a flavonoid with anti-inflammatory properties, have not been thoroughly examined in liver fibrosis. Therefore, we used cholestasis model to study the effect of naringenin on liver fibrosis. Our findings demonstrated a significant exacerbation of liver tissue damage and fibrosis in mice subjected to bile duct ligation (BDL), accompanied by a substantial upregulation of fibrogenesis-related gene expression. Notably, naringenin administration markedly alleviated liver injury and fibrosis in these mice. Furthermore, naringenin exhibited inhibitory effects on the activation of HSCs, concurrently inducing ferroptosis. Importantly, naringenin significantly increased autophagic activity in HSCs. This effect was counteracted by co-administration of the autophagy inhibitor 3-MA, leading to a notable reduction in naringenin-induced HSC ferroptosis. In BDL model mice, naringenin demonstrated a mitigating effect on liver fibrosis, suggesting a potential correlation with naringenin-induced ferroptosis of HSCs. These results provide novel insights into the molecular mechanisms of naringenin-induced ferroptosis and highlight autophagy-dependent ferroptosis as a promising therapeutic strategy for liver fibrosis.
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Affiliation(s)
- Ting Yu
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, No. 87 Dingjiaqiao, Nanjing, Jiangsu, 210009, People's Republic of China
| | - Xuejia Lu
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, No. 87 Dingjiaqiao, Nanjing, Jiangsu, 210009, People's Republic of China
| | - Yan Liang
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, No. 87 Dingjiaqiao, Nanjing, Jiangsu, 210009, People's Republic of China
| | - Lin Yang
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, No. 87 Dingjiaqiao, Nanjing, Jiangsu, 210009, People's Republic of China
| | - Yuehan Yin
- China HuaYou Group Corporation, Beijing, 100724, People's Republic of China
| | - Hong Chen
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, No. 87 Dingjiaqiao, Nanjing, Jiangsu, 210009, People's Republic of China
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Khalaf SE, Abdelfattah SN, Khaliefa AK, Daoud SA, Yahia E, Hasona NA. Expression of PVT-1 and miR-29a/29b as reliable biomarkers for liver cirrhosis and their correlation with the inflammatory biomarkers profile. Hum Exp Toxicol 2024; 43:9603271241251451. [PMID: 38685136 DOI: 10.1177/09603271241251451] [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: 05/02/2024]
Abstract
BACKGROUND & AIMS The liver is a vital organ responsible for numerous metabolic processes, which can be significantly impacted by long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). These ribonucleic acid (RNA) molecules have been shown to play a crucial role in regulating gene expression, and their dysregulation has been implicated in numerous liver disorders. Our study aimed to investigate the diagnostic accuracy of plasmacytoma variant translocation-1 (PVT-1), microRNA-29a/29b (miR-29a/miR-29b), and inflammatory biomarkers [ interleukine-6 (IL-6), tumor necrosis factor-alpha (TNF-α), transforming growth factor-beta (TGF-β), and insulin growth factor-1 (IGF-1)] as diagnostic and prognostic biomarkers for liver cirrhosis. Therefore, understanding the mechanisms by which lncRNAs and miRNAs influence liver metabolism is of paramount importance in developing effective treatments for liver-related diseases. METHODS Serum samples were collected from 164 participants, comprising 114 cirrhotic patients with varying grades (35 grade I, 35 grade II, and 44 grade III) and 50 healthy controls. PVT-1 and miR-29a/miR-29b expression was analyzed by reverse transcription-quantitative polymerase chain reaction (RT-PCR), while the serum levels of inflammatory biomarkers were assessed using enzyme-linked immunosorbent assay (ELISA). RESULTS The study participants exhibited notable differences in PVT-1 and miR-29a/miR-29b expression. ROC analysis revealed excellent discriminative power for PVT-1 and miR-29a/miR-29b in distinguishing cirrhotic patients from healthy controls. CONCLUSION This study demonstrates the promising potential of PVT-1 and miR-29a/miR-29b as early diagnostic biomarkers for liver cirrhosis detection, requiring further validation in larger cohorts. Our findings also reinforce the diagnostic value of circulating inflammatory biomarkers (IL-6, TNF-α, TGF-β, and IGF-1) levels for liver cirrhosis screening.
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Affiliation(s)
- Shaza E Khalaf
- Department of Biochemistry, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | | | - Amal K Khaliefa
- Department of Biochemistry, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Sahar A Daoud
- Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt
- Faculty of Medicine, Beni Suef National University, Beni-Suef, Egypt
| | - Enas Yahia
- Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt
- Faculty of Medicine, Beni Suef National University, Beni-Suef, Egypt
| | - Nabil A Hasona
- Department of Biochemistry, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
- Biochemistry Department, Faculty of Science, Beni Suef National University, Beni-Suef, Egypt
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Zhang X, Zhao L, Ying K, Xu J, Huang Y, Zhu R, Ding Y, Cai W, Wu X, Miao D, Xu Q, Zeng Y, Yu F. TUG1 protects against ferroptosis of hepatic stellate cells by upregulating PDK4-mediated glycolysis. Chem Biol Interact 2023; 383:110673. [PMID: 37582412 DOI: 10.1016/j.cbi.2023.110673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/21/2023] [Accepted: 08/12/2023] [Indexed: 08/17/2023]
Abstract
The induction of ferroptosis in hepatic stellate cells (HSCs) has shown promise in reversing liver fibrosis. And ferroptosis has been confirmed to be associated with glycolysis. The objective of this study is to determine whether ferroptosis inhibition in HSCs, induced by elevation of recombinant pyruvate dehydrogenase kinase isozyme 4 (PDK4)-mediated glycolysis, could mediate the pathogenesis of liver fibrosis. Liver fibrosis was induced using CCl4, the level of which was assessed through histochemical staining. Lentivirus was used to modulate the expression of specific genes. And underlying mechanisms were explored using primary HSCs extracted from normal mice. The results confirmed that Taurine up-regulated gene 1 (TUG1) expression was upregulated in liver fibrotic tissues and HSCs, showing a positive correlation with fibrosis. In addition, TUG1 attenuated ferroptosis in HSCs by promoting PDK4-mediated glycolysis, thereby promoting the progression of liver fibrosis. Moreover, TUG1 was observed to impact HSCs activation, exacerbating liver fibrosis to some extent. In conclusion, our study revealed that TUG1 expression was elevated in mouse models of liver fibrosis and activated HSCs, which inhibited ferroptosis in HSCs through PDK4-mediated glycolysis. This finding may open up a new therapeutic strategy for liver fibrosis.
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Affiliation(s)
- Xiangting Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Luying Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Kanglei Ying
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jun Xu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yangjin Huang
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ruhuang Zhu
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yinrong Ding
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Weimin Cai
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiao Wu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Dan Miao
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qian Xu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yuan Zeng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Fujun Yu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
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Jafari S, Ravan M, Karimi-Sani I, Aria H, Hasan-Abad AM, Banasaz B, Atapour A, Sarab GA. Screening and identification of potential biomarkers for pancreatic cancer: An integrated bioinformatics analysis. Pathol Res Pract 2023; 249:154726. [PMID: 37591067 DOI: 10.1016/j.prp.2023.154726] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023]
Abstract
Pancreatic cancer is one of the highly invasive and the seventh most common cause of death among cancers worldwide. To identify essential genes and the involved mechanisms in pancreatic cancer, we used bioinformatics analysis to identify potential biomarkers for pancreatic cancer management. Gene expression profiles of pancreatic cancer patients and normal tissues were screened and downloaded from The Cancer Genome Atlas (TCGA) bioinformatics database. The Differentially expressed genes (DEGs) were identified among gene expression signatures of normal and pancreatic cancer, using R software. Then, enrichment analysis of the DEGs, including Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, was performed by an interactive and collaborative HTML5 gene list enrichment analysis tool (enrichr) and ToppGene. The protein-protein interaction (PPI) network was also constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) database and ToppGenet web based tool followed by identifying hub genes of the top 100 DEGs in pancreatic cancer using Cytoscape software. Over 2000 DEGs with variable log2 fold (LFC) were identified among 34,706 genes. Principal component analysis showed that the top 20 DEGs, including H1-4, H1-5, H4C3, H4C2, RN7SL2, RN7SL3, RN7SL4P, RN7SKP80, SCARNA12, SCARNA10, SCARNA5, SCARNA7, SCARNA6, SCARNA21, SCARNA9, SCARNA13, SNORA73B, SNORA53, SNORA54 might distinguish pancreatic cancer from normal tissue. GO analysis showed that the top DEGs have more enriched in the negative regulation of gene silencing, negative regulation of chromatin organization, negative regulation of chromatin silencing, nucleosome positioning, regulation of chromatin silencing, and nucleosomal DNA binding. KEGG analysis identified an association between pancreatic cancer and systemic lupus erythematosus, alcoholism, neutrophil extracellular trap formation, and viral carcinogenesis. In PPI network analysis, we found that the different types of histone-encoding genes are involved as hub genes in the carcinogenesis of pancreatic cancer. In conclusion, our bioinformatics analysis identified genes that were significantly related to the prognosis of pancreatic cancer patients. These genes and pathways could serve as new potential prognostic markers and be used to develop treatments for pancreatic cancer patients.
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Affiliation(s)
- Somayeh Jafari
- Department of Molecular Medicine, School of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Milad Ravan
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Iman Karimi-Sani
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Aria
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran; Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Amin Moradi Hasan-Abad
- Autoimmune Diseases Research Center, Shahid Beheshti Hospital, Kashan University of Medical Sciences, Kashan, Iran
| | - Bahar Banasaz
- Internal Medicine Department, Babol University of Medical Sciences, Babol, Iran.
| | - Amir Atapour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Gholamreza Anani Sarab
- Cellular & Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran.
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Abstract
Hepatic fibrosis is a reversible wound healing process following liver injury. Although this process is necessary for maintaining liver integrity, severe excessive extracellular matrix accumulation (ECM) could lead to permanent scar formation and destroy the liver structure. The activation of hepatic stellate cells (HSCs) is a key event in hepatic fibrosis. Previous studies show that most antifibrotic therapies focus on the apoptosis of HSCs and the prevention of HSC activation. Noncoding RNAs (ncRNAs) play a substantial role in HSC activation and are likely to be biomarkers or therapeutic targets for the treatment of hepatic fibrosis. This review summarizes and discusses the previously reported ncRNAs, including the microRNAs, long noncoding RNAs, and circular RNAs, highlighting their regulatory roles and interactions in the signaling pathways that regulate HSC activation in hepatic fibrosis.
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Identification of plasma lncRNA-ATB levels in hepatitis B virus-related cirrhosis and non-cirrhotic chronic hepatitis B patients. Virus Res 2021; 303:198503. [PMID: 34331990 DOI: 10.1016/j.virusres.2021.198503] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/19/2022]
Abstract
Long non-coding RNA-ATB (LncRNA-ATB) which is activated by transforming growth factor-β (TGF-β), is a key regulator of TGF-β signaling pathway. TGF-β plays an important role in various pathogenic processes, from inflammation and fibrosis to cirrhosis and cancer. In this study, we evaluated the plasma levels of lncRNA-ATB in patients with hepatitis B virus (HBV)-related cirrhosis and non-cirrhotic patients with chronic hepatitis B (CHB) and investigated the clinical values. Plasma samples were collected from 44 HBV-related cirrhosis patients, 45 non-cirrhotic CHB and 75 healthy controls. Briefly, after total RNA extraction and cDNA synthesis, quantitative real-time PCR (qPCR) was performed to detect plasma lncRNA-ATB levels. Results show the plasma levels of lncRNA-ATB in HBV-related cirrhosis patients were significantly higher in comparison to healthy controls (Fold change=2.60, p value=0.04). Also, we determined plasma levels of lncRNA-ATB as a specific biomarker of HBV-related cirrhosis (AUC=0.65, p value=0.03, Sensitivity 61.36%; Specificity 70.00%). In addition to, we investigated the plasma levels of lncRNA-ATB in non-cirrhotic CHB patients were significantly lower than healthy controls (Fold change= 0.33, p value=0.01). We also indicated plasma lncRNA-ATB levels were as a sensitive biomarker for diagnosis of non-cirrhotic CHB patients compared with healthy (AUC=0.66, p value=0.00, Sensitivity 71.11%; Specificity 57.78%). According to our results, circulating lncRNA-ATB has good specificity for diagnosing hepatitis B virus (HBV)-related cirrhosis and good sensitivity for diagnosis of non-cirrhotic chronic hepatitis B (CHB) patients.
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