1
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Wang S, Pan C, Sheng H, Yang M, Yang C, Feng X, Hu C, Ma Y. Construction of a molecular regulatory network related to fat deposition by multi-tissue transcriptome sequencing of Jiaxian red cattle. iScience 2023; 26:108346. [PMID: 38026203 PMCID: PMC10665818 DOI: 10.1016/j.isci.2023.108346] [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: 08/02/2023] [Revised: 09/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Intramuscular fat (IMF) refers to the fat that accumulates between muscle bundles or within muscle cells, whose content significantly impacts the taste, tenderness, and flavor of meat products, making it a crucial economic characteristic in livestock production. However, the intricate mechanisms governing IMF deposition, involving non-coding RNAs (ncRNAs), genes, and complex regulatory networks, remain largely enigmatic. Identifying adipose tissue-specific genes and ncRNAs is paramount to unravel these molecular mysteries. This study, conducted on Jiaxian red cattle, harnessed whole transcriptome sequencing to unearth the nuances of circRNAs and miRNAs across seven distinct tissues. The interplay of these ncRNAs was assessed through differential expression analysis and network analysis. These findings are not only pivotal in unveiling the intricacies of fat deposition mechanisms but also lay a robust foundation for future research, setting the stage for enhancing IMF content in Jiaxian red cattle breeding.
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Affiliation(s)
- Shuzhe Wang
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Cuili Pan
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Hui Sheng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Mengli Yang
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chaoyun Yang
- Xichang College, Liangshan Prefecture, Sichuan Province, China
| | - Xue Feng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chunli Hu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
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2
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Rungratanawanich W, Ballway JW, Wang X, Won KJ, Hardwick JP, Song BJ. Post-translational modifications of histone and non-histone proteins in epigenetic regulation and translational applications in alcohol-associated liver disease: Challenges and research opportunities. Pharmacol Ther 2023; 251:108547. [PMID: 37838219 DOI: 10.1016/j.pharmthera.2023.108547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/30/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Epigenetic regulation is a process that takes place through adaptive cellular pathways influenced by environmental factors and metabolic changes to modulate gene activity with heritable phenotypic variations without altering the DNA sequences of many target genes. Epigenetic regulation can be facilitated by diverse mechanisms: many different types of post-translational modifications (PTMs) of histone and non-histone nuclear proteins, DNA methylation, altered levels of noncoding RNAs, incorporation of histone variants, nucleosomal positioning, chromatin remodeling, etc. These factors modulate chromatin structure and stability with or without the involvement of metabolic products, depending on the cellular context of target cells or environmental stimuli, such as intake of alcohol (ethanol) or Western-style high-fat diets. Alterations of epigenetics have been actively studied, since they are frequently associated with multiple disease states. Consequently, explorations of epigenetic regulation have recently shed light on the pathogenesis and progression of alcohol-associated disorders. In this review, we highlight the roles of various types of PTMs, including less-characterized modifications of nuclear histone and non-histone proteins, in the epigenetic regulation of alcohol-associated liver disease (ALD) and other disorders. We also describe challenges in characterizing specific PTMs and suggest future opportunities for basic and translational research to prevent or treat ALD and many other disease states.
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Affiliation(s)
- Wiramon Rungratanawanich
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Jacob W Ballway
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Xin Wang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kyoung-Jae Won
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, 90069, USA
| | - James P Hardwick
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA.
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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3
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Domi E, Barchiesi R, Barbier E. Epigenetic Dysregulation in Alcohol-Associated Behaviors: Preclinical and Clinical Evidence. Curr Top Behav Neurosci 2023. [PMID: 36717533 DOI: 10.1007/7854_2022_410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Alcohol use disorder (AUD) is characterized by loss of control over intake and drinking despite harmful consequences. At a molecular level, AUD is associated with long-term neuroadaptations in key brain regions that are involved in reward processing and decision-making. Over the last decades, a great effort has been made to understand the neurobiological basis underlying AUD. Epigenetic mechanisms have emerged as an important mechanism in the regulation of long-term alcohol-induced gene expression changes. Here, we review the literature supporting a role for epigenetic processes in AUD. We particularly focused on the three most studied epigenetic mechanisms: DNA methylation, Histone modification and non-coding RNAs. Clinical studies indicate an association between AUD and DNA methylation both at the gene and global levels. Using behavioral paradigms that mimic some of the characteristics of AUD, preclinical studies demonstrate that changes in epigenetic mechanisms can functionally impact alcohol-associated behaviors. While many studies support a therapeutic potential for targeting epigenetic enzymes, more research is needed to fully understand their role in AUD. Identification of brain circuits underlying alcohol-associated behaviors has made major advances in recent years. However, there are very few studies that investigate how epigenetic mechanisms can affect these circuits or impact the neuronal ensembles that promote alcohol-associated behaviors. Studies that focus on the role of circuit-specific and cell-specific epigenetic changes for clinically relevant alcohol behaviors may provide new insights on the functional role of epigenetic processes in AUD.
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Affiliation(s)
- Esi Domi
- Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience, Linköping University, Linköping, Sweden
- School of Pharmacy, Pharmacology Unit, Center for Neuroscience, University of Camerino, Camerino, Italy
| | - Riccardo Barchiesi
- Department of Neuroscience, Waggoner Center for Alcohol and Alcohol Addiction Research, University of Texas at Austin, Austin, TX, USA
| | - Estelle Barbier
- Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience, Linköping University, Linköping, Sweden.
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4
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Zhang X, Song W, Zhang M, Song Y, Di Y, Chen B, Tian H, Yuan X, Jin S. Identification of differentially expressed miRNAs and key genes involved in the progression of alcoholic fatty liver disease using rat models. Clin Res Hepatol Gastroenterol 2022; 46:102012. [PMID: 36030034 DOI: 10.1016/j.clinre.2022.102012] [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: 06/22/2022] [Revised: 08/02/2022] [Accepted: 08/24/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Alcoholic fatty liver disease (AFLD) is a liver disease caused by prolonged heavy drinking and has a poor prognosis in the clinic. This study aimed to explore the differential miRNAs expression profiles in the AFLD rat model. METHODS The rat model of AFLD was established by ethanol intragastric administration and was used to explore the differential miRNAs expression profiles. We further analyzed the potential target mRNAs using the bioinformatics technique. GO and KEGG pathway enrichment analyses were carried out to better understand the biological function of differential expression genes (DEGs). We used the human Gene Expression Omnibus (GEO) dataset GSE28619 to further screen the key differentially expressed genes. The integration between the differentially expressed genes from the AFLD model and GEO was conducted and the key genes were identified. RESULTS The serum ALT, AST, TG, and TC levels in the AFLD model group were significantly higher than those in the normal control group. There are 45 miRNAs with significant changes including 26 upregulated and 19 down-regulated miRNAs. GO and KEGG enrichment showed various metabolic processes and signaling pathways were enriched in the progression of AFLD. After integrating the results of GSE28619 and DEGs, we observed that there are 12 genes with significant changes in two data sets, including PSAT1, TKFC, PTTG1, LCN2, CXCL1, NR4A1, RGS1, VCAN, FOS, CXCL10, ATF3, and CYP1A1. CONCLUSION AFLD showed differentially expressed miRNAs, which may be involved in the occurrence and progression of AFLD. Meanwhile, some signal metabolic pathways may be related to the pathogenesis of AFLD.
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Affiliation(s)
- Xuemei Zhang
- Department of Gastroenterology, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang 154002, China; Department of Gastroenterology and Hepatology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Wenqi Song
- School of Basic Medicine, Jiamusi University, Jiamusi 154000, China
| | - Mingxuan Zhang
- School of Basic Medicine, Jiamusi University, Jiamusi 154000, China
| | - Yuanhang Song
- Department of Gastroenterology, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang 154002, China
| | - Yuzhu Di
- Department of Gastroenterology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Bo Chen
- Department of Medical Imaging, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, 154002, China
| | - Hao Tian
- Department of General surgery, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, 154002 China
| | - Xixian Yuan
- Department of Gastroenterology, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang 154002, China
| | - Shizhu Jin
- Department of Gastroenterology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
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Zeng S, Li SQ, Li QH. Progress in research of alcoholic liver disease. Shijie Huaren Xiaohua Zazhi 2022; 30:535-540. [DOI: 10.11569/wcjd.v30.i12.535] [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] [Indexed: 02/06/2023] Open
Abstract
Alcoholic liver disease (ALD) refers to the damage to the liver and its functions that result from excessive drinking, including alcoholic fatty liver/steatosis, alcoholic hepatitis, alcoholic liver fibrosis or cirrhosis, and even hepatocellular carcinoma. However, the pathogenesis of ALD is particularly complex due to the involvement of the toxic effects of alcohol and its metabolites, immune reaction, oxidative stress, autophagy, intestinal microbes, genetic factors, non-coding RNAs, etc. This paper reviews the new progress in the understanding of the pathogenesis and molecular mechanism of ALD, and provides perspectives on its clinical treatment.
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Affiliation(s)
- Shang Zeng
- Molecular Medicine Key Laboratory of Liver Injury and Repair Medical College, Henan University of Science and Technology, Henan Center for Engineering and Technology Research on Prevention and Treatment of Liver Diseases, Luoyang 471003, Henan Province, China
| | - San-Qiang Li
- Molecular Medicine Key Laboratory of Liver Injury and Repair Medical College, Henan University of Science and Technology, Henan Center for Engineering and Technology Research on Prevention and Treatment of Liver Diseases, Luoyang 471003, Henan Province, China
| | - Qian-Hui Li
- The First Affiliated Hospital of Henan University of Science and Technology, Luoyang 471003, Henan Province, China
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6
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Meng H, Niu R, Huang C, Li J. Circular RNA as a Novel Biomarker and Therapeutic Target for HCC. Cells 2022; 11:cells11121948. [PMID: 35741077 PMCID: PMC9222032 DOI: 10.3390/cells11121948] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/11/2022] [Accepted: 06/14/2022] [Indexed: 02/01/2023] Open
Abstract
Circular RNA (circRNA) is a kind of endogenous non-coding RNA (ncRNA), which is produced by the reverse splicing of precursor mRNA (pre mRNA). It is widely expressed in a variety of biological cells. Due to the special formation mode, circRNA does not have a 5′ terminal cap and 3′ poly (A) tail structure. Compared with linear RNA, circRNA is more stable to exonuclease and ribonuclease. In addition, circRNA is structurally conserved, has a stable sequence and is tissue-specific. With the development of high-throughput sequencing and bioinformatics technology, more and more circRNAs have been found. CircRNA plays an important pathophysiological role in the occurrence and development of alcoholic liver injury (ALI), hepatic fibrosis (HF), hepatocellular carcinoma (HCC), and other liver diseases. Our group has been committed to the research of liver disease diagnosis and treatment targets. We review the function and mechanism of circRNA in ALI, HF and HCC, expecting to provide new ideas for the diagnosis, treatment, and prognosis of liver diseases.
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Affiliation(s)
- Hongwu Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China;
| | - Ruowen Niu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China;
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China;
- Correspondence: (C.H.); (J.L.)
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China;
- Correspondence: (C.H.); (J.L.)
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7
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Li S, Song Z, Yao P, Qin J. Editorial: Alcohol Consumption and Liver Diseases: From Pathology to Phytotherapy. Front Pharmacol 2022; 13:848334. [PMID: 35250600 PMCID: PMC8889066 DOI: 10.3389/fphar.2022.848334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Songtao Li
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China
- *Correspondence: Songtao Li,
| | - Zhenyuan Song
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL, United States
| | - Ping Yao
- School of Public Health, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Jiangjiang Qin
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
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8
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Vornholt E, Drake J, Mamdani M, McMichael G, Taylor ZN, Bacanu S, Miles MF, Vladimirov VI. Identifying a novel biological mechanism for alcohol addiction associated with circRNA networks acting as potential miRNA sponges. Addict Biol 2021; 26:e13071. [PMID: 34164896 PMCID: PMC8590811 DOI: 10.1111/adb.13071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/21/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022]
Abstract
Our lab and others have shown that chronic alcohol use leads to gene and miRNA expression changes across the mesocorticolimbic (MCL) system. Circular RNAs (circRNAs) are noncoding RNAs that form closed-loop structures and are reported to alter gene expression through miRNA sequestration, thus providing a potentially novel neurobiological mechanism for the development of alcohol dependence (AD). Genome-wide expression of circRNA was assessed in the nucleus accumbens (NAc) from 32 AD-matched cases/controls. Significant circRNAs (unadj. p ≤ 0.05) were identified via regression and clustered in circRNA networks via weighted gene co-expression network analysis (WGCNA). CircRNA interactions with previously generated mRNA and miRNA were detected via correlation and bioinformatic analyses. Significant circRNAs (N = 542) clustered in nine significant AD modules (FWER p ≤ 0.05), within which we identified 137 circRNA hubs. We detected 23 significant circRNA-miRNA-mRNA interactions (FDR ≤ 0.10). Among these, circRNA-406742 and miR-1200 significantly interact with the highest number of mRNA, including genes associated with neuronal functioning and alcohol addiction (HRAS, PRKCB, HOMER1, and PCLO). Finally, we integrate genotypic information that revealed 96 significant circRNA expression quantitative trait loci (eQTLs) (unadj. p ≤ 0.002) that showed significant enrichment within recent alcohol use disorder (AUD) and smoking genome-wide association study (GWAS). To our knowledge, this is the first study to examine the role of circRNA in the neuropathology of AD. We show that circRNAs impact mRNA expression by interacting with miRNA in the NAc of AD subjects. More importantly, we provide indirect evidence for the clinical importance of circRNA in the development of AUD by detecting a significant enrichment of our circRNA eQTLs among GWAS of substance abuse.
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Affiliation(s)
- Eric Vornholt
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
- Integrative Life Sciences Doctoral ProgramVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - John Drake
- Department of Psychiatry and Behavioral SciencesTexas A&M UniversityCollege StationTexasUSA
| | - Mohammed Mamdani
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Gowon McMichael
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Zachary N. Taylor
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Silviu‐Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of PsychiatryVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Michael F. Miles
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
- VCU‐Alcohol Research CenterVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of Pharmacology and ToxicologyVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of NeurologyVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Vladimir I. Vladimirov
- Virginia Institute for Psychiatric and Behavioral GeneticsVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Center for Biomarker Research and Precision MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA
- Department of Physiology & BiophysicsVirginia Commonwealth UniversityRichmondVirginiaUSA
- School of PharmacyVirginia Commonwealth UniversityRichmondVirginiaUSA
- Lieber Institute for Brain DevelopmentJohns Hopkins UniversityBaltimoreMarylandUSA
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9
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Pi A, Jiang K, Ding Q, Lai S, Yang W, Zhu J, Guo R, Fan Y, Chi L, Li S. Alcohol Abstinence Rescues Hepatic Steatosis and Liver Injury via Improving Metabolic Reprogramming in Chronic Alcohol-Fed Mice. Front Pharmacol 2021; 12:752148. [PMID: 34603062 PMCID: PMC8481816 DOI: 10.3389/fphar.2021.752148] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/01/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Alcoholic liver disease (ALD) caused by chronic ethanol overconsumption is a common type of liver disease with a severe mortality burden throughout the world. The pathogenesis of ALD is complex, and no effective clinical treatment for the disease has advanced so far. Prolonged alcohol abstinence is the most effective therapy to attenuate the clinical course of ALD and even reverse liver damage. However, the molecular mechanisms involved in alcohol abstinence-improved recovery from alcoholic fatty liver remain unclear. This study aims to systematically evaluate the beneficial effect of alcohol abstinence on pathological changes in ALD. Methods: Using the Lieber-DeCarli mouse model of ALD, we analysed whether 1-week alcohol withdrawal reversed alcohol-induced detrimental alterations, including oxidative stress, liver injury, lipids metabolism, and hepatic inflammation, by detecting biomarkers and potential targets. Results: Alcohol withdrawal ameliorated alcohol-induced hepatic steatosis by improving liver lipid metabolism reprogramming via upregulating phosphorylated 5′-AMP -activated protein kinase (p-AMPK), peroxisome proliferator-activated receptor-α (PPAR-α), and carnitine palmitoyltransferase-1 (CPT-1), and downregulating fatty acid synthase (FAS) and diacylglycerol acyltransferase-2 (DGAT-2). The activities of antioxidant enzymes, including superoxide dismutase (SOD) and glutathione peroxidase (GSH-px), were significantly enhanced by alcohol withdrawal. Importantly, the abstinence recovered alcohol-fed induced liver injury, as evidenced by the improvements in haematoxylin and eosin (H&E) staining, plasma alanine aminotransferase (ALT) levels, and liver weight/body weight ratio. Alcohol-stimulated toll-like receptor 4/mitogen-activated protein kinases (TLR4/MAPKs) were significantly reversed by alcohol withdrawal, which might mechanistically contribute to the amelioration of liver injury. Accordingly, the hepatic inflammatory factor represented by tumour necrosis factor-alpha (TNF-α) was improved by alcohol abstinence. Conclusion: In summary, we reported that alcohol withdrawal effectively restored hepatic lipid metabolism and reversed liver injury and inflammation by improving metabolism reprogramming. These findings enhanced our understanding of the biological mechanisms involved in the beneficial role of alcohol abstinence as an effective treatment for ALD.
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Affiliation(s)
- Aiwen Pi
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.,School of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Kai Jiang
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Molecular Medicine Institute, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qinchao Ding
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Shanglei Lai
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.,School of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Wenwen Yang
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.,School of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinyan Zhu
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Rui Guo
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yibin Fan
- Department of Dermatology, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Linfeng Chi
- School of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Songtao Li
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.,Molecular Medicine Institute, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
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10
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Circular RNA as An Epigenetic Regulator in Chronic Liver Diseases. Cells 2021; 10:cells10081945. [PMID: 34440714 PMCID: PMC8392363 DOI: 10.3390/cells10081945] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 02/05/2023] Open
Abstract
Circular RNA (circRNA) is a type of non-coding RNA characterized by a covalently closed continuous loop. CircRNA is generated by pre-mRNA through back-splicing and is probably cleared up by extracellular vesicles. CircRNAs play a pivotal role in the epigenetic regulation of gene expression at transcriptional and post-transcriptional levels. Recently, circRNAs have been demonstrated to be involved in the regulation of liver homeostasis and diseases. However, the epigenetic role and underlying mechanisms of circRNAs in chronic liver diseases remain unclear. This review discussed the role of circRNAs in non-neoplastic chronic liver diseases, including alcoholic liver disease (ALD), metabolic-associated fatty liver disease (MAFLD), viral hepatitis, liver injury and regeneration, liver cirrhosis, and autoimmune liver disease. The review also highlighted that further efforts are urgently needed to develop circRNAs as novel diagnostics and therapeutics for chronic liver diseases.
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11
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Dou X, Yang W, Ding Q, Han Q, Qian Q, Du Z, Fan Y, Wang C, Li S. Comprehensive Analysis of the Expression Profiles of Hepatic lncRNAs in the Mouse Model of Alcoholic Liver Disease. Front Pharmacol 2021; 12:709287. [PMID: 34393788 PMCID: PMC8358650 DOI: 10.3389/fphar.2021.709287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Background and Aim: The worldwide prevalence of alcoholic liver disease (ALD) due to escalating alcohol consumption has presented an unprecedented pressure on human health. A few studies have determined long non-coding RNAs (lncRNAs) involved in the pathogenesis of liver diseases. However, the roles of lncRNAs in ALD development is still poorly understood. Methods: An ALD mouse model was established and confirmed. Expression profiles of lncRNAs were obtained by whole transcriptome sequencing. The altered lncRNAs in ALD mice were further verified by qRT-PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to enrich the functions of these lncRNAs. In combination with miRNA and mRNA profiles, we constructed concise endogenous RNA (ceRNA) networks. The function of the most up/downregulated lnRNA was further verified and investigated in both ALD model and AML-12 cells. Results: Totally, five downregulated lncRNAs were obtained and verified in ALD mice. The GO term and KEGG pathway analyses revealed that the identified lncRNAs were associated with alcohol-induced hepatic oxidative damage, cellular inflammation, and lipid metabolism. Combination the differentially modulated miRNAs and mRNAs with ceRNA network analysis, we constructed five ceRNA networks and obtained 30 miRNAs and 25 mRNAs that may participate in ALD. Further, we verified and investigate the function of the most downregulated lnc_1700023H06Rik. Depletion lnc_1700023H06Rik reduced genes encoding for lipid metabolism, especially mRNA Acat2 (ENSMUST00000159697) and Pgrmc2 (ENSMUST00000058578) both in vivo and in vitro. Knocking down lnc_1700023H06Rik induced triglyceride accumulation and lactate dehydrogenase leakage in AML12 cells, consisting with that in alcohol-treated cells. Conclusion: The five remarkably downregulated lncRNAs in ALD mouse model were identified as novel biomarkers, highlighting the key role of lncRNAs in the development of ALD. The effect of lnc_1700023H06Rik plays a pivotal role in lipid deposition and its pathological pathway in ALD needs further investigation.
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Affiliation(s)
- Xiaobing Dou
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.,School of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Molecular Medicine Institute, Zhejiang Chinese Medical University, Hangzhou, China
| | - Wenwen Yang
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.,School of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qinchao Ding
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qiang Han
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qianyu Qian
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Molecular Medicine Institute, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhongyan Du
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yibin Fan
- Department of Dermatology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Cui Wang
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Molecular Medicine Institute, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Songtao Li
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, China.,Molecular Medicine Institute, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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Epigenetic and non-coding regulation of alcohol abuse and addiction. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 156:63-86. [PMID: 33461665 DOI: 10.1016/bs.irn.2020.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alcohol use disorder is a chronic debilitated condition adversely affecting the lives of millions of individuals throughout the modern world. Individuals suffering from an alcohol use disorder diagnosis frequently have serious cooccurring conditions, which often further exacerbates problematic drinking behavior. Comprehending the biochemical processes underlying the progression and perpetuation of disease is essential for mitigating maladaptive behavior in order to restore both physiological and psychological health. The range of cellular and biological systems contributing to, and affected by, alcohol use disorder and other comorbid disorders necessitates a fundamental grasp of intricate functional relationships that govern molecular biology. Epigenetic factors are recognized as essential mediators of cellular behavior, orchestrating a symphony of gene expression changes within multicellular environments that are ultimately responsible for directing human behavior. Understanding the epigenetic and transcriptional regulatory mechanisms involved in the pathogenesis of disease is important for improving available pharmacotherapies and reducing the incidence of alcohol abuse and cooccurring conditions.
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Disease-Associated Circular RNAs: From Biology to Computational Identification. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6798590. [PMID: 32908906 PMCID: PMC7450300 DOI: 10.1155/2020/6798590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are endogenous RNAs with a covalently closed continuous loop, generated through various backsplicing events of pre-mRNA. An accumulating number of studies have shown that circRNAs are potential biomarkers for major human diseases such as cancer and Alzheimer's disease. Thus, identification and prediction of human disease-associated circRNAs are of significant importance. To this end, a computational analysis-assisted strategy is indispensable to detect, verify, and quantify circRNAs for downstream applications. In this review, we briefly introduce the biology of circRNAs, including the biogenesis, characteristics, and biological functions. In addition, we outline about 30 recent bioinformatic analysis tools that are publicly available for circRNA study. Principles for applying these computational strategies and considerations will be briefly discussed. Lastly, we give a complete survey on more than 20 key computational databases that are frequently used. To our knowledge, this is the most complete and updated summary on publicly available circRNA resources. In conclusion, this review summarizes key aspects of circRNA biology and outlines key computational strategies that will facilitate the genome-wide identification and prediction of circRNAs.
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