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Zhang X, Hu S, Xiang X, Li Z, Chen Z, Xia C, He Q, Jin J, Chen H. Bulk and single-cell transcriptome profiling identify potential cellular targets of the long noncoding RNA Gas5 in renal fibrosis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167206. [PMID: 38718848 DOI: 10.1016/j.bbadis.2024.167206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/05/2024] [Accepted: 04/27/2024] [Indexed: 05/18/2024]
Abstract
The long noncoding RNA growth arrest-specific 5 (lncRNA Gas5) is implicated in various kidney diseases. In this study, we investigated the lncRNA Gas5 expression profile and its critical role as a potential biomarker in the progression of chronic kidney disease. Subsequently, we assessed the effect of lncRNA Gas5 deletion on renal fibrosis induced by unilateral ureteral obstruction (UUO). The results indicated that loss of lncRNA Gas5 exacerbates UUO-induced renal injury and extracellular matrix deposition. Notably, the deletion of lncRNA Gas5 had a similar effect on control mice. The fibrogenic phenotype observed in mice lacking lncRNA Gas5 correlates with peroxisome proliferator-activated receptor (PPAR) signaling pathway activation and aberrant cytokine and chemokine reprogramming. Single-cell RNA sequencing analysis revealed key transcriptomic features of fibroblasts after Gas5 deletion, revealing heterogeneous cellular states suggestive of a propensity for renal fibrosis. Our findings indicate that lncRNA Gas5 regulates the differentiation and activation of immune cells and the transcription of key genes in the PPAR signaling pathway. These data offer novel insights into the involvement of lncRNA Gas5 in renal fibrosis, potentially paving the way for innovative diagnostic and therapeutic targets.
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Affiliation(s)
- Xiang Zhang
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Shouci Hu
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Xiaojun Xiang
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Zhiyu Li
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Zhejun Chen
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Cong Xia
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Qiang He
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Juan Jin
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Hongbo Chen
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China.
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Liao W, Li Y, Liu J, Mou Y, Zhao M, Liu J, Zhang T, Sun Q, Tang J, Wang Z. Homotherapy for heteropathy: therapeutic effect of Butein in NLRP3-driven diseases. Cell Commun Signal 2024; 22:315. [PMID: 38849890 PMCID: PMC11158000 DOI: 10.1186/s12964-024-01695-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 06/02/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Aberrant inflammatory responses drive the initiation and progression of various diseases, and hyperactivation of NLRP3 inflammasome is a key pathogenetic mechanism. Pharmacological inhibitors of NLRP3 represent a potential therapy for treating these diseases but are not yet clinically available. The natural product butein has excellent anti-inflammatory activity, but its potential mechanisms remain to be investigated. In this study, we aimed to evaluate the ability of butein to block NLRP3 inflammasome activation and the ameliorative effects of butein on NLRP3-driven diseases. METHODS Lipopolysaccharide (LPS)-primed bone-marrow-derived macrophages were pretreated with butein and various inflammasome stimuli. Intracellular potassium levels, ASC oligomerization and reactive oxygen species production were also detected to evaluate the regulatory mechanisms of butein. Moreover, mouse models of LPS-induced peritonitis, dextran sodium sulfate-induced colitis, and high-fat diet-induced non-alcoholic steatohepatitis were used to test whether butein has protective effects on these NLRP3-driven diseases. RESULTS Butein blocks NLRP3 inflammasome activation in mouse macrophages by inhibiting ASC oligomerization, suppressing reactive oxygen species production, and upregulating the expression of the antioxidant pathway nuclear factor erythroid 2-related factor 2 (Nrf2). Importantly, in vivo experiments demonstrated that butein administration has a significant protective effect on the mouse models of LPS-induced peritonitis, dextran sodium sulfate-induced colitis, and high-fat diet-induced non-alcoholic steatohepatitis. CONCLUSION Our study illustrates the connotation of homotherapy for heteropathy, i.e., the application of butein to broaden therapeutic approaches and treat multiple inflammatory diseases driven by NLRP3.
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Affiliation(s)
- Wenhao Liao
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Yuchen Li
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Jingwen Liu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Yu Mou
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Mei Zhao
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Juan Liu
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Tianxin Zhang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Qin Sun
- National Traditional Chinese Medicine Clinical Research Base of the Affiliated Traditional Chinese Medicine, Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Jianyuan Tang
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China.
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China.
| | - Zhilei Wang
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China.
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China.
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Wang X, Ye S, Tong L, Gao J, Zhang Y, Qin Y. Inhibition of ROS/caspase-3/GSDME-mediated pyroptosis alleviates high glucose-induced injury in AML-12 cells. Toxicol In Vitro 2024; 98:105840. [PMID: 38723977 DOI: 10.1016/j.tiv.2024.105840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 05/14/2024]
Abstract
Diabetic liver injury (DLI) is a chronic complication of the liver caused by diabetes, and its has become one of the main causes of nonalcoholic fatty liver disease (NAFLD). The gasdermin E (GSDME)-dependent pyroptosis signaling pathway is involved in various physiological and pathological processes; however, its role and mechanism in DLI are still unknown. This study was performed to investigate the role of GSDME-mediated pyroptosis in AML-12 cell injury induced by high glucose and to evaluate the therapeutic potential of caspase-3 inhibition for DLI. The results showed that high glucose activated apoptosis by regulating the apoptotic protein levels including Bax, Bcl-2, and enhanced cleavage of caspase-3 and PARP. Notably, some of the hepatocytes treated with high glucose became swollen, accompanied by GSDME-N generation, indicating that pyroptosis was further induced by active caspase-3. Moreover, the effects of high glucose on AML-12 cells could be partly reversed by a reactive oxygen scavenger (NAC) and caspase-3 specific inhibitor (Z-DEVD-FMK), which suggests high glucose induced GSDME-dependent pyroptosis in AML-12 cells through increasing ROS levels and activating caspase-3. In conclusion, our results show that high glucose can induce pyroptosis in AML-12 cells, at least in part, through the ROS/caspase-3/GSDME pathway,and inhibition of caspase-3 can ameliorate high glucose-induced hepatocyte injury, providing an important basis for clarifying the pathogenesis and treatment of DLI.
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Affiliation(s)
- Xinrui Wang
- Department of Physiology and Pathophysiology, School of Basic Medicine, Dali University, Dali, Yunnan 671000, China
| | - Shengying Ye
- Department of Physiology and Pathophysiology, School of Basic Medicine, Dali University, Dali, Yunnan 671000, China
| | - Linge Tong
- Department of Physiology and Pathophysiology, School of Basic Medicine, Dali University, Dali, Yunnan 671000, China
| | - Jingwen Gao
- Department of Physiology and Pathophysiology, School of Basic Medicine, Dali University, Dali, Yunnan 671000, China
| | - Yixin Zhang
- Department of Physiology and Pathophysiology, School of Basic Medicine, Dali University, Dali, Yunnan 671000, China
| | - Yan Qin
- Department of Physiology and Pathophysiology, School of Basic Medicine, Dali University, Dali, Yunnan 671000, China.
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Liu J, Song K, Lin B, Chen Z, Liu Y, Qiu X, He Q, Zuo Z, Yao X, Huang X, Liu Z, Liu Z, Huang Q, Guo X. The suppression of HSPA8 attenuates NLRP3 ubiquitination through SKP2 to promote pyroptosis in sepsis-induced lung injury. Cell Biosci 2024; 14:56. [PMID: 38698431 PMCID: PMC11064404 DOI: 10.1186/s13578-024-01239-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/25/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Acute lung injury (ALI) is strongly associated with hospitalization and mortality in patients with sepsis. Recent evidence suggests that pyroptosis mediated by NLRP3(NOD-, LRR- and pyrin domain-containing 3) inflammasome activation plays a key role in sepsis. However, the mechanism of NLRP3 inflammasome activation in sepsis-induced lung injury remains unclear. RESULTS in this study, we demonstrated that NLRP3 inflammasome was activated by the down-regulation of heat shock protein family A member 8 (HSPA8) in Lipopolysaccharide (LPS) and adenosine triphosphate (ATP)-treated mouse alveolar epithelial cells (AECs). Geranylgeranylacetone (GGA)-induced HSPA8 overexpression in cecum ligation and puncture (CLP) mice could significantly reduce systemic inflammatory response and mortality, effectively protect lung function, whilst HSPA8 inhibitor VER155008 aggravated this effect. The inhibition of HSPA8 was involved in sepsis induced acute lung injury by promoting pyroptosis of AECs. The down-regulation of HSPA8 activated NLRP3 inflammasome to mediate pyroptosis by promoting the degradation of E3 ubiquitin ligase S-phase kinase-associated protein 2 (SKP2). In addition, when stimulated by LPS and ATP, down-regulated SKP2 promoted pyroptosis of AECs by further attenuating ubiquitination of NLRP3. Adeno-associated virus 9-SKP2(AAV9-SKP2) could promote NLRP3 ubiquitination and degradation, alleviate lung injury and inhibit systemic inflammatory response in vivo. CONCLUSION in summary, our study shows there is strong statistical evidence that the suppression of HSPA8 mediates alveolar epithelial pyroptosis by promoting the degradation of E3 ubiquitin ligase SKP2 and subsequently attenuating the ubiquitination of NLRP3 to activate the NLRP3 inflammasome, which provides a new perspective and therapeutic target for the treatment of sepsis-induced lung injury.
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Affiliation(s)
- Jinlian Liu
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ke Song
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Bingqi Lin
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhenfeng Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yan Liu
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xianshuai Qiu
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qi He
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zirui Zuo
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaodan Yao
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoxia Huang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhuanhua Liu
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhifeng Liu
- Department of Medicine intensive care unit , National Clinical Research Center for Geriatric Diseases (Chinese PLA General Hospital), General Hospital of Southern Theatre Command of PLA, Guangdong Branch Center, Guangzhou, Guangdong, China.
| | - Qiaobing Huang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- School of Basic Medical Sciences, Southern Medical University, 1023 Shatai Road, Tonghe, Guangzhou, 510515, China.
| | - Xiaohua Guo
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of Proteomics, State Key Laboratory of Organ Failure Research, School of Basic Medical Sciences, National Experimental Education Demonstration Center for Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- School of Basic Medical Sciences, Southern Medical University, 1023 Shatai Road, Tonghe, Guangzhou, 510515, China.
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Xu D, Jiang J, Liu Y, Pang J, Suo J, Li Y, Peng Z. TIMP2 protects against sepsis-associated acute kidney injury by cAMP/NLRP3 axis-mediated pyroptosis. Am J Physiol Cell Physiol 2024; 326:C1353-C1366. [PMID: 38497110 DOI: 10.1152/ajpcell.00577.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
The tissue inhibitor of metalloproteinases 2 (TIMP2) has emerged as a promising biomarker for predicting the risk of sepsis-associated acute kidney injury (SA-AKI). However, its exact role in SA-AKI and the underlying mechanism remains unclear. In this study, we investigated the impact of kidney tubule-specific Timp2 knockout mice on kidney injury and inflammation. Our findings demonstrated that Timp2-knockout mice exhibited more severe kidney injury than wild-type mice, along with elevated levels of pyroptosis markers NOD-like receptor protein 3 (NLRP3), Caspase1, and gasdermin D (GSDMD) in the early stage of SA-AKI. Conversely, the expression of exogenous TIMP2 in TIMP2-knockout mice still protected against kidney damage and inflammation. In in vitro experiments, using recombinant TIMP2 protein, TIMP2 knockdown demonstrated that exogenous TIMP2 inhibited pyroptosis of renal tubular cells stimulated by lipopolysaccharide (LPS). Mechanistically, TIMP2 promoted the ubiquitination and autophagy-dependent degradation of NLRP3 by increasing intracellular cyclic adenosine monophosphate (cAMP), which mediated NLRP3 degradation through recruiting the E3 ligase MARCH7, attenuating downstream pyroptosis, and thus alleviating primary tubular cell damage. These results revealed the renoprotective role of extracellular TIMP2 in SA-AKI by attenuating tubular pyroptosis, and suggested that exogenous administration of TIMP2 could be a promising therapeutic intervention for SA-AKI treatment.NEW & NOTEWORTHY Tissue inhibitor of metalloproteinase 2 (TIMP-2) has been found to be the best biomarker for predicting the risk of sepsis-associated acute kidney injury (SA-AKI). However, its role and the underlying mechanism in SA-AKI remain elusive. The authors demonstrated in this study using kidney tubule-specific knockout mice model of SA-AKI and primary renal tubule cells stimulated with lipopolysaccharide (LPS) that extracellular TIMP-2 promoted NOD-like receptor protein 3 (NLRP3) ubiquitination and autophagy-dependent degradation by increasing intracellular cyclic adenosine monophosphate (cAMP), thus attenuated pyroptosis and alleviated renal damage.
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Affiliation(s)
- Dongxue Xu
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jun Jiang
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ye Liu
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jingjing Pang
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jinmeng Suo
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yiming Li
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhiyong Peng
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Research Center of Hubei Critical Care Medicine, Wuhan, China
- Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- Intensive Care Unit of the second affiliated Hospital of Hainan Medical College, Haikou, China
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Mononen J, Taipale M, Malinen M, Velidendla B, Niskanen E, Levonen AL, Ruotsalainen AK, Heikkinen S. Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice. Nucleic Acids Res 2024; 52:2904-2923. [PMID: 38153160 PMCID: PMC11014276 DOI: 10.1093/nar/gkad1225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/09/2023] [Accepted: 12/12/2023] [Indexed: 12/29/2023] Open
Abstract
Most common genetic variants associated with disease are located in non-coding regions of the genome. One mechanism by which they function is through altering transcription factor (TF) binding. In this study, we explore how genetic variation is connected to differences in the regulatory landscape of livers from C57BL/6J and 129S1/SvImJ mice fed either chow or a high-fat diet. To identify sites where regulatory variation affects TF binding and nearby gene expression, we employed an integrative analysis of H3K27ac ChIP-seq (active enhancers), ATAC-seq (chromatin accessibility) and RNA-seq (gene expression). We show that, across all these assays, the genetically driven (i.e. strain-specific) differences in the regulatory landscape are more pronounced than those modified by diet. Most notably, our analysis revealed that differentially accessible regions (DARs, N = 29635, FDR < 0.01 and fold change > 50%) are almost always strain-specific and enriched with genetic variation. Moreover, proximal DARs are highly correlated with differentially expressed genes. We also show that TF binding is affected by genetic variation, which we validate experimentally using ChIP-seq for TCF7L2 and CTCF. This study provides detailed insights into how non-coding genetic variation alters the gene regulatory landscape, and demonstrates how this can be used to study the regulatory variation influencing TF binding.
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Affiliation(s)
- Juho Mononen
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Mari Taipale
- A.I. Virtanen Institute, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Marjo Malinen
- Department of Environmental and Biological Sciences, Faculty of Science and Forestry, University of Eastern Finland, Joensuu FI- 80101, Finland
- Department of Forestry and Environmental Engineering, South-Eastern Finland University of Applied Sciences, Kouvola FI-45100, Finland
| | - Bharadwaja Velidendla
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Einari Niskanen
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Anna-Liisa Levonen
- A.I. Virtanen Institute, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Anna-Kaisa Ruotsalainen
- A.I. Virtanen Institute, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Sami Heikkinen
- Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio FI-70211, Finland
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Andersen SL. Increasing CB2 Receptor Activity after Early Life Stress Prevents Depressive Behavior in Female Rats. Biomolecules 2024; 14:464. [PMID: 38672480 PMCID: PMC11047932 DOI: 10.3390/biom14040464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/28/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Early adversity, the loss of the inhibitory GABAergic interneuron parvalbumin, and elevated neuroinflammation are associated with depression. Individuals with a maltreatment history initiate medicinal cannabis use earlier in life than non-maltreated individuals, suggesting self-medication. Female rats underwent maternal separation (MS) between 2 and 20 days of age to model early adversity or served as colony controls. The prelimbic cortex and behavior were examined to determine whether MS alters the cannabinoid receptor 2 (CB2), which has anti-inflammatory properties. A reduction in the CB2-associated regulatory enzyme MARCH7 leading to increased NLRP3 was observed with Western immunoblots in MS females. Immunohistochemistry with stereology quantified numbers of parvalbumin-immunoreactive cells and CB2 at 25, 40, and 100 days of age, revealing that the CB2 receptor associated with PV neurons initially increases at P25 and subsequently decreases by P40 in MS animals, with no change in controls. Confocal and triple-label microscopy suggest colocalization of these CB2 receptors to microglia wrapped around the parvalbumin neuron. Depressive-like behavior in MS animals was elevated at P40 and reduced with the CB2 agonist HU-308 or a CB2-overexpressing lentivirus microinjected into the prelimbic cortex. These results suggest that increasing CB2 expression by P40 in the prelimbic cortex prevents depressive behavior in MS female rats.
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Affiliation(s)
- Susan L Andersen
- Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Du G, Jiang Z, Xia T, Liu M, Liu Z, Zhou H, Zhang H, Zhai X, Jin B. lincRNA00907 promotes NASH progression by targeting miRNA-942-5p/TAOK1. Aging (Albany NY) 2024; 16:6868-6882. [PMID: 38613803 PMCID: PMC11087098 DOI: 10.18632/aging.205730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/27/2024] [Indexed: 04/15/2024]
Abstract
OBJECTIVE The study aims to examine the involvement of lincRNA00907 in the advancement of non-alcoholic steatohepatitis (NASH). METHODS The examination was conducted to assess the expression of linc00907 in liver tissues from NASH patients and healthy individuals. High-fat diets induced NASH in mouse models, while palmitic acid/oleic acid treatment was used to create in vitro cell models. Various techniques, such as qRT-PCR, Oil Red O staining and gene knockdown/overexpression, were used to assess the impact of linc00907 on genes related to lipid metabolism and immunity, as well as intracellular lipid accumulation. Furthermore, dual-luciferase reporter assays were carried out to confirm the connection between miRNA-942-5p and linc00907 or TAOK1 mRNA. RESULTS Linc00907 was found to be significantly upregulated in both NASH patients and NASH mouse models. Overexpression of linc00907 led to an increase in intracellular lipid accumulation, while knockdown of linc00907 resulted in decreased lipid content. It was found that miRNA-942-5p binds with linc00907, and their interaction was confirmed in dual-luciferase reporter assays. Additionally, TAOK1 was predicted to be a downstream target of miRNA-942-5p, and the upregulation of TAOK1 due to linc00907 was reversed by miRNA-942-5p overexpression. linc00907 overexpression reduces apoptosis but can be reversed by TAOK1 knockdown. The reduction of TAOK1 counteracted the impact of linc00907 on gene expression associated with lipid metabolism and immunity, as well as on the accumulation of intracellular lipids. CONCLUSIONS Our research suggests that linc00907 functions as a competitive endogenous RNA (ceRNA) by sequestering miRNA-942-5p, thus increasing the expression of TAOK1 and encouraging lipid accumulation in hepatocytes, leading to the aggravation of NASH development. Targeting the linc00907/miRNA-942-5p/TAOK1 axis may hold therapeutic potential for the treatment of NASH.
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Affiliation(s)
- Gang Du
- Organ Transplant Department, Qilu Hospital of Shangdong University, Jinan 250012, China
| | - Zhaochen Jiang
- Organ Transplant Department, Qilu Hospital of Shangdong University, Jinan 250012, China
| | - Tong Xia
- Organ Transplant Department, Qilu Hospital of Shangdong University, Jinan 250012, China
| | - Mingkun Liu
- Organ Transplant Department, Qilu Hospital of Shangdong University, Jinan 250012, China
| | - Zeyang Liu
- Organ Transplant Department, Qilu Hospital of Shangdong University, Jinan 250012, China
| | - Huaxin Zhou
- Department of Hepatobiliary Surgery, The Second Hospital of Shangdong University, Jinan 250033, China
| | - Hao Zhang
- Organ Transplant Department, Qilu Hospital of Shangdong University, Jinan 250012, China
| | - Xiangyu Zhai
- Department of Hepatobiliary Surgery, The Second Hospital of Shangdong University, Jinan 250033, China
| | - Bin Jin
- Organ Transplant Department, Qilu Hospital of Shangdong University, Jinan 250012, China
- Department of Hepatobiliary Surgery, The Second Hospital of Shangdong University, Jinan 250033, China
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Ma X, Mei S, Wuyun Q, Zhou L, Sun D, Yan J. Epigenetics in diabetic cardiomyopathy. Clin Epigenetics 2024; 16:52. [PMID: 38581056 PMCID: PMC10996175 DOI: 10.1186/s13148-024-01667-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/28/2024] [Indexed: 04/07/2024] Open
Abstract
Diabetic cardiomyopathy (DCM) is a critical complication that poses a significant threat to the health of patients with diabetes. The intricate pathological mechanisms of DCM cause diastolic dysfunction, followed by impaired systolic function in the late stages. Accumulating researches have revealed the association between DCM and various epigenetic regulatory mechanisms, including DNA methylation, histone modifications, non-coding RNAs, and other epigenetic molecules. Recently, a profound understanding of epigenetics in the pathophysiology of DCM has been broadened owing to advanced high-throughput technologies, which assist in developing potential therapeutic strategies. In this review, we briefly introduce the epigenetics regulation and update the relevant progress in DCM. We propose the role of epigenetic factors and non-coding RNAs (ncRNAs) as potential biomarkers and drugs in DCM diagnosis and treatment, providing a new perspective and understanding of epigenomics in DCM.
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Affiliation(s)
- Xiaozhu Ma
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Shuai Mei
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Qidamugai Wuyun
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Li Zhou
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Dating Sun
- Department of Cardiology, Wuhan No. 1 Hospital, Wuhan Hospital of Traditional Chinese and Western Medicine, Wuhan, China
| | - Jiangtao Yan
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China.
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China.
- Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Deng J, Qin L, Qin S, Wu R, Huang G, Fang Y, Huang L, Zhou Z. NcRNA Regulated Pyroptosis in Liver Diseases and Traditional Chinese Medicine Intervention: A Narrative Review. J Inflamm Res 2024; 17:2073-2088. [PMID: 38585470 PMCID: PMC10999193 DOI: 10.2147/jir.s448723] [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: 11/24/2023] [Accepted: 03/19/2024] [Indexed: 04/09/2024] Open
Abstract
Pyroptosis is a novel pro-inflammatory mode of programmed cell death that differs from ferroptosis, necrosis, and apoptosis in terms of its onset and regulatory mechanisms. Pyroptosis is dependent on cysteine aspartate protein hydrolase (caspase)-mediated activation of GSDMD, NLRP3, and the release of pro-inflammatory cytokines, interleukin-1 (IL-1β), and interleukin-18 (IL-18), ultimately leading to cell death. Non-coding RNA (ncRNA) is a type of RNA that does not encode proteins in gene transcription but plays an important regulatory role in other post-transcriptional links. NcRNA mediates pyroptosis by regulating various related pyroptosis factors, which we termed the pyroptosis signaling pathway. Previous researches have manifested that pyroptosis is closely related to the development of liver diseases, and is essential for liver injury, alcoholic fatty liver disease (ALD), non-alcoholic fatty liver disease (NAFLD), liver fibrosis, and liver cancer. In this review, we attempt to address the role of the ncRNA-mediated pyroptosis pathway in the above liver diseases and their pathogenesis in recent years, and briefly outline that TCM (Traditional Chinese Medicine) intervene in liver diseases by modulating ncRNA-mediated pyroptosis, which will provide a strategy to find new therapeutic targets for the prevention and treatment of liver diseases in the future.
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Affiliation(s)
- Jiasheng Deng
- School of Pharmacy, Guangxi University of Chinese Medicine, Nanning, Guangxi, 530200, People’s Republic of China
| | - Le Qin
- Department of Pharmacy, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, People’s Republic of China
| | - Sulang Qin
- School of Graduate Studies, Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, People’s Republic of China
| | - Ruisheng Wu
- School of Pharmacy, Guangxi University of Chinese Medicine, Nanning, Guangxi, 530200, People’s Republic of China
| | - Guidong Huang
- School of Pharmacy, Guangxi University of Chinese Medicine, Nanning, Guangxi, 530200, People’s Republic of China
| | - Yibin Fang
- Department of Pharmacy, Liuzhou People’s Hospital, Liuzhou, Guangxi, 545006, People’s Republic of China
| | - Lanlan Huang
- Department of Pharmacy, Liuzhou People’s Hospital, Liuzhou, Guangxi, 545006, People’s Republic of China
| | - Zhipin Zhou
- Department of Pharmacy, Liuzhou People’s Hospital, Liuzhou, Guangxi, 545006, People’s Republic of China
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Sun Q, Hu Z, Huang W, Liu X, Wu X, Chang W, Tang Y, Peng F, Yang Y. CircMLH3 induces mononuclear macrophage pyroptosis in sepsis by sponging miR-590-3p to regulate TAK1 expression. Int J Biol Macromol 2024; 263:130179. [PMID: 38378118 DOI: 10.1016/j.ijbiomac.2024.130179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/03/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
Sepsis is a fatal syndrome characterized by uncontrolled systemic inflammatory responses. Circular RNAs (circRNAs) are involved in the modulation of various pathophysiological processes, but their potential role in sepsis has largely been unexplored. In this study, we observed differential expression of circMLH3 between healthy volunteers and septic patients, and revealed the value of circMLH3 for sepsis diagnosis and prognostic prediction. Interestingly, we discovered a correlation between the expression level of circMLH3 and the degree of pyroptosis, a critical mechanism contributing to uncontrolled inflammation in sepsis patients. Knocking down circMLH3 alleviated macrophage pyroptosis whereas overexpressing circMLH3 aggravated pyroptosis. circMLH3 regulated macrophage pyroptosis by sponging miR-590-3p and subsequently modulating TAK1 expression. Furthermore, we found that the miR-590-3p/TAK1 axis inhibited the activation of pro-caspase-1 and the NLRP3 inflammasome. miR-590-3p overexpression had a protective effect by reducing macrophage pyroptosis, thereby alleviating sepsis-induced lung injury and systemic inflammatory responses. In conclusion, our study elucidated the circMLH3/miR-590-3p/TAK1 signaling pathway and identified its role in regulating mononuclear macrophage pyroptosis, thus providing potential novel targets and strategies for sepsis diagnosis and therapy.
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Affiliation(s)
- Qin Sun
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Zihan Hu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Wei Huang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Xu Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Xiao Wu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Wei Chang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Ying Tang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China.
| | - Fei Peng
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China.
| | - Yi Yang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
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Yang S, Zhang Y, Zhang Y, Yin L, Han X, Zhao X, Wang N, Xu L. LncRNA Gm28382 promotes lipogenesis by interacting with miR-326-3p to regulate ChREBP signaling pathway in NAFLD. Int Immunopharmacol 2024; 127:111444. [PMID: 38157698 DOI: 10.1016/j.intimp.2023.111444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to play vital roles in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). However, their biological roles and function mechanisms in NAFLD remain largely unknown. In this study, we found that Gm28382 may be a potential pathogenic lncRNA of NAFLD and highly expressed in NAFLD through RNA-seq. Overexpression of Gm28382 significantly enhanced the lipid accumulation in AML12 cells, whereas Gm28382 silencing reduced lipogenesis both in palmitic acid (PA)-induced AML12 cells and high fat diet (HFD)-induced mice. Then, bioinformatics were employed to speculate the potential interacting genes of Gm28382, and found that Gm28382 may regulate ChREBP expression through binding with miR-326-3p. Fluorescence in situ hybridization (FISH), dual luciferase reporter assay, immunofluorescence RNA pull-down and RNA immunoprecipitation (RIP) assays were used to validate the binding and targeting relationship of these genes, and we confirmed that Gm28382 competitively binds to miR-326-3p to increase ChREBP expression as a ceRNA. Mechanistically, overexpression of Gm28382 upregulated the ChREBP-mediated lipid synthesis signaling pathway, but the function was sabotaged by miR-326-3p deletion or ChREBP overexpression. Furthermore, in PA-challenged AML12 cells or HFD-induced mice, silencing of Gm28382 reversed the aberrant ChREBP signaling pathway and lipid accumulation, whereas ChREBP overexpression or liver-specific silencing of miR-326-3p blocked this function of Gm28382. Collectively, these findings reveal a critical role of Gm28382 in the promotion of lipogenesis in NAFLD by regulating the ChREBP signaling pathway through interaction with miR-326-3p, which could serve as a potential therapeutic target for NAFLD treatment.
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Affiliation(s)
- Sen Yang
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Yang Zhang
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Yan Zhang
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Lianhong Yin
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Xu Han
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Xuerong Zhao
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Ning Wang
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China
| | - Lina Xu
- College of Pharmacy, Dalian Medical University, Western 9 Lvshunnan Road, Dalian 116044, China.
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Ramezani M, Zobeiry M, Abdolahi S, Hatami B, Zali MR, Baghaei K. A crosstalk between epigenetic modulations and non-alcoholic fatty liver disease progression. Pathol Res Pract 2023; 251:154809. [PMID: 37797383 DOI: 10.1016/j.prp.2023.154809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) has recently emerged as a major public health concern worldwide due to its rapidly rising prevalence and its potential to progress into end-stage liver disease. While the precise pathophysiology underlying NAFLD remains incompletely understood, it is strongly associated with various environmental triggers and other metabolic disorders. Epigenetics examines changes in gene expression that are not caused by alterations in the DNA sequence itself. There is accumulating evidence that epigenetics plays a key role in linking environmental cues to the onset and progression of NAFLD. Our understanding of how epigenetic mechanisms contribute to NAFLD pathophysiology has expanded considerably in recent years as research on the epigenetics of NAFLD has developed. This review summarizes recent insights into major epigenetic processes that have been implicated in NAFLD pathogenesis including DNA methylation, histone acetylation, and microRNAs that have emerged as promising targets for further investigation. Elucidating epigenetic mechanisms in NAFLD may uncover novel diagnostic biomarkers and therapeutic targets for this disease. However, many questions have remained unanswered regarding how epigenetics promotes NAFLD onset and progression. Additional studies are needed to further characterize the epigenetic landscape of NAFLD and validate the potential of epigenetic markers as clinical tools. Nevertheless, an enhanced understanding of the epigenetic underpinnings of NAFLD promises to provide key insights into disease mechanisms and pave the way for novel prognostic and therapeutic approaches.
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Affiliation(s)
- Meysam Ramezani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Shahrokh Abdolahi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Behzad Hatami
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Baghaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Gastroenterology and Liver Diseases Research center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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