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Dong Y, Hu M, Tan K, Dai R. ZNF143 inhibits hepatocyte mitophagy and promotes non-alcoholic fatty liver disease by targeting increased lncRNA NEAT1 expression to activate ROCK2 pathway. Epigenetics 2023; 18:2239592. [PMID: 37566742 PMCID: PMC10424604 DOI: 10.1080/15592294.2023.2239592] [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: 02/17/2023] [Revised: 05/04/2023] [Accepted: 05/16/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) is the most common hepatic disorders worldwide. The mitophagy is suggested to be repressed in NAFLD, but the mechanism remains to be elucidated. METHODS NAFLD cell and mouse models were established by treating with free fatty acid (FFA) and feeding a high fat diet (HFD), respectively. QRT-PCR, Western blotting, or IHC measured the expression of ZNF143, lncRNA NEAT1, ROCK2, and lipid formation/mitophagy-related proteins. Cell viability and mitophagy were evaluated by MTT and immunofluorescence. The chloroform-methanol extraction method measured triglyceride and total cholesterol levels. ELISA detected ALT and AST levels. The interactions among ZNF143, lncRNA NEAT1 and SND1 were analysed by ChIP, dual-luciferase reporter, pull-down, and RIP. The lipid droplets were determined by Oil-red O and HE staining. RESULTS ZNF143 and lncRNA NEAT1 were upregulated in hepatic cells treated with FFA (p < 0.01 and p < 0.001). Knockdown of ZNF143 or lncRNA NEAT1 inhibited lipid droplets formation, while promoting mitophagy (p < 0.01 and p < 0.001). ZNF143 promoted lncRNA NEAT1 transcriptional expression through binding to its promoter. LncRNA NEAT1 increased ROCK2 mRNA stability by targeting SND1. LncRNA NEAT1 or ROCK2 overexpression reversed the effect of ZNF143 or lncRNA NEAT1 knockdown on hepatic steatosis and mitophagy (p < 0.01 and p < 0.001). ZNF143 or lncRNA NEAT1 knockdown inhibited HFD-induced steatosis and promoted mitophagy in vivo (p < 0.01 and p < 0.001). CONCLUSION The upregulation of lncRNA NEAT1 caused by ZNF143 promoted NAFLD through inhibiting mitophagy via activating ROCK2 pathway by targeting SND1, providing potential targets for NAFLD therapy.
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Affiliation(s)
- Yujie Dong
- The First Affiliated Hospital, Department of Ultrasound Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Minjie Hu
- The First Affiliated Hospital, Department of Cardiothoracic Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
| | - Kewei Tan
- The No.922 Hospital of the People Liberation Army Joint Logistics Support Force, Department of the Laboratory and Blood Transfusion, Hengyang, Hunan421002, China
| | - Rongjuan Dai
- The First Affiliated Hospital, Department of Infectious Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan421001, China
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Yang Y, Liu X, Chen H, Wang P, Yao S, Zhou B, Yin R, Li C, Wu C, Yang X, Yu M. HPS protects the liver against steatosis, cell death, inflammation, and fibrosis in mice with steatohepatitis. FEBS J 2022; 289:5279-5304. [PMID: 35285180 DOI: 10.1111/febs.16430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/20/2022] [Accepted: 03/10/2022] [Indexed: 12/14/2022]
Abstract
Hepassocin (HPS) is a hepatokine associated with metabolic regulation and development of non-alcoholic steatohepatitis (NASH). However, previous reports on HPS are controversial and its true function is not yet understood. Here, we demonstrated that hepatic HPS expression levels were upregulated in short-term feeding and downregulated in long-term feeding in high-fat diet (HFD)- and methionine- and choline-deficient (MCD) diet-fed mice, as well as in genetically obese (ob/ob) mice. HFD- and MCD-induced hepatic steatosis, inflammation, apoptosis, and fibrosis were more pronounced in HPS knockout mice than in the wild-type mice. Moreover, HPS depletion aggravated HFD-induced insulin resistance. By contrast, HPS administration improved MCD- or HFD-induced liver phenotypes and insulin resistance in HPS knockout and wild-type mice. Mechanistic studies revealed that MCD-induced hepatic oxidative stress was significantly increased by HPS deficiency and could be attenuated by HPS administration. Furthermore, palmitic acid-induced lipid accumulation and oxidative stress were exclusively enhanced in HPS knockout hepatocytes and diminished by HPS cotreatment. These data suggest that HPS ameliorates NASH in mice, at least in part, by inhibiting the oxidative stress. HPS expression levels are downregulated in human fatty liver tissues, suggesting that it may play an important protective role in NASH. Collectively, our findings provide clear genetic evidence that HPS has beneficial effects on the development of steatohepatitis in mice and suggest that upregulating HPS signaling may represent an effective treatment strategy for NASH.
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Affiliation(s)
- Yang Yang
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, China
| | - Xian Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Hui Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Pengjun Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Songhui Yao
- Institute of Life Sciences, HeBei University, Baoding, China
| | - Bin Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Ronghua Yin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Changyan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Chutse Wu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, China.,Beijing Institute of Radiation Medicine, China
| | - Xiaoming Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China
| | - Miao Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Beijing, China.,Institute of Life Sciences, HeBei University, Baoding, China
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3
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Liu F, Zhu X, Jiang X, Li S, Lv Y. Transcriptional control by HNF-1: Emerging evidence showing its role in lipid metabolism and lipid metabolism disorders. Genes Dis 2022; 9:1248-1257. [PMID: 35873023 DOI: 10.1016/j.gendis.2021.06.010.ecollection] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/10/2021] [Accepted: 06/29/2021] [Indexed: 05/25/2023] Open
Abstract
The present review focuses on the roles and underlying mechanisms of action of hepatic nuclear factor-1 (HNF-1) in lipid metabolism and the development of lipid metabolism disorders. HNF-1 is a transcriptional regulator that can form homodimers, and the HNF-1α and HNF-1β isomers can form heterodimers. Both homo- and heterodimers recognize and bind to specific cis-acting elements in gene promoters to transactivate transcription and to coordinate the expression of target lipid-related genes, thereby influencing the homeostasis of lipid metabolism. HNF-1 was shown to restrain lipid anabolism, including synthesis, absorption, and storage, by inhibiting the expression of lipogenesis-related genes, such as peroxisome proliferator-activated receptor γ (PPARγ) and sterol regulatory element-binding protein-1/2 (SREBP-1/2). Moreover, HNF-1 enhances the expression of various genes, such as proprotein convertase subtilisin/kexin type 9 (PCSK9), glutathione peroxidase 1 (GPx1), and suppressor of cytokine signaling-3 (SOCS-3) and negatively regulates signal transducer and activator of transcription (STAT) to facilitate lipid catabolism in hepatocytes. HNF-1 reduces hepatocellular lipid decomposition, which alleviates the progression of nonalcoholic fatty liver disease (NAFLD). HNF-1 impairs preadipocyte differentiation to reduce the number of adipocytes, stunting the development of obesity. Furthermore, HNF-1 reduces free cholesterol levels in the plasma to inhibit aortic lipid deposition and lipid plaque formation, relieving dyslipidemia and preventing the development of atherosclerotic cardiovascular disease (ASCVD). In summary, HNF-1 transcriptionally regulates lipid-related genes to manipulate intracorporeal balance of lipid metabolism and to suppress the development of lipid metabolism disorders.
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Affiliation(s)
- Fang Liu
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guangxi Province Postgraduate Co-training Base for Cooperative Innovation in Basic Medicine (Guilin Medical University and Yueyang Women & Children's Medical Center), Guilin Medical University, Guilin, Guangxi 541199, PR China
| | - Xiao Zhu
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guangxi Province Postgraduate Co-training Base for Cooperative Innovation in Basic Medicine (Guilin Medical University and Yueyang Women & Children's Medical Center), Guilin Medical University, Guilin, Guangxi 541199, PR China
| | - Xiaping Jiang
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guangxi Province Postgraduate Co-training Base for Cooperative Innovation in Basic Medicine (Guilin Medical University and Yueyang Women & Children's Medical Center), Guilin Medical University, Guilin, Guangxi 541199, PR China
| | - Shan Li
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guangxi Province Postgraduate Co-training Base for Cooperative Innovation in Basic Medicine (Guilin Medical University and Yueyang Women & Children's Medical Center), Guilin Medical University, Guilin, Guangxi 541199, PR China
| | - Yuncheng Lv
- Guangxi Key Laboratory of Diabetic Systems Medicine, Guangxi Province Postgraduate Co-training Base for Cooperative Innovation in Basic Medicine (Guilin Medical University and Yueyang Women & Children's Medical Center), Guilin Medical University, Guilin, Guangxi 541199, PR China
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Kang B, Kang B, Roh TY, Seong RH, Kim W. The Chromatin Accessibility Landscape of Nonalcoholic Fatty Liver Disease Progression. Mol Cells 2022; 45:343-352. [PMID: 35422452 PMCID: PMC9095509 DOI: 10.14348/molcells.2022.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 12/03/2022] Open
Abstract
The advent of the assay for transposase-accessible chromatin using sequencing (ATAC-seq) has shown great potential as a leading method for analyzing the genome-wide profiling of chromatin accessibility. A comprehensive reference to the ATAC-seq dataset for disease progression is important for understanding the regulatory specificity caused by genetic or epigenetic changes. In this study, we present a genome-wide chromatin accessibility profile of 44 liver samples spanning the full histological spectrum of nonalcoholic fatty liver disease (NAFLD). We analyzed the ATAC-seq signal enrichment, fragment size distribution, and correlation coefficients according to the histological severity of NAFLD (healthy control vs steatosis vs fibrotic nonalcoholic steatohepatitis), demonstrating the high quality of the dataset. Consequently, 112,303 merged regions (genomic regions containing one or multiple overlapping peak regions) were identified. Additionally, we found differentially accessible regions (DARs) and performed transcription factor binding motif enrichment analysis and de novo motif analysis to determine new biomarker candidates. These data revealed the generegulatory interactions and noncoding factors that can affect NAFLD progression. In summary, our study provides a valuable resource for the human epigenome by applying an advanced approach to facilitate diagnosis and treatment by understanding the non-coding genome of NAFLD.
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Affiliation(s)
- Byeonggeun Kang
- Department of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul 08826, Korea
| | - Byunghee Kang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Rho Hyun Seong
- Department of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul 08826, Korea
| | - Won Kim
- Department of Internal Medicine, SMG-SNU Boramae Medical Center, Seoul National University College of Medicine, Seoul 07061, Korea
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5
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Yeh MM, Shi X, Yang J, Li M, Fung KM, Daoud SS. Perturbation of Wnt/β-catenin signaling and sexual dimorphism in non-alcoholic fatty liver disease. Hepatol Res 2022; 52:433-448. [PMID: 35120274 PMCID: PMC10874498 DOI: 10.1111/hepr.13754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 02/08/2023]
Abstract
AIMS The prevalence of non-alcoholic fatty liver disease (NAFLD) and its progression to non-alcoholic steatohepatitis (NASH) is higher in postmenopausal women than men. The aim of this study was to determine the molecular mechanisms underlying this sexual dimorphism in NAFLD. METHODS A total of 24 frozen liver samples of both sexes (normal and NAFLD/NASH) were used in this study. Total RNAseq was first used to identify differentially expressed genes (DEGs) between samples. Enrichment analysis of Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome were used to analyze biological pathways. RT2 profiler polymerase chain reaction (PCR) arrays were used to identify genes associated with the biological pathways. Immunoblotting was used to validate protein expression of certain genes. RESULTS We identified 4362 genes that are differentially expressed between NAFLD/NASH and normal samples; of those 745 genes were characterized as sex specific in NAFLD/NASH. Multiple pathway analysis platforms showed that Wnt-signaling is a candidate shared for a common biological pathway-associated with NAFLD/NASH. Using Wnt pathway focused PCR array we identified many genes involved in canonical pathway (Wnt/β-catenin activation) such as CTNNB1, c-Myc and CCND2 are overexpressed in female cases, whereas these genes are either not detected or downregulated in male cases. Immunoblot analysis validated the expression of CTNNB1 in female cases but not in male protein samples. CONCLUSIONS Our study suggests, for the first time, that the activation of canonical Wnt signaling could be one of the main pathways associated with sexual dimorphism in NAFLD and NASH.
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Affiliation(s)
- Matthew M Yeh
- Department of Laboratory Medicine and Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Xiuhui Shi
- Department of Medicine and Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Jingxuan Yang
- Department of Medicine and Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Min Li
- Department of Medicine and Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Kar-Ming Fung
- Department of Pathology and Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Sayed S. Daoud
- Department of Pharmaceutical Sciences, Washington State University Health Sciences, Spokane, Washington, USA
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6
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Liu F, Zhu X, Jiang X, Li S, Lv Y. Transcriptional control by HNF-1: Emerging evidence showing its role in lipid metabolism and lipid metabolism disorders. Genes Dis 2021; 9:1248-1257. [PMID: 35873023 PMCID: PMC9293700 DOI: 10.1016/j.gendis.2021.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/10/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
The present review focuses on the roles and underlying mechanisms of action of hepatic nuclear factor-1 (HNF-1) in lipid metabolism and the development of lipid metabolism disorders. HNF-1 is a transcriptional regulator that can form homodimers, and the HNF-1α and HNF-1β isomers can form heterodimers. Both homo- and heterodimers recognize and bind to specific cis-acting elements in gene promoters to transactivate transcription and to coordinate the expression of target lipid-related genes, thereby influencing the homeostasis of lipid metabolism. HNF-1 was shown to restrain lipid anabolism, including synthesis, absorption, and storage, by inhibiting the expression of lipogenesis-related genes, such as peroxisome proliferator-activated receptor γ (PPARγ) and sterol regulatory element-binding protein-1/2 (SREBP-1/2). Moreover, HNF-1 enhances the expression of various genes, such as proprotein convertase subtilisin/kexin type 9 (PCSK9), glutathione peroxidase 1 (GPx1), and suppressor of cytokine signaling-3 (SOCS-3) and negatively regulates signal transducer and activator of transcription (STAT) to facilitate lipid catabolism in hepatocytes. HNF-1 reduces hepatocellular lipid decomposition, which alleviates the progression of nonalcoholic fatty liver disease (NAFLD). HNF-1 impairs preadipocyte differentiation to reduce the number of adipocytes, stunting the development of obesity. Furthermore, HNF-1 reduces free cholesterol levels in the plasma to inhibit aortic lipid deposition and lipid plaque formation, relieving dyslipidemia and preventing the development of atherosclerotic cardiovascular disease (ASCVD). In summary, HNF-1 transcriptionally regulates lipid-related genes to manipulate intracorporeal balance of lipid metabolism and to suppress the development of lipid metabolism disorders.
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7
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Matboli M, Gadallah SH, Rashed WM, Hasanin AH, Essawy N, Ghanem HM, Eissa S. mRNA-miRNA-lncRNA Regulatory Network in Nonalcoholic Fatty Liver Disease. Int J Mol Sci 2021; 22:ijms22136770. [PMID: 34202571 PMCID: PMC8269036 DOI: 10.3390/ijms22136770] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
AIM we aimed to construct a bioinformatics-based co-regulatory network of mRNAs and non coding RNAs (ncRNAs), which is implicated in the pathogenesis of non-alcoholic fatty liver disease (NAFLD), followed by its validation in a NAFLD animal model. MATERIALS AND METHODS The mRNAs-miRNAs-lncRNAs regulatory network involved in NAFLD was retrieved and constructed utilizing bioinformatics tools. Then, we validated this network using an NAFLD animal model, high sucrose and high fat diet (HSHF)-fed rats. Finally, the expression level of the network players was assessed in the liver tissues using reverse transcriptase real-time polymerase chain reaction. RESULTS in-silico constructed network revealed six mRNAs (YAP1, FOXA2, AMOTL2, TEAD2, SMAD4 and NF2), two miRNAs (miR-650 and miR-1205), and two lncRNAs (RPARP-AS1 and SRD5A3-AS1) that play important roles as a co-regulatory network in NAFLD pathogenesis. Moreover, the expression level of these constructed network-players was significantly different between NAFLD and normal control. Conclusion and future perspectives: this study provides new insight into the molecular mechanism of NAFLD pathogenesis and valuable clues for the potential use of the constructed RNA network in effective diagnostic or management strategies of NAFLD.
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Affiliation(s)
- Marwa Matboli
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt
- Correspondence: (M.M.); (S.E.)
| | - Shaimaa H. Gadallah
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo 11382, Egypt; (S.H.G.); (H.M.G.)
| | - Wafaa M. Rashed
- Department of Research, Children’s Cancer Hospital-57357, Cairo 11382, Egypt;
| | - Amany Helmy Hasanin
- Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt;
| | - Nada Essawy
- Institut Pasteur, CEDEX 15, 75724 Paris, France;
| | - Hala M. Ghanem
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo 11382, Egypt; (S.H.G.); (H.M.G.)
| | - Sanaa Eissa
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo 11382, Egypt
- Correspondence: (M.M.); (S.E.)
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The Gene Signature Associated with Hepatocellular Carcinoma in Patients with Nonalcoholic Fatty Liver Disease. JOURNAL OF ONCOLOGY 2021; 2021:6630535. [PMID: 33868403 PMCID: PMC8035011 DOI: 10.1155/2021/6630535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 11/28/2022]
Abstract
Background Nonalcoholic fatty liver disease (NAFLD) is becoming a critical risk of hepatocellular carcinoma (HCC). As both NAFLD and HCC are heterogeneous diseases, this study aims to identify the similarity between the subtypes of NAFLD and HCC based on gene modules. Methods Coexpressed gene modules were extracted for both NAFLD and HCC. The association between the coexpressed gene modules of NAFLD and HCC was evaluated by Fisher's exact test. The overlapping coexpressed gene module was validated in three independent human NAFLD datasets. Furthermore, the preserved gene module was assessed in four independent NAFLD mouse datasets. The significantly enriched motifs within the gene module were inferred from upstream sequences. Results Four coexpressed gene modules were extracted from NAFLD. Of the four coexpressed gene modules, one was significantly overlapping with a module of HCC. This overlapping gene module was regarded as the HCC-associated NAFLD gene module (HANM). Enrichment analysis of biological processes revealed inflammatory response in HANM. Specifically, within the inflammatory response biological process, IL-17, TNF-α, and NF-κB signaling pathways were enriched. HANM was found to be strongly or moderately conserved across four mouse NAFLD datasets. Motif analysis of the upstream genomic sequences of HANM revealed nine transcription factors (FLI1, NRF1, ZBTB33, ELK1, YY1, ZNF143, TAF1, SF1, and E2F1), of which three transcription factors (YY1, E2F1, and ZNF143) were significantly highly expressed in the NAFLD patients and exhibited survival significance in HCC. Conclusion This study demonstrated a robust way to identify the sharing gene signature between subtypes of NAFLD and HCC, which contributed to a comprehensive understanding of pathogenesis from NAFLD to HCC.
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Sahoo S, Singh D, Chakraborty P, Jolly MK. Emergent Properties of the HNF4α-PPARγ Network May Drive Consequent Phenotypic Plasticity in NAFLD. J Clin Med 2020; 9:E870. [PMID: 32235813 PMCID: PMC7141525 DOI: 10.3390/jcm9030870] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/15/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common form of chronic liver disease in adults and children. It is characterized by excessive accumulation of lipids in the hepatocytes of patients without any excess alcohol intake. With a global presence of 24% and limited therapeutic options, the disease burden of NAFLD is increasing. Thus, it becomes imperative to attempt to understand the dynamics of disease progression at a systems-level. Here, we decoded the emergent dynamics of underlying gene regulatory networks that were identified to drive the initiation and the progression of NAFLD. We developed a mathematical model to elucidate the dynamics of the HNF4α-PPARγ gene regulatory network. Our simulations reveal that this network can enable multiple co-existing phenotypes under certain biological conditions: an adipocyte, a hepatocyte, and a "hybrid" adipocyte-like state of the hepatocyte. These phenotypes may also switch among each other, thus enabling phenotypic plasticity and consequently leading to simultaneous deregulation of the levels of molecules that maintain a hepatic identity and/or facilitate a partial or complete acquisition of adipocytic traits. These predicted trends are supported by the analysis of clinical data, further substantiating the putative role of phenotypic plasticity in driving NAFLD. Our results unravel how the emergent dynamics of underlying regulatory networks can promote phenotypic plasticity, thereby propelling the clinically observed changes in gene expression often associated with NAFLD.
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Affiliation(s)
- Sarthak Sahoo
- Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Divyoj Singh
- Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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Cebola I. Liver gene regulatory networks: Contributing factors to nonalcoholic fatty liver disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1480. [PMID: 32020788 DOI: 10.1002/wsbm.1480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 12/17/2022]
Abstract
Metabolic diseases such as nonalcoholic fatty liver disease (NAFLD) result from complex interactions between intrinsic and extrinsic factors, including genetics and exposure to obesogenic environments. These risk factors converge in aberrant gene expression patterns in the liver, which are underlined by altered cis-regulatory networks. In homeostasis and in disease states, liver cis-regulatory networks are established by coordinated action of liver-enriched transcription factors (TFs), which define enhancer landscapes, activating broad gene programs with spatiotemporal resolution. Recent advances in DNA sequencing have dramatically expanded our ability to map active transcripts, enhancers and TF cistromes, and to define the 3D chromatin topology that contains these elements. Deployment of these technologies has allowed investigation of the molecular processes that regulate liver development and metabolic homeostasis. Moreover, genomic studies of NAFLD patients and NAFLD models have demonstrated that the liver undergoes pervasive regulatory rewiring in NAFLD, which is reflected by aberrant gene expression profiles. We have therefore achieved an unprecedented level of detail in the understanding of liver cis-regulatory networks, particularly in physiological conditions. Future studies should aim to map active regulatory elements with added levels of resolution, addressing how the chromatin landscapes of different cell lineages contribute to and are altered in NAFLD and NAFLD-associated metabolic states. Such efforts would provide additional clues into the molecular factors that trigger this disease. This article is categorized under: Biological Mechanisms > Metabolism Biological Mechanisms > Regulatory Biology Laboratory Methods and Technologies > Genetic/Genomic Methods.
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Affiliation(s)
- Inês Cebola
- Department of Metabolism, Digestion and Reproduction, Section of Genetics and Genomics, Imperial College London, London, UK
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11
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Pan G, Cavalli M, Carlsson B, Skrtic S, Kumar C, Wadelius C. rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression. iScience 2020; 23:100808. [PMID: 31928966 PMCID: PMC7033636 DOI: 10.1016/j.isci.2019.100808] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 11/26/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
Long-chain polyunsaturated fatty acids (LC-PUFAs) influence human health in several areas, including cardiovascular disease, diabetes, fatty liver disease, and cancer. ELOVL2 encodes one of the key enzymes in the in vivo synthesis of LC-PUFAs from their precursors. Variants near ELOVL2 have repeatedly been associated with levels of LC-PUFA-derived metabolites in genome-wide association studies (GWAS), but the mechanisms behind these observations remain poorly defined. In this study, we found that rs953413, located in the first intron of ELOVL2, lies within a functional FOXA and HNF4α cooperative binding site. The G allele of rs953413 increases binding of FOXA1/FOXA2 and HNF4α to an evolutionarily conserved enhancer element, conferring allele-specific upregulation of the rs953413-associated gene ELOVL2. The expression of ELOVL2 was significantly downregulated by both FOXA1 and HNF4α knockdown and CRISPR/Cas9-mediated direct mutation to the enhancer element. Our results suggest that rs953413 regulates LC-PUFAs metabolism by altering ELOVL2 expression through FOXA1/FOXA2 and HNF4α cooperation. rs953413 resides in an evolutionarily conserved enhancer region rs953413 mediates the cooperative binding of FOXA and HNF4α to the enhancer region The rs953413 locus plays a key role in regulating ELOVL2 expression rs953413 is implicated in PUFA metabolism by regulating ELOVL2 expression
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Affiliation(s)
- Gang Pan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Björn Carlsson
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Stanko Skrtic
- Pharmaceutical Technology & Development, AstraZeneca AB, Gothenburg, Sweden; Department of Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Chanchal Kumar
- Translational Science & Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden; Karolinska Institutet/AstraZeneca Integrated CardioMetabolic Center (KI/AZ ICMC), Department of Medicine, Novum, Huddinge, Sweden
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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12
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Abo El-khair SM, Ghoneim FM, Shabaan DA, Elsamanoudy AZ. Molecular and ultrastructure study of endoplasmic reticulum stress in hepatic steatosis: role of hepatocyte nuclear factor 4α and inflammatory mediators. Histochem Cell Biol 2019; 153:49-62. [DOI: 10.1007/s00418-019-01823-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2019] [Indexed: 12/15/2022]
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13
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Hardesty JE, Wahlang B, Falkner KC, Shi H, Jin J, Zhou Y, Wilkey DW, Merchant ML, Watson CT, Feng W, Morris AJ, Hennig B, Prough RA, Cave MC. Proteomic Analysis Reveals Novel Mechanisms by Which Polychlorinated Biphenyls Compromise the Liver Promoting Diet-Induced Steatohepatitis. J Proteome Res 2019; 18:1582-1594. [PMID: 30807179 DOI: 10.1021/acs.jproteome.8b00886] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Environmental pollution contributes to fatty liver disease pathogenesis. Polychlorinated biphenyl (PCB) exposures have been associated with liver enzyme elevation and suspected steatohepatitis in cohort studies. Male mice treated with the commercial PCB mixture, Aroclor 1260 (20 mg/kg), and fed high fat diet (HFD) for 12 weeks developed steatohepatitis. Receptor-based modes of action including inhibition of the epidermal growth factor (EGF) receptor were previously proposed, but other mechanisms likely exist. Objectives were to identify and validate the pathways, transcription factors, and mechanisms responsible for the steatohepatitis associated with PCB and HFD coexposures. Comparative proteomics analysis was performed in archived mouse liver samples from the aforementioned chronic exposure study. Pathway and transcription factor analysis (TFA) was performed, and selected results were validated. Liver proteomics detected 1103 unique proteins. Aroclor 1260 upregulated 154 and downregulated 93 of these. Aroclor 1260 + HFD coexposures affected 55 pathways including glutathione metabolism, intermediary metabolism, and cytoskeletal remodeling. TFA of Aroclor 1260 treatment demonstrated alterations in the function of 42 transcription factors including downregulation of NRF2 and key nuclear receptors previously demonstrated to protect against steatohepatitis (e.g., HNF4α, FXR, PPARα/δ/γ, etc.). Validation studies demonstrated that Aroclor 1260 significantly reduced HNF4α protein levels, while Aroclor 1260 + HFD reduced expression of the HNF4α target gene, albumin, in vivo. Aroclor 1260 attenuated EGF-dependent HNF4α phosphorylation and target gene activation in vitro. Aroclor 1260 reduced levels of NRF2, its target genes, and glutathione in vivo. Aroclor 1260 attenuated EGF-dependent NRF2 upregulation, in vitro. Aroclor 1260 indirectly activated hepatic stellate cells in vitro via induction of hepatocyte-derived TGFβ. PCB exposures adversely impacted transcription factors regulating liver protection, function, and fibrosis. PCBs, thus, compromised the liver by reducing its protective responses against nutritional stress to promote diet-induced steatohepatitis. The identified mechanisms by which environmental pollutants influence fatty liver disease pathogenesis require confirmation in humans.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Andrew J Morris
- Superfund Research Center , University of Kentucky , Lexington , Kentucky 40536 , United States
| | - Bernhard Hennig
- Superfund Research Center , University of Kentucky , Lexington , Kentucky 40536 , United States
| | | | - Matthew C Cave
- The Robley Rex Veterans Affairs Medical Center , Louisville , Kentucky 40206 , United States.,The Jewish Hospital Liver Transplant Program , Louisville , Kentucky 40202 , United States
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14
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Li H, Toth E, Cherrington NJ. Asking the Right Questions With Animal Models: Methionine- and Choline-Deficient Model in Predicting Adverse Drug Reactions in Human NASH. Toxicol Sci 2019; 161:23-33. [PMID: 29145614 DOI: 10.1093/toxsci/kfx253] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In the past few decades, great conceptual and technological advances have been made in the field of toxicology, but animal model-based research still remains one of the most widely used and readily available tools for furthering our current knowledge. However, animal models are not perfect in predicting all systemic toxicity in humans. Extrapolating animal data to accurately predict human toxicities remains a challenge, and researchers are obligated to question the appropriateness of their chosen animal model. This paper provides an assessment of the utility of the methionine- and choline-deficient (MCD) diet fed animal model in reflecting human nonalcoholic steatohepatitis (NASH) and the potential risks of adverse drug reactions and toxicities that are associated with the disease. As a commonly used NASH model, the MCD model fails to exhibit most metabolic abnormalities in a similar manner to the human disease. The MCD model, on the other hand, closely resembles human NASH histology and reflects signatures of drug transporter alterations in humans. Due to the nature of the MCD model, it should be avoided in studies of NASH pathogenesis, metabolic parameter evaluation, and biomarker identification. But it can be used to accurately predict altered drug disposition due to NASH-associated transporter alterations.
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Affiliation(s)
- Hui Li
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721
| | - Erica Toth
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721
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15
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Systematic integrative analysis of gene expression identifies HNF4A as the central gene in pathogenesis of non-alcoholic steatohepatitis. PLoS One 2017; 12:e0189223. [PMID: 29216278 PMCID: PMC5720788 DOI: 10.1371/journal.pone.0189223] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/21/2017] [Indexed: 12/18/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in the Western world, and encompasses a spectrum from simple steatosis to steatohepatitis (NASH). There is currently no approved pharmacologic therapy against NASH, partly due to an incomplete understanding of its molecular basis. The goal of this study was to determine the key differentially expressed genes (DEGs), as well as those genes and pathways central to its pathogenesis. We performed an integrative computational analysis of publicly available gene expression data in NASH from GEO (GSE17470, GSE24807, GSE37031, GSE89632). The DEGs were identified using GEOquery, and only the genes present in at least three of the studies, to a total of 190 DEGs, were considered for further analyses. The pathways, networks, molecular interactions, functional analyses were generated through the use of Ingenuity Pathway Analysis (IPA). For selected networks, we computed the centrality using igraph package in R. Among the statistically significant predicted networks (p-val < 0.05), three were of most biological interest: the first is involved in antimicrobial response, inflammatory response and immunological disease, the second in cancer, organismal injury and development and the third in metabolic diseases. We discovered that HNF4A is the central gene in the network of NASH connected to metabolic diseases and that it regulates HNF1A, an additional transcription regulator also involved in lipid metabolism. Therefore, we show, for the first time to our knowledge, that HNF4A is central to the pathogenesis of NASH. This adds to previous literature demonstrating that HNF4A regulates the transcription of genes involved in the progression of NAFLD, and that HNF4A genetic variants play a potential role in NASH progression.
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