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Younesi FS, Miller AE, Barker TH, Rossi FMV, Hinz B. Fibroblast and myofibroblast activation in normal tissue repair and fibrosis. Nat Rev Mol Cell Biol 2024; 25:617-638. [PMID: 38589640 DOI: 10.1038/s41580-024-00716-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2024] [Indexed: 04/10/2024]
Abstract
The term 'fibroblast' often serves as a catch-all for a diverse array of mesenchymal cells, including perivascular cells, stromal progenitor cells and bona fide fibroblasts. Although phenotypically similar, these subpopulations are functionally distinct, maintaining tissue integrity and serving as local progenitor reservoirs. In response to tissue injury, these cells undergo a dynamic fibroblast-myofibroblast transition, marked by extracellular matrix secretion and contraction of actomyosin-based stress fibres. Importantly, whereas transient activation into myofibroblasts aids in tissue repair, persistent activation triggers pathological fibrosis. In this Review, we discuss the roles of mechanical cues, such as tissue stiffness and strain, alongside cell signalling pathways and extracellular matrix ligands in modulating myofibroblast activation and survival. We also highlight the role of epigenetic modifications and myofibroblast memory in physiological and pathological processes. Finally, we discuss potential strategies for therapeutically interfering with these factors and the associated signal transduction pathways to improve the outcome of dysregulated healing.
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Affiliation(s)
- Fereshteh Sadat Younesi
- Keenan Research Institute for Biomedical Science of the St. Michael's Hospital, Toronto, Ontario, Canada
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrew E Miller
- Department of Biomedical Engineering, School of Engineering and Applied Science, University of Virginia, Charlottesville, VA, USA
| | - Thomas H Barker
- Department of Biomedical Engineering, School of Engineering and Applied Science, University of Virginia, Charlottesville, VA, USA
| | - Fabio M V Rossi
- School of Biomedical Engineering and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Boris Hinz
- Keenan Research Institute for Biomedical Science of the St. Michael's Hospital, Toronto, Ontario, Canada.
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.
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Chen N, Sun Y, Luo P, Tang Y, Fan Y, Han L, Wang K. Association of CXCR4 gene expression and promoter methylation with chronic hepatitis B-related fibrosis/cirrhosis. Int Immunopharmacol 2024; 139:112686. [PMID: 39053226 DOI: 10.1016/j.intimp.2024.112686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/30/2024] [Accepted: 07/11/2024] [Indexed: 07/27/2024]
Abstract
OBJECTIVE Chronic hepatitis B (CHB) virus infection remains a major public health concern. In this study, the diagnostic capability of C-X-C chemokine receptor type 4 promoter methylation in patients with CHB-associated liver fibrosis/cirrhosis was evaluated. METHODS Two hundred participants were recruited, including 25 healthy controls (HCs), 60 patients with CHB and 115 patients with hepatitis B virus (HBV)-related liver fibrosis/LC. Researchers monitored the methylation and messenger ribonucleic acid (mRNA) levels of C-X-C chemokine receptor type 4 (CXCR4) in peripheral blood mononuclear cells (PBMCs). In addition, we utilized single cell sequencing to analyze the cell types highly expressing CXCR4 in HBV-related liver fibrosis/LC. RESULTS HBV-related fibrosis/cirrhosis patients exhibited a significant elevation in the expression level of CXCR4 mRNA in PBMCs compared to CHB ones. The CXCR4 promoter showed a significantly lower methylation level in patients with CHB-related fibrosis/cirrhosis than in patients with CHB. Additionally, the diagnostic area under the area under the curve (AUC) of methylation of the CXCR4 promoter for CHB -related liver fibrosis/LC exceeded liver stiffness measurement (LSM), aspartate aminotransferase-to-platelet ratio index (APRI) and fibrosis-4 score (FIB-4). Furthermore, single-cell analysis demonstrated that CXCR4 expression is closely associated with Natural Killer cells(NK cells), T lymphocytes (T cells), and monocytes. CONCLUSION The low methylation of the CXCR4 promoter holds promise as a non-invasive biomarker for detecting CHB-associated liver fibrosis/LC.
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Affiliation(s)
- Nan Chen
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, PR China
| | - Yu Sun
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, PR China
| | - Pengyu Luo
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, PR China
| | - Yuna Tang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, PR China
| | - Yuchen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, PR China
| | - Liyan Han
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, PR China; Institute of Hepatology, Shandong University, Jinan 250012, PR China.
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, PR China; Institute of Hepatology, Shandong University, Jinan 250012, PR China.
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Li D, Yang W, Pang J, Yu G. Differential DNA methylation landscape of miRNAs genes in mice liver fibrosis. Mol Biol Rep 2024; 51:475. [PMID: 38553662 DOI: 10.1007/s11033-024-09416-6] [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: 10/30/2023] [Accepted: 03/05/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Patients with chronic liver disease were found nearly all to have liver fibrosis, which is characterized by excess accumulation of extracellular matrix (ECM) proteins. While ECM accumulation can prevent liver infection and injury, it can destroy normal liver function and architecture. miRNA's own regulation was involved in DNA methylation change. The purpose of this study is to detect DNA methylation landscape of miRNAs genes in mice liver fibrosis tissues. METHODS Male mice (10-12 weeks) were injected CCl4 from abdominal cavity to induced liver fibrosis. 850 K BeadChips were used to examine DNA methylation change in whole genome. The methylation change of 16 CpG dinucleotides located in promoter regions of 4 miRNA genes were detected by bisulfite sequencing polymerase chain reaction (BSP) to verify chip data accuracy, and these 4 miRNA genes' expressions were detected by RT-qPCR methods. RESULTS There are 769 differential methylation sites (DMS) in total between fibrotic liver tissue and normal mice liver tissue, which were related with 148 different miRNA genes. Chips array data were confirmed by bisulfite sequencing polymerase chain reaction (R = 0.953; P < 0.01). GO analysis of the target genes of 2 miRNA revealed that protein binding, cytoplasm and chromatin binding activity were commonly enriched; KEGG pathway enrichment analysis displayed that TGF-beta signaling pathway was commonly enriched. CONCLUSION The DNA of 148 miRNA genes was found to have methylation change in liver fibrosis tissue. These discoveries in miRNA genes are beneficial to future miRNA function research in liver fibrosis.
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Affiliation(s)
- Deming Li
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Wentong Yang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Jiaojiao Pang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China.
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Wang C, Liu T, Wang Z, Li W, Zhao Q, Mi Z, Xue X, Shi P, Sun Y, Zhang Y, Wang N, Bao F, Chen W, Liu H, Zhang F. IL-23/IL-23R Promote Macrophage Pyroptosis and T Helper 1/T Helper 17 Cell Differentiation in Mycobacterial Infection. J Invest Dermatol 2023; 143:2264-2274.e18. [PMID: 37187409 DOI: 10.1016/j.jid.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 04/08/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Pathogen-induced epigenetic modifications can reshape anti-infection immune processes and control the magnitude of host responses. DNA methylation profiling has identified crucial aberrant methylation changes associated with diseases, thus providing biological insights into the roles of epigenetic factors in mycobacterial infection. In this study, we performed a genome-wide methylation analysis of skin biopsies from patients with leprosy and healthy controls. T helper 17 differentiation pathway was found to be significantly associated with leprosy through functional enrichment analysis. As a key gene in this pathway, IL-23R was found to be critical to mycobacterial immunity in leprosy, according to integrated analysis with DNA methylation, RNA sequencing, and GWASs. Functional analysis revealed that IL-23/IL-23R-enhanced bacterial clearance by activating caspase-1/GSDMD-mediated pyroptosis in a manner dependent on NLRP3 through signal transducer and activator of transcription 3 signaling in macrophages. Moreover, IL23/IL-23R promoted T helper 1 and T helper 17 cell differentiation and proinflammatory cytokine secretion, thereby increasing host bactericidal activity. IL-23R knockout attenuated the effects and increased susceptibility to mycobacterial infection mentioned earlier. These findings illustrate the biological functions of IL-23/IL-23R in modulating intracellular bacterial clearance in macrophages and further support their regulatory effects in T helper cell differentiation. Our study highlights that IL-23/IL-23R might serve as potential targets for the prevention and treatment of leprosy and other mycobacterial infections.
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Affiliation(s)
- Chuan Wang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Tingting Liu
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zhenzhen Wang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Wenchao Li
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Qing Zhao
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zihao Mi
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xiaotong Xue
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Peidian Shi
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yonghu Sun
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yuan Zhang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Na Wang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Fangfang Bao
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Wenjie Chen
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Hong Liu
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Furen Zhang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
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Hamidi N, Feizi F, Azadmehr A, Zabihi E, Khafri S, Zarei-Behjani Z, Babazadeh Z. Disulfiram ameliorates bleomycin induced pulmonary inflammation and fibrosis in rats. Biotech Histochem 2023; 98:584-592. [PMID: 37779489 DOI: 10.1080/10520295.2023.2261367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
Bleomycin (BL) is a widely used anticancer drug that can cause pulmonary fibrosis due to increased fibroblast proliferation and increased secretion of extracellular matrix. RASSF1A is a tumor suppressor gene that is down-regulated by DNA methylation during fibrosis. Disulfiram (DSF), a noncytosine DNA methyltransferase inhibitor, can revert epigenetic biomarkers and re-express silenced genes. We investigated anti-inflammatory and anti-fibrotic effects of DSF on regulation of epigenetic molecules and histopathology in a rat model of BL induced pulmonary fibrosis. We used six groups of rats: sesame oil (SO) control (Co) group, BL group, BL + SO group and three BL + DSF groups administered 1 mg/kg DSF (BL + DSF), 10 mg/kg DSF (BL + DSF10) or 100 mg/kg DSF (BL + DSF100), respectively. BL was administered intratracheally to induce pulmonary fibrosis. DSF and SO were injected intraperitoneally (i.p.) 2 days before BL administration; these injections were continued for 3 weeks. At the end of the study, lung tissues were removed for molecular and histopathologic studies. Administration of 10 or 100 mg/kg DSF after BL induced pulmonary inflammation and fibrosis, and up-regulated RASSF1A and down-regulated TNF-α and IL-1 β compared to the BL and BL + SO groups. A RASSF1A unmethylated band was observed using the methylation-specific PCR technique in rats that had been administered 10 and 100 mg/kg DSF, which indicated partial DNA demethylation. Histopathologic evaluation revealed that fibrosis and all inflammatory scores were decreased significantly in the BL + DSF10 and BL + DSF100 groups compared to the BL group. Our findings indicate that DSF modified DNA methylation by up-regulating RASSF1A, which reduced inflammation and fibrosis in BL induced pulmonary inflammation and fibrosis.
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Affiliation(s)
- Negar Hamidi
- Cellular and Molecular Biology Research Center, Institute of Health, Babol University of Medical Sciences, Babol, Iran
- Department of Anatomical Science, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Farideh Feizi
- Cellular and Molecular Biology Research Center, Institute of Health, Babol University of Medical Sciences, Babol, Iran
- Department of Anatomical Science, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Abbas Azadmehr
- Cellular and Molecular Biology Research Center, Institute of Health, Babol University of Medical Sciences, Babol, Iran
- Department of Immunology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Ebrahim Zabihi
- Cellular and Molecular Biology Research Center, Institute of Health, Babol University of Medical Sciences, Babol, Iran
| | - Soraya Khafri
- Department of Biostatistics and Epidemiology, Faculty of Medicine, Babol University of Medical Science, Babol, Iran
| | - Zeinab Zarei-Behjani
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Babazadeh
- Cellular and Molecular Biology Research Center, Institute of Health, Babol University of Medical Sciences, Babol, Iran
- Department of Anatomical Science, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
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6
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Majid A, Hassan FO, Hoque MM, Gbadegoye JO, Lebeche D. Bioactive Compounds and Cardiac Fibrosis: Current Insight and Future Prospect. J Cardiovasc Dev Dis 2023; 10:313. [PMID: 37504569 PMCID: PMC10380727 DOI: 10.3390/jcdd10070313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
Cardiac fibrosis is a pathological condition characterized by excessive deposition of collagen and other extracellular matrix components in the heart. It is recognized as a major contributor to the development and progression of heart failure. Despite significant research efforts in characterizing and identifying key molecular mechanisms associated with myocardial fibrosis, effective treatment for this condition is still out of sight. In this regard, bioactive compounds have emerged as potential therapeutic antifibrotic agents due to their anti-inflammatory and antioxidant properties. These compounds exhibit the ability to modulate fibrogenic processes by inhibiting the production of extracellular matrix proteins involved in fibroblast to myofibroblast differentiation, or by promoting their breakdown. Extensive investigation of these bioactive compounds offers new possibilities for preventing or reducing cardiac fibrosis and its detrimental consequences. This comprehensive review aims to provide a thorough overview of the mechanisms underlying cardiac fibrosis, address the limitations of current treatment strategies, and specifically explore the potential of bioactive compounds as therapeutic interventions for the treatment and/or prevention of cardiac fibrosis.
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Affiliation(s)
- Abdul Majid
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Fasilat Oluwakemi Hassan
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Md Monirul Hoque
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Joy Olaoluwa Gbadegoye
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Djamel Lebeche
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
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Sumey JL, Johnston PC, Harrell AM, Caliari SR. Hydrogel mechanics regulate fibroblast DNA methylation and chromatin condensation. Biomater Sci 2023; 11:2886-2897. [PMID: 36880435 PMCID: PMC10329270 DOI: 10.1039/d2bm02058k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Cellular mechanotransduction plays a central role in fibroblast activation during fibrotic disease progression, leading to increased tissue stiffness and reduced organ function. While the role of epigenetics in disease mechanotransduction has begun to be appreciated, little is known about how substrate mechanics, particularly the timing of mechanical inputs, regulate epigenetic changes such as DNA methylation and chromatin reorganization during fibroblast activation. In this work, we engineered a hyaluronic acid hydrogel platform with independently tunable stiffness and viscoelasticity to model normal (storage modulus, G' ∼ 0.5 kPa, loss modulus, G'' ∼ 0.05 kPa) to increasingly fibrotic (G' ∼ 2.5 and 8 kPa, G'' ∼ 0.05 kPa) lung mechanics. Human lung fibroblasts exhibited increased spreading and nuclear localization of myocardin-related transcription factor-A (MRTF-A) with increasing substrate stiffness within 1 day, with these trends holding steady for longer cultures. However, fibroblasts displayed time-dependent changes in global DNA methylation and chromatin organization. Fibroblasts initially displayed increased DNA methylation and chromatin decondensation on stiffer hydrogels, but both of these measures decreased with longer culture times. To investigate how culture time affected the responsiveness of fibroblast nuclear remodeling to mechanical signals, we engineered hydrogels amenable to in situ secondary crosslinking, enabling a transition from a compliant substrate mimicking normal tissue to a stiffer substrate resembling fibrotic tissue. When stiffening was initiated after only 1 day of culture, fibroblasts rapidly responded and displayed increased DNA methylation and chromatin decondensation, similar to fibroblasts on static stiffer hydrogels. Conversely, when fibroblasts experienced later stiffening at day 7, they showed no changes in DNA methylation and chromatin condensation, suggesting the induction of a persistent fibroblast phenotype. These results highlight the time-dependent nuclear changes associated with fibroblast activation in response to dynamic mechanical perturbations and may provide mechanisms to target for controlling fibroblast activation.
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Affiliation(s)
- Jenna L Sumey
- Department of Chemical Engineering, University of Virginia, USA.
| | | | | | - Steven R Caliari
- Department of Chemical Engineering, University of Virginia, USA.
- Department of Biomedical Engineering, University of Virginia, USA
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Yang J, Liang C, Liu L, Wang L, Yu G. High-Fat Diet Related Lung Fibrosis-Epigenetic Regulation Matters. Biomolecules 2023; 13:biom13030558. [PMID: 36979493 PMCID: PMC10046645 DOI: 10.3390/biom13030558] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/12/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Pulmonary fibrosis (PF) is an interstitial lung disease characterized by the destruction of the pulmonary parenchyma caused by excessive extracellular matrix deposition. Despite the well-known etiological factors such as senescence, aberrant epithelial cell and fibroblast activation, and chronic inflammation, PF has recently been recognized as a metabolic disease and abnormal lipid signature was observed both in serum and bronchoalveolar lavage fluid (BALF) of PF patients and mice PF model. Clinically, observational studies suggest a significant link between high-fat diet (HFD) and PF as manifested by high intake of saturated fatty acids (SFAs) and meat increases the risk of PF and mice lung fibrosis. However, the possible mechanisms between HFD and PF remain unclear. In the current review we emphasize the diversity effects of the epigenetic dysregulation induced by HFD on the fibrotic factors such as epithelial cell injury, abnormal fibroblast activation and chronic inflammation. Finally, we discuss the potential ways for patients to improve their conditions and emphasize the prospect of targeted therapy based on epigenetic regulation for scientific researchers or drug developers.
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Affiliation(s)
- Juntang Yang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
| | - Chenxi Liang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
| | - Lulu Liu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
| | - Lan Wang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453007, China
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Duan J, Zhong B, Fan Z, Zhang H, Xu M, Zhang X, Sanders YY. DNA methylation in pulmonary fibrosis and lung cancer. Expert Rev Respir Med 2022; 16:519-528. [PMID: 35673969 DOI: 10.1080/17476348.2022.2085091] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Juan Duan
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Baiyun Zhong
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhihua Fan
- Xiangya Medical school of Central South University, Changsha, Hunan, China
| | - Hao Zhang
- Xiangya Medical school of Central South University, Changsha, Hunan, China
| | - Mengmeng Xu
- Xiangya Medical school of Central South University, Changsha, Hunan, China
| | - Xiangyu Zhang
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Y Sanders
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, 901 19 Street South, BMRII Room 408, Birmingham, AL 35294, USA
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Wen D, Gao Y, Ho C, Yu L, Zhang Y, Lyu G, Hu D, Li Q, Zhang Y. Focusing on Mechanoregulation Axis in Fibrosis: Sensing, Transduction and Effecting. Front Mol Biosci 2022; 9:804680. [PMID: 35359592 PMCID: PMC8963247 DOI: 10.3389/fmolb.2022.804680] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/09/2022] [Indexed: 11/24/2022] Open
Abstract
Fibrosis, a pathologic process featured by the excessive deposition of connective tissue components, can affect virtually every organ and has no satisfactory therapy yet. Fibrotic diseases are often associated with organ dysfunction which leads to high morbidity and mortality. Biomechanical stmuli and the corresponding cellular response havebeen identified in fibrogenesis, as the fibrotic remodeling could be seen as the incapacity to reestablish mechanical homeostasis: along with extracellular matrix accumulating, the physical property became more “stiff” and could in turn induce fibrosis. In this review, we provide a comprehensive overview of mechanoregulation in fibrosis, from initialing cellular mechanosensing to intracellular mechanotransduction and processing, and ends up in mechanoeffecting. Our contents are not limited to the cellular mechanism, but further expand to the disorders involved and current clinical trials, providing an insight into the disease and hopefully inspiring new approaches for the treatment of tissue fibrosis.
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Affiliation(s)
- Dongsheng Wen
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ya Gao
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chiakang Ho
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Yu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuguang Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guozhong Lyu
- Department of Burns and Plastic Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Dahai Hu
- Burns Centre of PLA, Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Qingfeng Li
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Qingfeng Li, ; Yifan Zhang,
| | - Yifan Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Qingfeng Li, ; Yifan Zhang,
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Wei A, Gao Q, Chen F, Zhu X, Chen X, Zhang L, Su X, Dai J, Shi Y, Cao W. Inhibition of DNA methylation derepresses PPARγ and attenuates pulmonary fibrosis. Br J Pharmacol 2021; 179:1304-1318. [PMID: 34378791 DOI: 10.1111/bph.15655] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/13/2021] [Accepted: 08/02/2021] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND AND PURPOSE Development of pulmonary fibrosis is associated with altered DNA methylation modifications of fibrogenic gene expressions; however, their causal relationships and the underlying mechanisms remain unclear. This study investigates the critical role of DNA methylation aberration-associated suppression of PPARγ (peroxisome proliferator-activated receptor-gamma) in pulmonary fibrosis. EXPERIMENTAL APPROACH Expressions of PPARγ and bioactive DNA methyltranferases, and PPARγ promoter methylation status were examined from fibrotic lungs of idiopathic pulmonary fibrosis (IPF) patients and bleomycin (Blm)-treated mice. DNA demethylating agent 5-Aza-2'-deoxycytidine (5aza) and glycyrrhizic acid (GA) derived from medicinal plant were assessed for their PPARγ derepression and anti-pulmonary fibrosis activities. PPARγ knockout mice were created to determine the critical role of PPARγ in the protections. KEY RESULTS Lung PPARγ expressions were markedly suppressed in IPF patients and Blm mice, accompanied by increased methyltransferase (DNMT) 1/DNMT3a and PPARγ promoter hypermethylation. Administrations of 5aza and GA similarly demethylated PPARγ promoter, recovered the PPARγ loss and alleviated the fibrotic lung pathologies, including structural alterations and adverse expressions of fibrotic mediators and inflammatory cytokines. In cultured lung fibroblast and alveolar epithelial cells, GA alleviated the fibrotic PPARγ suppression in a gain of DNMT-sensitive manner, and in PPARγ knockout mice, the anti-fibrotic effects of 5aza and GA were significantly reduced, suggesting that PPARγ is a critical mediator of epigenetic pulmonary fibrogenesis. CONCLUSION AND IMPLICATIONS Aberrant DNMT1/3a elevations and the resultant PPARγ suppression contribute significantly to the development of pulmonary fibrosis, and strategies targeting DNMT/PPARγ axis by synthetic or natural small compounds might benefit patients with pulmonary fibrotic disorders.
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Affiliation(s)
- Ai Wei
- Organ Fibrosis and Remodeling Research Center, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China.,Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Qi Gao
- Organ Fibrosis and Remodeling Research Center, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
| | - Fang Chen
- Organ Fibrosis and Remodeling Research Center, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
| | - Xiaobo Zhu
- Organ Fibrosis and Remodeling Research Center, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
| | - Xingren Chen
- Organ Fibrosis and Remodeling Research Center, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
| | - Lijun Zhang
- Organ Fibrosis and Remodeling Research Center, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
| | - Xin Su
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Jinghong Dai
- Department of Pulmonary and Critical Care Medicine, The Affiliated Drum Tower Hospital of Nanjing University School of Medicine, Nanjing, China
| | - Yi Shi
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Wangsen Cao
- Organ Fibrosis and Remodeling Research Center, Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, China
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12
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Johnson ND, Wu X, Still CD, Chu X, Petrick AT, Gerhard GS, Conneely KN, DiStefano JK. Differential DNA methylation and changing cell-type proportions as fibrotic stage progresses in NAFLD. Clin Epigenetics 2021; 13:152. [PMID: 34353365 PMCID: PMC8340447 DOI: 10.1186/s13148-021-01129-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is characterized by changes in cell composition that occur throughout disease pathogenesis, which includes the development of fibrosis in a subset of patients. DNA methylation (DNAm) is a plausible mechanism underlying these shifts, considering that DNAm profiles differ across tissues and cell types, and DNAm may play a role in cell-type differentiation. Previous work investigating the relationship between DNAm and fibrosis in NAFLD has been limited by sample size and the number of CpG sites interrogated. RESULTS Here, we performed an epigenome-wide analysis using Infinium MethylationEPIC array data from 325 individuals with NAFLD, including 119 with severe fibrosis and 206 with no histological evidence of fibrosis. After adjustment for latent confounders, we identified 7 CpG sites whose DNAm associated with fibrosis (p < 5.96 × 10-8). Analysis of RNA-seq data collected from a subset of individuals (N = 56) revealed that gene expression at 288 genes associated with DNAm at one or more of the 7 fibrosis-related CpGs. DNAm-based estimates of cell-type proportions showed that estimated proportions of natural killer cells increased, while epithelial cell proportions decreased with disease stage. Finally, we used an elastic net regression model to assess DNAm as a biomarker of fibrotic stage and found that our model predicted fibrosis with a sensitivity of 0.93 and provided information beyond a model based solely on cell-type proportions. CONCLUSION These findings are consistent with DNAm as a mechanism underpinning or marking fibrosis-related shifts in cell composition and demonstrate the potential of DNAm as a possible biomarker of NAFLD fibrosis.
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Affiliation(s)
- Nicholas D Johnson
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
| | - Xiumei Wu
- Diabetes and Fibrotic Disease Unit, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Xin Chu
- Geisinger Obesity Institute, Danville, PA, USA
| | | | - Glenn S Gerhard
- Lewis Katz School of Medicine, Temple University School of Medicine, Philadelphia, PA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
| | - Johanna K DiStefano
- Diabetes and Fibrotic Disease Unit, Translational Genomics Research Institute, Phoenix, AZ, USA.
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13
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Pastar I, Marjanovic J, Stone RC, Chen V, Burgess JL, Mervis JS, Tomic-Canic M. Epigenetic regulation of cellular functions in wound healing. Exp Dermatol 2021; 30:1073-1089. [PMID: 33690920 DOI: 10.1111/exd.14325] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023]
Abstract
Stringent spatiotemporal regulation of the wound healing process involving multiple cell types is associated with epigenetic mechanisms of gene regulation, such as DNA methylation, histone modification and chromatin remodelling, as well as non-coding RNAs. Here, we discuss the epigenetic changes that occur during wound healing and the rapidly expanding understanding of how these mechanisms affect healing resolution in both acute and chronic wound milieu. We provide a focussed overview of current research into epigenetic regulators that contribute to wound healing by specific cell type. We highlight the role of epigenetic regulators in the molecular pathophysiology of chronic wound conditions. The understanding of how epigenetic regulators can affect cellular functions during normal and impaired wound healing could lead to novel therapeutic approaches, and we outline questions that can provide guidance for future research on epigenetic-based interventions to promote healing. Dissecting the dynamic interplay between cellular subtypes involved in wound healing and epigenetic parameters during barrier repair will deepen our understanding of how to improve healing outcomes in patients affected by chronic non-healing wounds.
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Affiliation(s)
- Irena Pastar
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, Wound Healing and Regenerative Medicine Research Program, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jelena Marjanovic
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, Wound Healing and Regenerative Medicine Research Program, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Rivka C Stone
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, Wound Healing and Regenerative Medicine Research Program, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Vivien Chen
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, Wound Healing and Regenerative Medicine Research Program, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jamie L Burgess
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, Wound Healing and Regenerative Medicine Research Program, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Joshua S Mervis
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, Wound Healing and Regenerative Medicine Research Program, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Marjana Tomic-Canic
- Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, Wound Healing and Regenerative Medicine Research Program, University of Miami Miller School of Medicine, Miami, FL, USA
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14
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Dees C, Pötter S, Zhang Y, Bergmann C, Zhou X, Luber M, Wohlfahrt T, Karouzakis E, Ramming A, Gelse K, Yoshimura A, Jaenisch R, Distler O, Schett G, Distler JH. TGF-β-induced epigenetic deregulation of SOCS3 facilitates STAT3 signaling to promote fibrosis. J Clin Invest 2021; 130:2347-2363. [PMID: 31990678 DOI: 10.1172/jci122462] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 01/17/2020] [Indexed: 12/28/2022] Open
Abstract
Fibroblasts are key effector cells in tissue remodeling. They remain persistently activated in fibrotic diseases, resulting in progressive deposition of extracellular matrix. Although fibroblast activation may be initiated by external factors, prolonged activation can induce an "autonomous," self-maintaining profibrotic phenotype in fibroblasts. Accumulating evidence suggests that epigenetic alterations play a central role in establishing this persistently activated pathologic phenotype of fibroblasts. We demonstrated that in fibrotic skin of patients with systemic sclerosis (SSc), a prototypical idiopathic fibrotic disease, TGF-β induced the expression of DNA methyltransferase 3A (DNMT3A) and DNMT1 in fibroblasts in a SMAD-dependent manner to silence the expression of suppressor of cytokine signaling 3 (SOCS3) by promoter hypermethylation. Downregulation of SOCS3 facilitated activation of STAT3 to promote fibroblast-to-myofibroblast transition, collagen release, and fibrosis in vitro and in vivo. Reestablishment of the epigenetic control of STAT3 signaling by genetic or pharmacological inactivation of DNMT3A reversed the activated phenotype of SSc fibroblasts in tissue culture, inhibited TGF-β-dependent fibroblast activation, and ameliorated experimental fibrosis in murine models. These findings identify a pathway of epigenetic imprinting of fibroblasts in fibrotic disease with translational implications for the development of targeted therapies in fibrotic diseases.
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Affiliation(s)
- Clara Dees
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Sebastian Pötter
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Yun Zhang
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christina Bergmann
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Xiang Zhou
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Markus Luber
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Thomas Wohlfahrt
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Emmanuel Karouzakis
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, Zurich, Switzerland
| | - Andreas Ramming
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Kolja Gelse
- Department of Trauma Surgery - Orthopedic Surgery, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital of Zurich, Zurich, Switzerland
| | - Georg Schett
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Jörg Hw Distler
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
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15
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Ganguly N, Chakrabarti S. Role of long non‑coding RNAs and related epigenetic mechanisms in liver fibrosis (Review). Int J Mol Med 2021; 47:23. [PMID: 33495817 PMCID: PMC7846421 DOI: 10.3892/ijmm.2021.4856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
Liver fibrosis is one of the major liver pathologies affecting patients worldwide. It results from an improper tissue repair process following liver injury or inflammation. If left untreated, it ultimately leads to liver cirrhosis and liver failure. Long non‑coding RNAs (lncRNAs) have been implicated in a wide variety of diseases. They can regulate gene expression and modulate signaling. Some of the lncRNAs promote, while others inhibit liver fibrosis. Similarly, other epigenetic processes, such as methylation and acetylation regulate gene transcription and can modulate gene expression. Notably, there are several regulatory associations of lncRNAs with other epigenetic processes. A major mechanism of action of long non‑coding RNAs is to competitively bind to their target microRNAs (miRNAs or miRs), which in turn affects miRNA availability and bioactivity. In the present review, the role of lncRNAs and related epigenetic processes contributing to liver fibrosis is discussed. Finally, various potential therapeutic approaches targeting lncRNAs and related epigenetic processes, which are being considered as possible future treatment targets for liver fibrosis are identified.
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Affiliation(s)
- Niladri Ganguly
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Subrata Chakrabarti
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON N6A 5C1, Canada
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16
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Cui Z, Huang N, Liu L, Li X, Li G, Chen Y, Wu Q, Zhang J, Long S, Wang M, Sun F, Shi Y, Pan Q. Dynamic analysis of m6A methylation spectroscopy during progression and reversal of hepatic fibrosis. Epigenomics 2020; 12:1707-1723. [PMID: 33174480 DOI: 10.2217/epi-2019-0365] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: To dynamically analyze the differential m6A methylation during the progression and reversal of hepatic fibrosis. Materials & methods: We induced hepatic fibrosis in C57/BL6 mice by intraperitoneal injection of CCl4. The reversal model of hepatic fibrosis was established by stopping drug after continuous injection of CCl4. Dynamic m6A methylation was evaluated using MeRIP-Seq in the progression and reversal of hepatic fibrosis at different stages. Result: During the hepatic fibrosis, differential m6A methylation was mainly enriched in processes associated with oxidative stress and cytochrome metabolism, while differential m6A methylation was mainly enriched in processes associated with immune response and apoptosis in the hepatic fibrosis reversal. Conclusion: m6A methylation plays an important role in the progression and reversal of hepatic fibrosis.
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Affiliation(s)
- Zhongqi Cui
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Nan Huang
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Li Liu
- Department of Clinical Laboratory, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai 200081, China
| | - Xue Li
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Guohui Li
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Yan Chen
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Qi Wu
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Jie Zhang
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Shuping Long
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Minyi Wang
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Fenyong Sun
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Yi Shi
- Department of Clinical Laboratory, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai 200081, China
| | - Qiuhui Pan
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, China
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17
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Targeting chromatin dysregulation in organ fibrosis. Cytokine Growth Factor Rev 2020; 57:64-72. [PMID: 32900600 DOI: 10.1016/j.cytogfr.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Fibrosis leads to destruction of organ architecture accompanied by chronic inflammation and loss of function. Fibrosis affects nearly every organ in the body and accounts for ∼45% of total deaths worldwide. Over the past decade, tremendous progress has been made in understanding the basic mechanisms leading to organ fibrosis. However, we are limited with therapeutic options and there is a significant need to develop highly effective anti-fibrotic therapies. Recent advances in sequencing technologies have advanced the burgeoning field of epigenetics towards molecular understanding at a higher resolution. Here we provide a comprehensive review of the recent advances in chromatin regulatory processes, specifically DNA methylation, post-translational modification of histones, and chromatin remodeling complexes in kidney, liver and lung fibrosis. Although this research field is young, we discuss new strategies for potential therapeutic interventions for treating organ fibrosis.
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18
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Identification of Differentially Methylated CpG Sites in Fibroblasts from Keloid Scars. Biomedicines 2020; 8:biomedicines8070181. [PMID: 32605309 PMCID: PMC7400180 DOI: 10.3390/biomedicines8070181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
As a part of an abnormal healing process of dermal injuries and irritation, keloid scars arise on the skin as benign fibroproliferative tumors. Although the etiology of keloid scarring remains unsettled, considerable recent evidence suggested that keloidogenesis may be driven by epigenetic changes, particularly, DNA methylation. Therefore, genome-wide scanning of methylated cytosine-phosphoguanine (CpG) sites in extracted DNA from 12 keloid scar fibroblasts (KF) and 12 control skin fibroblasts (CF) (six normal skin fibroblasts and six normotrophic fibroblasts) was conducted using the Illumina Human Methylation 450K BeadChip in two replicates for each sample. Comparing KF and CF used a Linear Models for Microarray Data (Limma) model revealed 100,000 differentially methylated (DM) CpG sites, 20,695 of which were found to be hypomethylated and 79,305 were hypermethylated. The top DM CpG sites were associated with TNKS2, FAM45B, LOC723972, GAS7, RHBDD2 and CAMKK1. Subsequently, the most functionally enriched genes with the top 100 DM CpG sites were significantly (p ≤ 0.05) associated with SH2 domain binding, regulation of transcription, DNA-templated, nucleus, positive regulation of protein targeting to mitochondrion, nucleoplasm, Swr1 complex, histone exchange, and cellular response to organic substance. In addition, NLK, CAMKK1, LPAR2, CASP1, and NHS showed to be the most common regulators in the signaling network analysis. Taken together, these findings shed light on the methylation status of keloids that could be implicated in the underlying mechanism of keloid scars formation and remission.
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19
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Liu Y, Xu S, Zu T, Li F, Sang S, Liu C, An Y, Mi B, Orgill DP, Murphy GF, Lian CG. Reversal of TET-mediated 5-hmC loss in hypoxic fibroblasts by ascorbic acid. J Transl Med 2019; 99:1193-1202. [PMID: 30837678 DOI: 10.1038/s41374-019-0235-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/16/2018] [Accepted: 12/30/2018] [Indexed: 01/01/2023] Open
Abstract
Hypoxia resulting in hypoxia-inducible factor-1 alpha (HIF-1α) induction is known to drive scar formation during cutaneous wound healing, and may be responsible for excessive fibrosis inherent to hypertrophic scars and keloids. Because epigenetic pathways play an important role in regulation of fibrosing processes, we evaluated patient scars for DNA hydroxymethylation (5-hydroxymethylcytosine; 5-hmC) status and documented a significant decrease in scar fibroblasts. To test this finding in vitro, human fibroblasts were cultured with cobalt chloride (CoCl2), a known stimulant of HIF-1α. HIF-1α induced so resulted in loss of 5-hmC similar to that seen in naturally occurring scars and was associated with significant downregulation of one of the 5-hmC converting enzymes-ten-eleven translocation 3 (TET3)-as well as increased expression of phosphorylated focal adhesion kinase (p-FAK), which is important in wound contracture. These changes were partially reversed by exposure to ascorbic acid, a recognized epigenetic regulator potentially capable of minimizing excessive scar formation and promoting a more regenerative healing response. Our results provide a novel and translationally relevant mechanism whereby epigenetic regulation of scar formation may be manipulated at the level of fibroblast DNA hydroxymethylation.
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Affiliation(s)
- Yukun Liu
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Plastic Surgery, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shuyun Xu
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tingjian Zu
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Feng Li
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shengbo Sang
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Cynthia Liu
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yang An
- Division of Plastic Surgery, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bobin Mi
- Division of Plastic Surgery, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dennis P Orgill
- Division of Plastic Surgery, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - George F Murphy
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Christine G Lian
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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20
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Qiu Y, Gao Y, Yu D, Zhong L, Cai W, Ji J, Geng F, Tang G, Zhang H, Cao J, Zhang J, Zhang S. Genome-Wide Analysis Reveals Zinc Transporter ZIP9 Regulated by DNA Methylation Promotes Radiation-Induced Skin Fibrosis via the TGF-β Signaling Pathway. J Invest Dermatol 2019; 140:94-102.e7. [PMID: 31254515 DOI: 10.1016/j.jid.2019.04.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/16/2019] [Accepted: 04/29/2019] [Indexed: 01/12/2023]
Abstract
Radiation-induced skin fibrosis is a detrimental and chronic disorder that occurs after radiation exposure. DNA methylation has been characterized as an important regulatory mechanism of multiple pathological processes. In this study, we compared the genome-wide DNA methylation status in radiation-induced fibrotic skin and adjacent normal tissues of rats by methylated DNA immunoprecipitation sequencing. Radiation-induced fibrotic skin showed differentially methylated regions associated with 3,650 protein-coding genes, 72 microRNAs, 5,836 long noncoding RNAs and 3 piwi-interacting RNAs. By integrating the mRNA and methylation profiles, the zinc transporter SLC39A9/ZIP9 was investigated in greater detail. The protein level of ZIP9 was increased in irradiated skin tissues of humans, monkeys, and rats, especially in radiogenic fibrotic skin tissues. Radiation induced the demethylation of a CpG dinucleotide in exon 1 of ZIP9 that resulted in recruitment of the transcriptional factor Sp1 and increased ZIP9 expression. Overexpression of ZIP9 resulted in activation of the profibrotic transforming growth factor-β signaling pathway through protein kinase B in human fibroblasts. In addition, radiation-induced skin fibrosis was associated with increased zinc accumulation. The zinc chelator N,N,N',N'-tetrakis(2-pyridylmethyl)-1,2-ethylenediamine abrogated ZIP9-induced activation of the transforming growth factor-β signaling pathway and attenuated radiation-induced skin fibrosis in a rat model. In summary, our findings illustrate epigenetic regulation of ZIP9 and its critical role in promoting radiation-induced skin fibrosis.
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Affiliation(s)
- Yuyou Qiu
- Department of Radiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yiying Gao
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Daojiang Yu
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China; The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Zhong
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Weichao Cai
- The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jiang Ji
- The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Fenghao Geng
- Radiation Medicine Department of Institute of Preventive Medicine, Fourth Military Medical University, Xi'an, China
| | - Guangyu Tang
- Department of Radiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huojun Zhang
- Department of Radiation Oncology, Shanghai Changhai Hospital, the Second Military Medical University, Shanghai, China
| | - Jianping Cao
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China; The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jie Zhang
- Radiation Medicine Department of Institute of Preventive Medicine, Fourth Military Medical University, Xi'an, China.
| | - Shuyu Zhang
- State Key Lab of Radiation Medicine and Protection, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China; West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China; Second Affiliated Hospital of Chengdu Medical College (China National Nuclear Corporation 416 Hospital), Chengdu, China.
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Barcena-Varela M, Colyn L, Fernandez-Barrena MG. Epigenetic Mechanisms in Hepatic Stellate Cell Activation During Liver Fibrosis and Carcinogenesis. Int J Mol Sci 2019; 20:E2507. [PMID: 31117267 PMCID: PMC6566358 DOI: 10.3390/ijms20102507] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/17/2019] [Accepted: 05/19/2019] [Indexed: 02/06/2023] Open
Abstract
Liver fibrosis is an essential component of chronic liver disease (CLD) and hepatocarcinogenesis. The fibrotic stroma is a consequence of sustained liver damage combined with exacerbated extracellular matrix (ECM) accumulation. In this context, activation of hepatic stellate cells (HSCs) plays a key role in both initiation and perpetuation of fibrogenesis. These cells suffer profound remodeling of gene expression in this process. This review is focused on the epigenetic alterations participating in the transdifferentiation of HSCs from the quiescent to activated state. Recent advances in the field of DNA methylation and post-translational modifications (PTM) of histones (acetylation and methylation) patterns are discussed here, together with altered expression and activity of epigenetic remodelers. We also consider recent advances in translational approaches, including the use of epigenetic marks as biomarkers and the promising antifibrotic properties of epigenetic drugs that are currently being used in patients.
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Affiliation(s)
| | - Leticia Colyn
- Hepatology Program, CIMA, University of Navarra, 31180 Pamplona, Spain.
| | - Maite G Fernandez-Barrena
- Hepatology Program, CIMA, University of Navarra, 31180 Pamplona, Spain.
- CIBERehd, Instituto de Salud Carlos III, 28029 Madrid, Spain.
- Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, 31180 Pamplona, Spain.
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22
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He Y, Ling S, Sun Y, Sheng Z, Chen Z, Pan X, Ma G. DNA methylation regulates α-smooth muscle actin expression during cardiac fibroblast differentiation. J Cell Physiol 2018; 234:7174-7185. [PMID: 30362530 DOI: 10.1002/jcp.27471] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/30/2018] [Indexed: 12/12/2022]
Abstract
Cardiac fibroblast (CF) differentiation to myofibroblasts expressing α-smooth muscle actin (α-SMA) plays a key role in cardiac fibrosis. Therefore, a study of the mechanism regulating α-SMA expression is a means to understanding the mechanism of fibroblast differentiation and cardiac fibrosis. Previous studies have shown that DNA methylation is associated with gene expression and is related to the development of tissue fibrosis. However, the mechanisms by which CF differentiation is regulated by DNA methylation remain unclear. Here, we explored the epigenetic regulation of α-SMA expression and its relevance in CF differentiation. In this study, we demonstrated that α-SMA was overexpressed and DNMT1 expression was downregulated in the infarct area after myocardial infarction. Treatment of CFs with transforming growth factor-β1 (TGF-β1 ) in vitro upregulated α-SMA expression via epigenetic modifications. TGF-β1 also inhibited DNMT1 expression and activity during CF differentiation. In addition, α-SMA expression was regulated by DNMT1. Conversely, increasing DNMT1 expression levels rescued the TGF-β1 -induced upregulation of α-SMA expression. Finally, TGF-β1 regulated α-SMA expression by inhibiting the DNMT1-mediated DNA methylation of the α-SMA promoter. Taken together, our research showed that inhibition of the DNMT1-mediated DNA methylation of the α-SMA promoter plays an essential role in CF differentiation. In addition, DNMT1 may be a new target for the prevention and treatment of myocardial fibrosis.
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Affiliation(s)
- Yanru He
- Department of Cardiology, Zhongda Hospital Affiliated to Southeast University, Nanjing, China.,Department of Cardiology, School of Medicine, Southeast University, Nanjing, China
| | - Sunkai Ling
- Department of Cardiology, School of Medicine, Southeast University, Nanjing, China
| | - Yuning Sun
- Department of Cardiology, Zhongda Hospital Affiliated to Southeast University, Nanjing, China.,Department of Cardiology, School of Medicine, Southeast University, Nanjing, China
| | - Zulong Sheng
- Department of Cardiology, Zhongda Hospital Affiliated to Southeast University, Nanjing, China
| | - Zhongpu Chen
- Department of Cardiology, Zhongda Hospital Affiliated to Southeast University, Nanjing, China
| | - Xiaodong Pan
- Department of Cardiology, Zhongda Hospital Affiliated to Southeast University, Nanjing, China
| | - Genshan Ma
- Department of Cardiology, Zhongda Hospital Affiliated to Southeast University, Nanjing, China
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23
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Ricard-Blum S, Baffet G, Théret N. Molecular and tissue alterations of collagens in fibrosis. Matrix Biol 2018; 68-69:122-149. [DOI: 10.1016/j.matbio.2018.02.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/02/2018] [Accepted: 02/02/2018] [Indexed: 02/07/2023]
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24
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Komatsu M, Kanda T, Urai H, Kurokochi A, Kitahama R, Shigaki S, Ono T, Yukioka H, Hasegawa K, Tokuyama H, Kawabe H, Wakino S, Itoh H. NNMT activation can contribute to the development of fatty liver disease by modulating the NAD + metabolism. Sci Rep 2018; 8:8637. [PMID: 29872122 PMCID: PMC5988709 DOI: 10.1038/s41598-018-26882-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/22/2018] [Indexed: 12/15/2022] Open
Abstract
Nicotinamide N-methyltransferase (NNMT) catalyses the reaction between nicotinamide (NAM) and S-adenosylmethionine to produce 1-methylnicotinamide and S-adenosylhomocysteine. Recently, this enzyme has also been reported to modulate hepatic nutrient metabolism, but its role in the liver has not been fully elucidated. We developed transgenic mice overexpressing NNMT to elucidate its role in hepatic nutrient metabolism. When fed a high fat diet containing NAM, a precursor for nicotinamide adenine dinucleotide (NAD)+, these NNMT-overexpressing mice exhibit fatty liver deterioration following increased expression of the genes mediating fatty acid uptake and decreased very low-density lipoprotein secretion. NNMT overactivation decreased the NAD+ content in the liver and also decreased gene activity related to fatty acid oxidation by inhibiting NAD+-dependent deacetylase Sirt3 function. Moreover, the transgenic mice showed liver fibrosis, with the induction of inflammatory and fibrosis genes. Induced NNMT expression decreased the tissue methylation capacity, thereby reducing methylation of the connective tissue growth factor (CTGF) gene promoter, resulting in increased CTGF expression. These data indicate that NNMT links the NAD+ and methionine metabolic pathways and promotes liver steatosis and fibrosis. Therefore, targeting NNMT may serve as a therapeutic strategy for treating fatty liver and fibrosis.
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Affiliation(s)
- Motoaki Komatsu
- Department of Internal Medicine, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
| | - Takeshi Kanda
- Department of Internal Medicine, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
| | - Hidenori Urai
- Department of Internal Medicine, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
| | - Arata Kurokochi
- Department of Internal Medicine, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
| | - Rina Kitahama
- Department of Internal Medicine, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
| | | | | | | | - Kazuhiro Hasegawa
- Department of Internal Medicine, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
| | - Hirobumi Tokuyama
- Department of Internal Medicine, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
| | | | - Shu Wakino
- Department of Internal Medicine, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan.
| | - Hiroshi Itoh
- Department of Internal Medicine, School of Medicine, Keio University, Shinjuku-ku, Tokyo, Japan
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25
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Karouzakis E, Raza K, Kolling C, Buckley CD, Gay S, Filer A, Ospelt C. Analysis of early changes in DNA methylation in synovial fibroblasts of RA patients before diagnosis. Sci Rep 2018; 8:7370. [PMID: 29743579 PMCID: PMC5943364 DOI: 10.1038/s41598-018-24240-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/26/2018] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an important epigenetic modification that is known to be altered in rheumatoid arthritis synovial fibroblasts (RASF). Here, we compared the status of promoter DNA methylation of SF from patients with very early RA with SF from patients with resolving arthritis, fully established RA and from non-arthritic patients. DNA was hybridized to Infinium Human methylation 450k and 850k arrays and differential methylated genes and pathways were identified. We could identify a significant number of CpG sites that differed between the SF of different disease stages, showing that epigenetic changes in SF occur early in RA development. Principal component analysis confirmed that the different groups of SF were separated according to their DNA methylation state. Furthermore, pathway analysis showed that important functional pathways were altered in both very early and late RASF. By focusing our analysis on CpG sites in CpG islands within promoters, we identified genes that have significant hypermethylated promoters in very early RASF. Our data show that changes in DNA methylation differ in RASF compared to other forms of arthritis and occur at a very early, clinically yet unspecific stage of disease. The identified differential methylated genes might become valuable prognostic biomarkers for RA development.
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Affiliation(s)
- Emmanuel Karouzakis
- Center of Experimental Rheumatology, Department of Rheumatology, University of Zurich, Zurich, CH-8952, Switzerland.
| | - Karim Raza
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, B15 2TT, UK.,Sandwell and West Birmingham Hospitals NHS Trust, West Bromwich, B71 4HJ, UK
| | | | - Christopher D Buckley
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Steffen Gay
- Center of Experimental Rheumatology, Department of Rheumatology, University of Zurich, Zurich, CH-8952, Switzerland
| | - Andrew Filer
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, B15 2TT, UK.,University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2 GW, UK
| | - Caroline Ospelt
- Center of Experimental Rheumatology, Department of Rheumatology, University of Zurich, Zurich, CH-8952, Switzerland
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Abstract
PURPOSE OF REVIEW Systemic sclerosis (SSc) is a heterogeneous autoimmune disease which has defined three hallmarks: Small vessel vasculopathy, production of autoantibodies and fibroblast dysfunction. The exact aetiology of the disease remains unknown, due to the complex nature of the cellular signalling pathways involved. However, there is strong and consistent evidence that the innate system, in particular toll-like receptor signalling, is contributing to the progression and perhaps onset of systemic sclerosis. In light of this evidence, this review examines the role of innate immunity in systemic sclerosis and where appropriate suggests avenues for therapeutic modulation in SSc. RECENT FINDINGS Multiple lines of evidence suggest that Toll-like receptors (TLRs) are dysregulated and emerging evidence suggests that many endogenous ligands are also elevated in the disease leading to 'sterile inflammation' and ultimately the induction of fibrosis. Currently, no effective therapy exists and exploiting the innate immune system perturbation may be one possible avenue. Innate immune dysregulation is key in SSc pathogenesis and may represent a novel target.
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27
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Zhang X, Hu M, Lyu X, Li C, Thannickal VJ, Sanders YY. DNA methylation regulated gene expression in organ fibrosis. Biochim Biophys Acta Mol Basis Dis 2017; 1863:2389-2397. [PMID: 28501566 PMCID: PMC5567836 DOI: 10.1016/j.bbadis.2017.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/08/2017] [Accepted: 05/09/2017] [Indexed: 01/05/2023]
Abstract
DNA methylation is a major epigenetic mechanism to regulate gene expression. Epigenetic regulation, including DNA methylation, histone modifications and RNA interference, results in heritable changes in gene expression independent of alterations in DNA sequence. Epigenetic regulation often occurs in response to aging and environment stimuli, including exposures and diet. Studies have shown that DNA methylation is critical in the pathogenesis of fibrosis involving multiple organ systems, contributing to significant morbidity and mortality. Aberrant DNA methylation can silence or activate gene expression patterns that drive the fibrosis process. Fibrosis is a pathological wound healing process in response to chronic injury. It is characterized by excessive extracellular matrix production and accumulation, which eventually affects organ architecture and results in organ failure. Fibrosis can affect a wide range of organs, including the heart and lungs, and have limited therapeutic options. DNA methylation, like other epigenetic process, is reversible, therefore regarded as attractive therapeutic interventions. Although epigenetic mechanisms are highly interactive and often reinforcing, this review discusses DNA methylation-dependent mechanisms in the pathogenesis of organ fibrosis, with focus on cardiac and pulmonary fibrosis. We discuss specific pro- and anti-fibrotic genes and pathways regulated by DNA methylation in organ fibrosis; we further highlight the potential benefits and side-effects of epigenetic therapies in fibrotic disorders.
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Affiliation(s)
- Xiangyu Zhang
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Min Hu
- Laboratory of Clinical Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Xing Lyu
- Laboratory of Clinical Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Chun Li
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Victor J Thannickal
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yan Y Sanders
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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