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Ren D, Ebert T, Kreher D, Ernst BLV, de Fallois J, Schmalz G. The Genetic Cross-Talk between Periodontitis and Chronic Kidney Failure Revealed by Transcriptomic Analysis. Genes (Basel) 2023; 14:1374. [PMID: 37510279 PMCID: PMC10379591 DOI: 10.3390/genes14071374] [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: 05/19/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Periodontitis and chronic kidney failure (CKF) are potentially related to each other. This bioinformatics analysis aimed at the identification of potential cross-talk genes and related pathways between periodontitis and CKF. Based on NCBI Gene Expression Omnibus (GEO), datasets GSE10334, GSE16134, and GSE23586 were extracted for periodontitis. A differential expression analysis (p < 0.05, |log2(FC)| > 0.5) was performed to assess deregulated genes (DEGs). CKF-related genes were extracted from DisGeNET and examined regarding their overlap with periodontitis-related DEGs. Cytoscape was used to construct and analyze a protein-protein interaction (PPI) network. Based on Cytoscape plugin MCODE and a LASSO regression analysis, the potential hub cross-talk genes were identified. Finally, a complex PPI of the hub genes was constructed. A total of 489 DEGs for periodontitis were revealed. With the 805 CKF-related genes, an overlap of 47 cross-talk genes was found. The PPI network of the potential cross-talk genes was composed of 1081 nodes and 1191 edges. The analysis with MCODE resulted in 10 potential hub genes, while the LASSO regression resulted in 22. Finally, five hub cross-talk genes, CCL5, FCGR3B, MMP-9, SAA1, and SELL, were identified. Those genes were significantly upregulated in diseased samples compared to controls (p ≤ 0.01). Furthermore, ROC analysis showed a high predictive value of those genes (AUC ≥ 73.44%). Potentially relevant processes and pathways were primarily related to inflammation, metabolism, and cardiovascular issues. In conclusion, five hub cross-talk genes, i.e., CCL5, FCGR3B, MMP-9, SAA1, and SELL, could be involved in the interplay between periodontitis and CKF, whereby primarily inflammation, metabolic, and vascular issues appear to be of relevance.
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Affiliation(s)
- Dandan Ren
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Thomas Ebert
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig, 04013 Leipzig, Germany
| | - Deborah Kreher
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, 04103 Leipzig, Germany
| | - Bero Luke Vincent Ernst
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, 04103 Leipzig, Germany
| | - Jonathan de Fallois
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig, 04013 Leipzig, Germany
| | - Gerhard Schmalz
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, 04103 Leipzig, Germany
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2
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Lagosz-Cwik KB, Melnykova M, Nieboga E, Schuster A, Bysiek A, Dudek S, Lipska W, Kantorowicz M, Tyrakowski M, Darczuk D, Kaczmarzyk T, Gilijamse M, de Vries TJ, Potempa J, Grabiec AM. Mapping of DNA methylation-sensitive cellular processes in gingival and periodontal ligament fibroblasts in the context of periodontal tissue homeostasis. Front Immunol 2023; 14:1078031. [PMID: 36776856 PMCID: PMC9909404 DOI: 10.3389/fimmu.2023.1078031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 01/04/2023] [Indexed: 01/27/2023] Open
Abstract
Interactions between gingival fibroblasts (GFs) and oral pathogens contribute to the chronicity of inflammation in periodontitis. Epigenetic changes in DNA methylation are involved in periodontitis pathogenesis, and recent studies indicate that DNA methyltransferase (DNMT) inhibitors may protect against epithelial barrier disruption and bone resorption. To assess the impact of DNMT inhibition on GFs, cells were cultured with decitabine (5-aza-2'-deoxycytidine, DAC) for 12 days to induce DNA hypomethylation. We observed several potentially detrimental effects of DAC on GF biological functions. First, extended treatment with DAC reduced GF proliferation and induced necrotic cell death. Second, DAC amplified Porphyromonas gingivalis- and cytokine-induced expression and secretion of the chemokine CCL20 and several matrix metalloproteinases (MMPs), including MMP1, MMP9, and MMP13. Similar pro-inflammatory effects of DAC were observed in periodontal ligament fibroblasts. Third, DAC upregulated intercellular adhesion molecule-1 (ICAM-1), which was associated with increased P. gingivalis adherence to GFs and may contribute to bacterial dissemination. Finally, analysis of DAC-induced genes identified by RNA sequencing revealed increased expression of CCL20, CCL5, CCL8, CCL13, TNF, IL1A, IL18, IL33, and CSF3, and showed that the most affected processes were related to immune and inflammatory responses. In contrast, the genes downregulated by DAC were associated with extracellular matrix and collagen fibril organization. Our observations demonstrate that studies of DNMT inhibitors provide important insights into the role of DNA methylation in cells involved in periodontitis pathogenesis. However, the therapeutic potential of hypomethylating agents in periodontal disease may be limited due to their cytotoxic effects on fibroblast populations and stimulation of pro-inflammatory pathways.
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Affiliation(s)
- Katarzyna B. Lagosz-Cwik
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Mariia Melnykova
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Elwira Nieboga
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Aureliusz Schuster
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Agnieszka Bysiek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Slawomir Dudek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Weronika Lipska
- Department of Periodontology, Preventive Dentistry and Oral Medicine, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
| | - Malgorzata Kantorowicz
- Department of Periodontology, Preventive Dentistry and Oral Medicine, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
| | - Michal Tyrakowski
- Chair of Oral Surgery, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
| | - Dagmara Darczuk
- Department of Periodontology, Preventive Dentistry and Oral Medicine, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
| | - Tomasz Kaczmarzyk
- Chair of Oral Surgery, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
| | - Marjolijn Gilijamse
- Department of Oral and Maxillofacial Surgery and Oral Pathology, Amsterdam University Medical Center (Amsterdam UMC), Amsterdam, Netherlands
- Department of Oral and Maxillofacial Surgery, OLVG Hospital, Amsterdam, Netherlands
| | - Teun J. de Vries
- Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States
| | - Aleksander M. Grabiec
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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3
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The Biology and Function of Tissue Inhibitor of Metalloproteinase 2 in the Lungs. Pulm Med 2022; 2022:3632764. [PMID: 36624735 PMCID: PMC9825218 DOI: 10.1155/2022/3632764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 01/02/2023] Open
Abstract
Tissue inhibitors of matrix metalloproteinases (TIMP) are a family of four endogenous proteins that primarily function to inhibit the activities of proteases such as the matrix metalloproteinases (MMP). Altered MMP/TIMP ratios are frequently observed in several human diseases. During aging and disease progression, the extracellular matrix (ECM) undergoes structural changes in which elastin and collagens serve an essential role. MMPs and TIMPs significantly influence the ECM. Classically, elevated levels of TIMPs are suggested to result in ECM accumulation leading to fibrosis, whereas loss of TIMP responses leads to enhanced matrix proteolysis. Here, we outline the known roles of the most abundant TIMP, TIMP2, in pulmonary diseases but also discuss future perspectives in TIMP2 research that could impact the lungs. TIMP2 directly inhibits MMPs, in particular MMP2, but TIMP2 is also required for the activation of MMP2 through its interaction with MMP14. The protease and antiprotease imbalance of MMPs and TIMPs are extensively studied in diseases but recent discoveries suggest that TIMPs, specifically, TIMP2 could play other roles in aging and inflammation processes.
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Shyamala N, Kongettira CL, Puranam K, Kupsal K, Kummari R, Padala C, Hanumanth SR. In silico identification of single nucleotide variations at CpG sites regulating CpG island existence and size. Sci Rep 2022; 12:3574. [PMID: 35246549 PMCID: PMC8897451 DOI: 10.1038/s41598-022-05198-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/03/2022] [Indexed: 12/20/2022] Open
Abstract
Genetic and epigenetic modifications of genes involved in the key regulatory pathways play a significant role in the pathophysiology and progression of multifactorial diseases. The present study is an attempt to identify single nucleotide variations (SNVs) at CpG sites of promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes influencing CpG island (CGI) existence and size associated with the pathophysiology of Diabetes mellitus, Coronary artery disease and Cancers. Promoter sequences located between -2000 to + 2000 bp were retrieved from the EPDnew database and predicted the CpG island using MethPrimer. Further, SNVs at CpG sites were accessed from NCBI, Ensembl while transcription factor (TF) binding sites were accessed using AliBaba2.1. CGI existence and size were determined for each SNV at CpG site with respect to wild type and variant allele by MethPrimer. A total of 200 SNVs at CpG sites were analyzed from the promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes. Of these, only 17 (8.5%) SNVs were found to influence the loss of CGI while 70 (35%) SNVs were found to reduce the size of CGI. It has also been found that 59% (10) of CGI abolishing SNVs are showing differences in binding of TFs. The findings of the study suggest that the candidate SNVs at CpG sites regulating CGI existence and size might influence the DNA methylation status and expression of genes involved in molecular pathways associated with several diseases. The insights of the present study may pave the way for new experimental studies to undertake challenges in DNA methylation, gene expression and protein assays.
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Affiliation(s)
- Nivas Shyamala
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Chaitra Lava Kongettira
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Kaushik Puranam
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Keerthi Kupsal
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Ramanjaneyulu Kummari
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Chiranjeevi Padala
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana State, India
| | - Surekha Rani Hanumanth
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India.
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5
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Cho YD, Kim WJ, Ryoo HM, Kim HG, Kim KH, Ku Y, Seol YJ. Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives. Clin Epigenetics 2021; 13:92. [PMID: 33902683 PMCID: PMC8077755 DOI: 10.1186/s13148-021-01074-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/12/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The Encyclopedia of DNA Elements (ENCODE) project has advanced our knowledge of the functional elements in the genome and epigenome. The aim of this article was to provide the comprehension about current research trends from ENCODE project and establish the link between epigenetics and periodontal diseases based on epigenome studies and seek the future direction. MAIN BODY Global epigenome research projects have emphasized the importance of epigenetic research for understanding human health and disease, and current international consortia show an improved interest in the importance of oral health with systemic health. The epigenetic studies in dental field have been mainly conducted in periodontology and have focused on DNA methylation analysis. Advances in sequencing technology have broadened the target for epigenetic studies from specific genes to genome-wide analyses. CONCLUSIONS In line with global research trends, further extended and advanced epigenetic studies would provide crucial information for the realization of comprehensive dental medicine and expand the scope of ongoing large-scale research projects.
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Affiliation(s)
- Young-Dan Cho
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Yeongeon-dong, Jongno-gu, Seoul, 03080, Korea
| | - Woo-Jin Kim
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Korea
| | - Hyun-Mo Ryoo
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Korea
| | - Hong-Gee Kim
- Biomedical Knowledge Engineering Laboratory, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Korea
| | - Kyoung-Hwa Kim
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Yeongeon-dong, Jongno-gu, Seoul, 03080, Korea
| | - Young Ku
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Yeongeon-dong, Jongno-gu, Seoul, 03080, Korea
| | - Yang-Jo Seol
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Yeongeon-dong, Jongno-gu, Seoul, 03080, Korea.
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6
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Zhang Y, Kuang W, Li D, Li Y, Feng Y, Lyu X, Huang GB, Lian JQ, Yang XF, Hu C, Xie Y, Xue S, Tan J. Natural Killer-Like B Cells Secreting Interleukin-18 Induces a Proinflammatory Response in Periodontitis. Front Immunol 2021; 12:641562. [PMID: 33679805 PMCID: PMC7930384 DOI: 10.3389/fimmu.2021.641562] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/27/2021] [Indexed: 12/23/2022] Open
Abstract
Natural killer-like B (NKB) cells, which are newly identified immune subsets, reveal a critical immunoregulatory property in the eradication of microbial infection via the secretion of interleukin (IL)-18. For the first time, this study investigated the role of NKB cells in secreting IL-18 in the pathogenesis of periodontitis. In this study, NKB cells' percentage and IL-18 concentration in peripheral blood and periodontium in periodontitis patients was measured using flow cytometry and ELISA. The role of IL-18 in regulating periodontal inflammation was examined in a Porphyromonas gingivalis (P. gingivalis)-induced periodontitis murine model. Peripheral and periodontal-infiltrating CD3-CD19+NKp46+ NKB cells, which were the main source of IL-18, were elevated and correlated with attachment loss in periodontitis patients. In vitro IL-18 stimulation promoted proinflammatory cytokine production in periodontal ligament cells. P. gingivalis infection induced elevation of IL-18 receptor in periodontium in a periodontitis murine model. IL-18 neutralization not only suppressed P. gingivalis-induced alveolar bone resorption, but also inhibited recruitment of antigen-non-specific inflammatory cells into the periodontium, probably via dampening expressions of cytokines, chemokines, and matrix metalloproteinases. NKB cells secreting IL-18 appeared to be an important mediator in the inflammatory response following intraoral P. gingivalis infection. These findings might be relevant to the development of immunotherapies for periodontitis.
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Affiliation(s)
- Ye Zhang
- Department of Orthodontics, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China.,Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Wei Kuang
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Department of Oral and Maxillofacial Surgery, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Danfeng Li
- Department of Orthodontics, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yu Li
- Department of Infectious Diseases, Shaanxi Provincial People's Hospital, The Affiliated Hospital of Xi'an Medical University, Xi'an, China
| | - Yi Feng
- Department of Orthodontics, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xinwei Lyu
- Department of Orthodontics, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Gao-Bo Huang
- Department of Hepatobiliary Surgery, Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jian-Qi Lian
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiao-Fei Yang
- Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Cheng Hu
- Department of Orthodontics, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yajuan Xie
- Department of Orthodontics, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Song Xue
- Department of Anesthesiology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jiali Tan
- Department of Orthodontics, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
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7
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Mei HX, Chen YL, Shi PL, Yang SR, Xu X, He JZ. [Advances in oral bacteria influencing host epigenetic regulation]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2020; 38:583-588. [PMID: 33085246 DOI: 10.7518/hxkq.2020.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Epigenetics refers to a steady change in the level of gene expression caused by non-DNA sequence changes. Microbes can modulate host inflammation through epigenetic pathways to evade or expend immune responses. As an important part of human microbes, oral bacteria also have various epigenetic regulation mechanisms to affect host inflammatory responses. This article reviews the common pathways of epigenetic regulation in microbe infection and the regulation of host epigenetics by using oral microbes to provide a reference for the study of epigenetic-related mechanisms in oral diseases.
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Affiliation(s)
- Hong-Xiang Mei
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yi-Lin Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Pei-Lei Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Si-Rui Yang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xin Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Jin-Zhi He
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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8
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Khouly I, Braun RS, Ordway M, Aouizerat BE, Ghassib I, Larsson L, Asa’ad F. The Role of DNA Methylation and Histone Modification in Periodontal Disease: A Systematic Review. Int J Mol Sci 2020; 21:ijms21176217. [PMID: 32867386 PMCID: PMC7503325 DOI: 10.3390/ijms21176217] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Despite a number of reports in the literature on the role of epigenetic mechanisms in periodontal disease, a thorough assessment of the published studies is warranted to better comprehend the evidence on the relationship between epigenetic changes and periodontal disease and its treatment. Therefore, the aim of this systematic review is to identify and synthesize the evidence for an association between DNA methylation/histone modification and periodontal disease and its treatment in human adults. A systematic search was independently conducted to identify articles meeting the inclusion criteria. DNA methylation and histone modifications associated with periodontal diseases, gene expression, epigenetic changes after periodontal therapy, and the association between epigenetics and clinical parameters were evaluated. Sixteen studies were identified. All included studies examined DNA modifications in relation to periodontitis, and none of the studies examined histone modifications. Substantial variation regarding the reporting of sample sizes and patient characteristics, statistical analyses, and methodology, was found. There was some evidence, albeit inconsistent, for an association between DNA methylation and periodontal disease. IL6, IL6R, IFNG, PTGS2, SOCS1, and TNF were identified as candidate genes that have been assessed for DNA methylation in periodontitis. While several included studies found associations between methylation levels and periodontal disease risk, there is insufficient evidence to support or refute an association between DNA methylation and periodontal disease/therapy in human adults. Further research must be conducted to identify reproducible epigenetic markers and determine the extent to which DNA methylation can be applied as a clinical biomarker.
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Affiliation(s)
- Ismael Khouly
- Department of Oral and Maxillofacial Surgery, College of Dentistry, New York University, New York, NY 10010, USA;
- Correspondence:
| | - Rosalie Salus Braun
- Department of Cariology and Comprehensive Care, College of Dentistry, New York University, New York, NY 10010, USA;
| | - Michelle Ordway
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Bradley Eric Aouizerat
- Department of Oral and Maxillofacial Surgery, College of Dentistry, New York University, New York, NY 10010, USA;
- Bluestone Center for Clinical Research, New York University College of Dentistry, New York, NY 10010, USA
| | - Iya Ghassib
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI 48104, USA;
| | - Lena Larsson
- Department of Periodontology, Institute of Odontology, The Sahlgrenska Academy at University of Gothenburg, SE-405 30 Göteborg, Sweden;
| | - Farah Asa’ad
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy at University of Gothenburg, SE-405 30 Göteborg, Sweden;
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9
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He J, Qin M, Chen Y, Hu Z, Xie F, Ye L, Hui T. Epigenetic regulation of matrix metalloproteinases in inflammatory diseases: a narrative review. Cell Biosci 2020; 10:86. [PMID: 32695308 PMCID: PMC7368751 DOI: 10.1186/s13578-020-00451-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/11/2020] [Indexed: 02/06/2023] Open
Abstract
With the acceleration of urbanization and aging and the change of lifestyle, inflammatory diseases have become one of the important threats to the health of the global population. Matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) are involved in the metabolism of extracellular matrix (ECM). They play a key role in inflammation-related diseases. Factors such as inflammation, oxidative stress and growth factors stimulate the production of MMPs with subsequent ECM remodeling. Recently, the studies of epigenetic regulation, including the ability to predict disease progression, important pathophysiological deficiencies as well as treatment methods have been extensively discussed. This article reviews the current studies on epigenetic alterations in MMPs during inflammatory response. It is likely to provide new insights into development of efficient medications of epigenetic therapy for inflammatory diseases.
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Affiliation(s)
- Jie He
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, No. 22, Zhongguancun South Avenue, Haidian District, Beijing, China
| | - Man Qin
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, No. 22, Zhongguancun South Avenue, Haidian District, Beijing, China
| | - Yingyi Chen
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, No. 22, Zhongguancun South Avenue, Haidian District, Beijing, China
| | - Ziqi Hu
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, No. 22, Zhongguancun South Avenue, Haidian District, Beijing, China
| | - Fei Xie
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, No. 22, Zhongguancun South Avenue, Haidian District, Beijing, China
| | - Ling Ye
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan China
| | - Tianqian Hui
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, No. 22, Zhongguancun South Avenue, Haidian District, Beijing, China
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10
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Azevedo AM, Carvalho Rocha LP, de Faria Amormino SA, Cavalieri Gomes C, Ornelas Dutra W, Santiago Gomez R, da Costa JE, Rocha Moreira P. DNA methylation profile of genes related to immune response in generalized periodontitis. J Periodontal Res 2020; 55:426-431. [PMID: 31943216 DOI: 10.1111/jre.12726] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/05/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND OBJECTIVE Epigenetic events, as the DNA methylation, may be related to development of inflammatory diseases. Due to the important role of host's response in the pathogenesis of periodontitis, the purpose of the present study was to investigate the methylation profile of genes related to immune response in gingival tissues from patients with generalized periodontitis (GP) compared to healthy individuals. METHODS Gingival tissues were collected from 20 individuals with GP and 20 healthy individuals. Genomic DNA was extracted and submitted to enzymatic digestions. An initial screening using a panel of genes involved with the response immune was performed in pools containing six samples of each group. Genes that presented different levels of methylation between the groups were selected for individual assays for validation. RESULTS The array results showed an unmethylated profile in the majority of genes evaluated in both groups. MALT1, LTB, and STAT5 genes presented a profile of partial methylation in the control compared with GP group. Validation individual assays using a larger number of samples (n = 20, each group) confirmed the hypomethylation of STAT5 in the GP group compared with control group (P < .001). CONCLUSION Generalized periodontitis is associated with hypomethylation of the STAT5 gene. Further studies are necessary to evaluate the functional impact these findings.
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Affiliation(s)
- Andrea Mara Azevedo
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luiz Paulo Carvalho Rocha
- Department of Morphology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Carolina Cavalieri Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Walderez Ornelas Dutra
- Department of Morphology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ricardo Santiago Gomez
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - José Eustáquio da Costa
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paula Rocha Moreira
- Department of Morphology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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11
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J.H. Martinez C, Villafuerte KR, Luchiari HR, O. Cruz J, Sales M, Palioto DB, Messora MR, Souza SL, Taba M, Ramos ES, Novaes AB. Effect of smoking on the DNA methylation pattern of the SOCS1 promoter in epithelial cells from the saliva of patients with chronic periodontitis. J Periodontol 2019; 90:1279-1286. [DOI: 10.1002/jper.18-0692] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/24/2019] [Accepted: 02/24/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Cristhiam J.H. Martinez
- Department of Oral & Maxillofacial Surgery, and PeriodontologySchool of Dentistry of Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Kelly R.V. Villafuerte
- Department of Oral & Maxillofacial Surgery, and PeriodontologySchool of Dentistry of Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Heloise R. Luchiari
- Laboratory of Epigenetics and ReproductionDepartment of GeneticsRibeirão Preto Medical SchoolUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Juliana O. Cruz
- Laboratory of Epigenetics and ReproductionDepartment of GeneticsRibeirão Preto Medical SchoolUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Mariana Sales
- Department of Oral & Maxillofacial Surgery, and PeriodontologySchool of Dentistry of Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Daniela B. Palioto
- Department of Oral & Maxillofacial Surgery, and PeriodontologySchool of Dentistry of Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Michel R. Messora
- Department of Oral & Maxillofacial Surgery, and PeriodontologySchool of Dentistry of Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Sergio L.S. Souza
- Department of Oral & Maxillofacial Surgery, and PeriodontologySchool of Dentistry of Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Mario Taba
- Department of Oral & Maxillofacial Surgery, and PeriodontologySchool of Dentistry of Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Ester S. Ramos
- Laboratory of Epigenetics and ReproductionDepartment of GeneticsRibeirão Preto Medical SchoolUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Arthur B. Novaes
- Department of Oral & Maxillofacial Surgery, and PeriodontologySchool of Dentistry of Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
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12
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de Oliveira Y, Lima RPA, Luna RCP, Monteiro MGCA, da Silva CSO, do Nascimento RAF, de Farias Lima KQ, Andrade E Silva AH, de Lima Ferreira FEL, de Toledo Vianna RP, de Moraes RM, de Oliveira NFP, de Almeida ATC, Silva AS, da Silva Diniz A, de Carvalho Costa MJ, da Conceição Rodrigues Gonçalves M. Decrease of the DNA methylation levels of the ADRB3 gene in leukocytes is related with serum folate in eutrophic adults. J Transl Med 2018; 16:152. [PMID: 29866117 PMCID: PMC5987450 DOI: 10.1186/s12967-018-1529-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/28/2018] [Indexed: 12/14/2022] Open
Abstract
Background DNA methylation has been evidenced as a potential epigenetic mechanism related to various candidate genes to development of obesity. Therefore, the objective of this study was to evaluate the DNA methylation levels of the ADRB3 gene by body mass index (BMI) in a representative adult population, besides characterizing this population as to the lipid profile, oxidative stress and food intake. Methods This was a cross-sectional population-based study, involving 262 adults aged 20–59 years, of both genders, representative of the East and West regions of the municipality of João Pessoa, Paraíba state, Brazil, in that were evaluated lifestyle variables and performed nutritional, biochemical evaluation and DNA methylation levels of the ADRB3 gene using high resolution melting method. The relationship between the study variables was performed using analyses of variance and multiple regression models. All results were obtained using the software R, 3.3.2. Results From the stratification of categories BMI, was observed a difference in the average variables values of age, waist-to-height ratio, waist-to-hip ratio, waist circumference, triglycerides and intake of trans fat, which occurred more frequently between the categories “eutrophic” and “obesity”. From the multiple regression analysis in the group of eutrophic adults, it was observed a negative relationship between methylation levels of the ADRB3 gene with serum levels of folic acid. However, no significant relation was observed among lipid profile, oxidative stress and food intake in individuals distributed in the three categories of BMI. Conclusions A negative relationship was demonstrated between methylation levels of the ADRB3 gene in eutrophic adults individuals with serum levels of folic acid, as well as with the independent gender of BMI, however, was not observed relation with lipid profile, oxidative stress and variables of food intake. Regarding the absence of relationship with methylation levels of the ADRB3 gene in the categories of overweight, mild and moderate obesity, the answer probably lies in the insufficient amount of body fat to initiate inflammatory processes and oxidative stress with a direct impact on methylation levels, what is differently is found most of the times in exacerbated levels in severe obesity. Electronic supplementary material The online version of this article (10.1186/s12967-018-1529-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yohanna de Oliveira
- Health Sciences Center (Centro de Ciências da Saúde), Departament of Nutrition, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil.
| | - Raquel Patrícia Ataíde Lima
- Health Sciences Center (Centro de Ciências da Saúde), Departament of Nutrition, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Rafaella Cristhine Pordeus Luna
- Health Sciences Center (Centro de Ciências da Saúde), Departament of Nutrition, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Mussara Gomes Cavalcanti Alves Monteiro
- Health Sciences Center (Centro de Ciências da Saúde), Departament of Nutrition, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Cássia Surama Oliveira da Silva
- Health Sciences Center (Centro de Ciências da Saúde), Departament of Nutrition, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Rayner Anderson Ferreira do Nascimento
- Center of Exact Sciences and Nature (Centro de Ciências Exatas e da Natureza), Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Keylha Querino de Farias Lima
- Health Sciences Center (Centro de Ciências da Saúde), Departament of Nutrition, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Ana Hermínia Andrade E Silva
- Departament of Statistics, Center of Exact Sciences and Nature (Centro de Ciências Exatas e da Natureza), Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Flávia Emília Leite de Lima Ferreira
- Health Sciences Center (Centro de Ciências da Saúde), Departament of Nutrition, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Rodrigo Pinheiro de Toledo Vianna
- Health Sciences Center (Centro de Ciências da Saúde), Departament of Nutrition, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Ronei Marcos de Moraes
- Departament of Statistics, Center of Exact Sciences and Nature (Centro de Ciências Exatas e da Natureza), Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Naila Francis Paulo de Oliveira
- Departament of Molecular Biology, Center of Exact Sciences and Nature (Centro de Ciências Exatas e da Natureza), Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Aléssio Tony Cavalcanti de Almeida
- Department of Economics, Center for Applied Social Sciences (Centro de Ciências Sociais Aplicadas), Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Alexandre Sérgio Silva
- Health Sciences Center (Centro de Ciências da Saúde), Departament of Nutrition, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Alcides da Silva Diniz
- Departament of Nutrition, Health Sciences Center (Centro de Ciências da Saúde), Federal University of Pernambuco (Universidade Federal de Pernambuco), Recife, Brazil
| | - Maria José de Carvalho Costa
- Health Sciences Center (Centro de Ciências da Saúde), Departament of Nutrition, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
| | - Maria da Conceição Rodrigues Gonçalves
- Health Sciences Center (Centro de Ciências da Saúde), Departament of Nutrition, Federal University of Paraíba (Universidade Federal da Paraíba), João Pessoa, Brazil
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