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Liu H, Ma L, Cao Z. DNA methylation and its potential roles in common oral diseases. Life Sci 2024; 351:122795. [PMID: 38852793 DOI: 10.1016/j.lfs.2024.122795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/26/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Oral diseases are among the most common diseases worldwide and are associated with systemic illnesses, and the rising occurrence of oral diseases significantly impacts the quality of life for many individuals. It is crucial to detect and treat these conditions early to prevent them from advancing. DNA methylation is a fundamental epigenetic process that contributes to a variety of diseases including various oral diseases. Taking advantage of its reversibility, DNA methylation becomes a viable therapeutic target by regulating various cellular processes. Understanding the potential role of this DNA alteration in oral diseases can provide significant advances and more opportunities for diagnosis and therapy. This article will review the biology of DNA methylation, and then mainly discuss the key findings on DNA methylation in oral cancer, periodontitis, endodontic disease, oral mucosal disease, and clefts of the lip and/or palate in the background of studies on global DNA methylation and gene-specific DNA methylation.
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Affiliation(s)
- Heyu Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, China
| | - Li Ma
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, China; Department of Periodontology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
| | - Zhengguo Cao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, China; Department of Periodontology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
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Rodas-Junco BA, Hernández-Solís SE, Serralta-Interian AA, Rueda-Gordillo F. Dental Stem Cells and Lipopolysaccharides: A Concise Review. Int J Mol Sci 2024; 25:4338. [PMID: 38673923 PMCID: PMC11049850 DOI: 10.3390/ijms25084338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Dental tissue stem cells (DTSCs) are well known for their multipotent capacity and regenerative potential. They also play an important role in the immune response of inflammatory processes derived from caries lesions, periodontitis, and gingivitis. These oral diseases are triggered by toxins known as lipopolysaccharides (LPS) produced by gram-negative bacteria. LPS present molecular patterns associated with pathogens and are recognized by Toll-like receptors (TLRs) in dental stem cells. In this review, we describe the effect of LPS on the biological behavior of DTSCs. We also focus on the molecular sensors, signaling pathways, and emerging players participating in the interaction of DTSCs with lipopolysaccharides. Although the scientific advances generated provide an understanding of the immunomodulatory potential of DTSCs, there are still new reflections to explore with regard to their clinical application in the treatment of oral inflammatory diseases.
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Affiliation(s)
- Beatriz A. Rodas-Junco
- CONAHCYT–Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingenierías, Universidad Autónoma de Yucatán, Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615 Chuburná de Hidalgo Inn, Mérida CP 97203, Yucatán, Mexico
- Laboratorio Traslacional de Células Troncales de la Cavidad Bucal, Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A #492-A X Av. Itzaes Costado Sur “Parque de la Paz”, Col. Centro, Mérida CP 97000, Yucatán, Mexico;
| | - Sandra E. Hernández-Solís
- Departamento de Microbiología Oral y Biología Molecular, Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A #492-A X Av. Itzaes Costado Sur “Parque de la Paz”, Col. Centro, Mérida CP 97000, Yucatán, Mexico; (S.E.H.-S.); (F.R.-G.)
| | - Angelica A. Serralta-Interian
- Laboratorio Traslacional de Células Troncales de la Cavidad Bucal, Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A #492-A X Av. Itzaes Costado Sur “Parque de la Paz”, Col. Centro, Mérida CP 97000, Yucatán, Mexico;
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingenierías, Universidad Autónoma de Yucatán, Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615 Chuburná de Hidalgo Inn, Mérida CP 97203, Yucatán, Mexico
| | - Florencio Rueda-Gordillo
- Departamento de Microbiología Oral y Biología Molecular, Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A #492-A X Av. Itzaes Costado Sur “Parque de la Paz”, Col. Centro, Mérida CP 97000, Yucatán, Mexico; (S.E.H.-S.); (F.R.-G.)
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3
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Ahmad P, Siqueira WL. Polymorphism of salivary proteins and risk of periodontal diseases: A systematic review and meta-analysis of clinical studies. J Dent 2024; 141:104804. [PMID: 38122885 DOI: 10.1016/j.jdent.2023.104804] [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: 10/19/2023] [Revised: 11/17/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023] Open
Abstract
OBJECTIVES The present systematic review and meta-analysis aimed to assess the association between salivary protein polymorphisms and the risk of periodontal diseases (PD). DATA The review incorporated cross-sectional, case-control, retrospective/prospective cohort, and randomized controlled trials assessing the influence of salivary protein polymorphisms on the risk of PD development were included in this review. SOURCES A thorough literature search was conducted across electronic databases, namely PubMed, Scopus, Embase, and Web of Science, without any restrictions on publication language and year. STUDY SELECTION A total of 168 studies were identified, of which 19 were eligible for inclusion. The risk of bias (RoB) assessment of the included studies was conducted at the methodological level. RESULTS A total of 16 studies were included. Polymorphism in the gene encoding TNF-α was found to be protective against gingivitis, while those encoding IL-1α and IL-1β were associated with developing gingivitis. Of the 42 proteins investigated, various gene polymorphisms were identified as protective or risk factors for periodontitis. Protective genes include CFH, DNMT1, OPRM1, and TLR9. Conversely, certain salivary protein genes (e.g., CRP, ERN1, FAM5C, IDH2, LTA, TET2, MPA, NLRP3, TLR4) were associated with periodontitis risk. Notably, IL6, MMP9, and MUC7 genes showed no association with PD, while MMP13 was linked to early implant loss. Overall, the meta-analysis found a statistically significant association between salivary proteins' polymorphisms and risk of PD. CONCLUSIONS Salivary protein polymorphisms significantly influence PD, revealing protective and risk-associated genotypes. Despite limitations, findings suggest therapeutic targets, emphasizing the complex genetics-periodontal health interplay. CLINICAL SIGNIFICANCE This study unveils salivary protein polymorphisms as pivotal factors in PD. Protective genes including CFH and TLR9, and risk-associated genes including CRP and TLR4, indicate a genetic basis for PD susceptibility.
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Affiliation(s)
- Paras Ahmad
- College of Dentistry, University of Saskatchewan, Saskatoon, S7N E5E, Saskatchewan, Canada
| | - Walter Luiz Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, S7N E5E, Saskatchewan, Canada.
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Almiñana-Pastor PJ, Alpiste-Illueca FM, Micó-Martinez P, García-Giménez JL, García-López E, López-Roldán A. MicroRNAs in Gingival Crevicular Fluid: An Observational Case-Control Study of Differential Expression in Periodontitis. Noncoding RNA 2023; 9:73. [PMID: 37987369 PMCID: PMC10660715 DOI: 10.3390/ncrna9060073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/01/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023] Open
Abstract
OBJECTIVES microRNAs (miRNAs) present in the gingival crevicular fluid (GCF) of patients with chronic periodontitis may serve as biomarkers of periodontal disease. The aim of this study was to perform a miRNA-sequencing study of all miRNAs present in GCF, comparing miRNA expression level profiles between advanced chronic periodontitis (CP) patients and healthy subjects (HS). MATERIALS AND METHODS GCF samples were collected from the single-rooted teeth of patients with severe CP (n = 11) and of HS (n = 12). miRNAs were isolated from GCF using an miRNeasy Serum/Plasma kit(Qiagen GmbH, Hilden, Germany). Reverse transcription polymerase chain reaction (qRT-PCR) was used to determine the expression levels of miRNA candidates involved in periodontal pathogenesis. RESULTS Of all the sequenced miRNAs, miR-199, miR-146a, miR-30a, and miR-338 were identified as best representing the CP patient samples. The validation study identified miR-199 as the most powerful biomarker used to define periodontitis. CONCLUSIONS Upon sequencing all known miRNAs in GCF for the first time, we uncovered several potential biomarkers to define periodontitis. Identifying miRNAS in the GCF using high-throughput approaches will clarify the role of these molecules in periodontitis and provide biomarkers with potential applications.
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Affiliation(s)
- Pedro J. Almiñana-Pastor
- Department of Stomatology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain; (P.J.A.-P.); (F.M.A.-I.); (P.M.-M.); (A.L.-R.)
| | - Francisco M. Alpiste-Illueca
- Department of Stomatology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain; (P.J.A.-P.); (F.M.A.-I.); (P.M.-M.); (A.L.-R.)
| | - Pablo Micó-Martinez
- Department of Stomatology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain; (P.J.A.-P.); (F.M.A.-I.); (P.M.-M.); (A.L.-R.)
| | - Jose Luis García-Giménez
- Biomedical Research Institute INCLIVA, Consortium Center for Biomedical Network Research on Rare Diseases, CIBERER-ISCIII, 46010 Valencia, Spain
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain;
| | - Eva García-López
- Department of Physiology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain;
| | - Andrés López-Roldán
- Department of Stomatology, Faculty of Medicine and Odontology, University of Valencia, 46010 Valencia, Spain; (P.J.A.-P.); (F.M.A.-I.); (P.M.-M.); (A.L.-R.)
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Asa'ad F, Petrenya N, Jönsson B, Holde GE, Oscarson N, Hadler-Olsen E, Vieira AR, Petzold M, Larsson L. Polymorphism in epigenetic regulating genes in relation to periodontitis, number of teeth, and levels of high-sensitivity C-reactive protein and glycated hemoglobin: The Tromsø Study 2015-2016. J Periodontol 2023; 94:1324-1337. [PMID: 37382343 DOI: 10.1002/jper.23-0108] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND The aim of this study was to investigate the association between periodontitis and four single nucleotide polymorphisms (SNPs) in genes involved in epigenetic regulation of DNA, and between these same SNPs and tooth loss, high-sensitivity C-reactive protein (hs-CRP), and glycated hemoglobin (HbA1c) levels. METHODS We included participants with periodontal examination (n = 3633, aged: 40-93 years) from the Tromsø Study seventh survey (2015-2016), Norway. Periodontitis was defined according to the 2017 AAP/EFP classification system as no periodontitis, grades A, B, or C. Salivary DNA was extracted and genotyping was performed to investigate four SNPs (rs2288349, rs35474715, rs34023346, and rs10010325) in the sequence of the genes DNMT1, IDH2, TET1, and TET2. Association between SNPs and periodontitis was analyzed by logistic regression adjusted for age, sex, and smoking. Subgroup analyses on participants aged 40-49 years were performed. RESULTS In participants aged 40-49 years, homozygous carriage of minor A-allele of rs2288349 (DNMT1) was associated with decreased susceptibility to periodontitis (grade A: odds ratio [OR] 0.55; p = 0.014: grade B/C OR 0.48; p = 0.004). The minor A-allele of rs10010325 (TET2) was associated with increased susceptibility to periodontitis (grade A OR 1.69; p = 0.035: grade B/C OR 1.90; p = 0.014). In the entire sample, homozygous carriage of the G-allele of rs35474715 (IDH2) was associated with having ≤24 teeth (OR 1.31; p = 0.018). Homozygous carriage of the A-allele of TET2 was associated with hs-CRP≥3 mg/L (OR 1.37; p = 0.025) and HbA1c≥6.5% (OR 1.62; p = 0.028). CONCLUSIONS In this Norwegian population, there were associations between polymorphism in genes related to DNA methylation and periodontitis, tooth loss, low-grade inflammation, and hyperglycemia.
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Affiliation(s)
- Farah Asa'ad
- Department of Biomaterials, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Oral Biochemistry, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Natalia Petrenya
- The Public Dental Health Service Competence Centre of Northern Norway, Tromsø, Norway
| | - Birgitta Jönsson
- The Public Dental Health Service Competence Centre of Northern Norway, Tromsø, Norway
- Department of Periodontology, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gro Eirin Holde
- The Public Dental Health Service Competence Centre of Northern Norway, Tromsø, Norway
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Nils Oscarson
- Clinic of Periodontology, The Public Dental Service, Region Västra Götaland, Skövde, Sweden
| | - Elin Hadler-Olsen
- The Public Dental Health Service Competence Centre of Northern Norway, Tromsø, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT the Artic University of Norway, Tromsø, Norway
| | - Alexandre R Vieira
- Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Max Petzold
- School of Public Health and Community Medicine, Institute of Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Lena Larsson
- Department of Periodontology, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Tian X, Zheng J, Luo Y, Wei C, Ma J, Wang D, Li K. Identification of abnormally methylated differentially expressed genes in chronic periodontitis by integrated bioinformatics analysis. Technol Health Care 2022; 31:809-819. [PMID: 36617795 DOI: 10.3233/thc-220137] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND DNA methylation plays a vital role as an epigenetic change that contributes to chronic periodontitis. OBJECTIVE This study aimed to integrate two methylation datasets (GSE173081 and GSE59962) and two gene expression datasets (GSE10334 and GES16134) to identify abnormally methylated differentially expressed genes related to chronic periodontitis. METHODS Differentially methylated genes were obtained. Functional enrichment analysis of DMGs was performed. The protein-protein interaction (PPI) network was constructed using STRING and Cytoscape software. Finally, the hub genes were selected from the PPI network by using CytoHubba. RESULTS In total, 122 hypomethylated and highly expressed genes were enriched in the biological mechanisms that are involved in the differentiation of extracellular matrix organization, extracellular structure organization, and cell chemotaxis. The three selected hub genes of the PPI network were IL1B, KDR, and MMP9. A total of 122 hypermethylated and lowly expressed genes were identified, and biological processes, such as cornification, epidermis development, skin development, and keratinocyte differentiation were enriched. CDSN DSG1, and KRT2 were identified as the top 3 hub genes of the PPI network. CONCLUSION Based on the comprehensive bioinformatics analysis, six hub genes (IL1B, KDR, MMP9, CDSN DSG1, and KRT2) were associated with chronic periodontitis. Our findings provide novel insights into the mechanisms underlying epigenetic changes in chronic periodontitis.
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Affiliation(s)
- Xiufen Tian
- Department of Stomatology, Liaocheng People's Hospital, Liaocheng, Shandong, China.,Department of Orthopaedics, School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Department of Stomatology, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Juan Zheng
- Department of Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, Shandong, China.,Department of Stomatology, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Yuanyuan Luo
- Department of Stomatology, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Chengshi Wei
- Department of Stomatology, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Jing Ma
- Department of Scientific Research, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Dawei Wang
- Department of Orthopaedics, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Keyi Li
- Department of Stomatology, Liaocheng People's Hospital, Liaocheng, Shandong, China
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Suzuki S, Yamada S. Epigenetics in susceptibility, progression, and diagnosis of periodontitis. JAPANESE DENTAL SCIENCE REVIEW 2022; 58:183-192. [PMID: 35754944 PMCID: PMC9218144 DOI: 10.1016/j.jdsr.2022.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/14/2022] [Accepted: 06/01/2022] [Indexed: 12/12/2022] Open
Abstract
Periodontitis is characterized by irreversible destruction of periodontal tissue. At present, the accepted etiology of periodontitis is based on a three-factor theory including pathogenic bacteria, host factors, and acquired factors. Periodontitis development usually takes a decade or longer and is therefore called chronic periodontitis (CP). To search for genetic factors associated with CP, several genome-wide association study (GWAS) analyses were conducted; however, polymorphisms associated with CP have not been identified. Epigenetics, on the other hand, involves acquired transcriptional regulatory mechanisms due to reversibly altered chromatin accessibility. Epigenetic status is a condition specific to each tissue and cell, mostly determined by the responses of host cells to stimulations by local factors, like bacterial inflammation, and systemic factors such as nutrition status, metabolic diseases, and health conditions. Significantly, epigenetic status has been linked with the onset and progression of several acquired diseases. Thus, epigenetic factors in periodontal tissues are attractive targets for periodontitis diagnosis and treatments. In this review, we introduce accumulating evidence to reveal the epigenetic background effects related to periodontitis caused by genetic factors, systemic diseases, and local environmental factors, such as smoking, and clarify the underlying mechanisms by which epigenetic alteration influences the susceptibility of periodontitis.
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Key Words
- 5mC, 5-methylcytocine
- AP, aggressive periodontitis
- ATAC-seq, assay for transposase-accessible chromatin sequencing
- CP, chronic periodontitis
- DNA methylation
- ECM, extracellular matrix
- Epigenetics
- Epigenome
- GWAS, genome-wide association study
- H3K27ac, acetylation of histone H3 lysine 27
- H3K27me3, trimethylation of histone H3 lysine 27
- H3K4me3, trimethylation of histone H3 lysine 4
- H3K9ac, histone H3 lysine 9
- HATs, histone acetyltransferases
- HDACs, histone deacetylases
- Histone modifications
- LPS, lipopolysaccharide
- PDL, periodontal ligament
- Periodontal ligament
- Periodontitis
- ceRNA, competing endogenous RNA
- lncRNAs, long ncRNAs
- m6A, N6-methyladenosine
- ncRNAs, non-coding RNAs
- sEV, small extracellular vesicles
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Affiliation(s)
- Shigeki Suzuki
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Satoru Yamada
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
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Wojciech Tynior, Joanna Katarzyna Strzelczyk. A Brief Landscape of Epigenetic Mechanisms in Dental Pathologies. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722050115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Larsson L, Kavanagh NM, Nguyen TVN, Castilho RM, Berglundh T, Giannobile WV. Influence of epigenetics on periodontitis and peri-implantitis pathogenesis. Periodontol 2000 2022; 90:125-137. [PMID: 35913702 DOI: 10.1111/prd.12453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Periodontitis is a disease characterized by tooth-associated microbial biofilms that drive chronic inflammation and destruction of periodontal-supporting tissues. In some individuals, disease progression can lead to tooth loss. A similar condition can occur around dental implants in the form of peri-implantitis. The immune response to bacterial challenges is not only influenced by genetic factors, but also by environmental factors. Epigenetics involves the study of gene function independent of changes to the DNA sequence and its associated proteins, and represents a critical link between genetic and environmental factors. Epigenetic modifications have been shown to contribute to the progression of several diseases, including chronic inflammatory diseases like periodontitis and peri-implantitis. This review aims to present the latest findings on epigenetic influences on periodontitis and to discuss potential mechanisms that may influence peri-implantitis, given the paucity of information currently available.
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Affiliation(s)
- Lena Larsson
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, USA.,Department of Periodontology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Nolan M Kavanagh
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Trang V N Nguyen
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, USA
| | - Rogerio M Castilho
- Department of Periodontics and Oral Medicine and Laboratory of Epithelial Biology, University of Michigan School of Dentistry, Ann Arbor, Michigan, USA
| | - Tord Berglundh
- Department of Periodontology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - William V Giannobile
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
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Bezerra B, Monajemzadeh S, Silva D, Pirih FQ. Modulating the Immune Response in Periodontitis. FRONTIERS IN DENTAL MEDICINE 2022. [DOI: 10.3389/fdmed.2022.879131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Periodontitis is a chronic inflammatory condition initiated by the accumulation of bacterial biofilm. It is highly prevalent and when left untreated can lead to tooth loss. The presence of bacterial biofilm is essential for the initiation of the inflammatory response but is not the sole initiator. Currently it is unknown which mechanisms drive the dysbiosis of the bacterial biofilm leading to the dysregulation of the inflammatory response. Other players in this equation include environmental, systemic, and genetic factors which can play a role in exacerbating the inflammatory response. Treatment of periodontal disease consists of removal of the bacterial biofilm with the goal of resolving the inflammatory response; however, this does not occur in every case. Understanding the way the inflammatory response does not return to a state of homeostasis has led investigators to consider both systemic and local pharmacological interventions. Nonetheless, a better understanding of the impact that genetics and environmental factors may have on the inflammatory response could be key to helping identify how inflammation can be modulated therefore stopping the destruction of the periodontium. In this article, we will explore the current evidence associating the microbial dysbiosis and the dysregulation of the immune response, potential mechanisms or pathways that may be targeted for the modulation of the inflammatory response, and discuss the advantages and drawbacks associated with local and systemic inflammatory modulation in the management of periodontal disease. This information will be valuable for those interested in understanding potential adjunct methods for managing periodontal diseases, but not limited to, dental professionals, clinical researchers and the public at large.
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Huang J, Zhou Y. Emerging role of epigenetic regulations in periodontitis: a literature review. Am J Transl Res 2022; 14:2162-2183. [PMID: 35559409 PMCID: PMC9091094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
Periodontitis is mainly initiated by periodontal pathogens including Porphyromonas gingivalis, and bad living habits such as smoking aggravate its incidence and severity. The development of periodontitis is closely related to the host's immune responses and the secretion of various cytokine networks. Moreover, periodontitis has an important connection with the development of systemic diseases. Recently, epigenetics which is a fast-developing hot research area has provided new insights into the research of various diseases including periodontitis. Epigenetics is an important supplement to the regulation of gene expression. The study of epigenetics is about causing heritable gene expression or cell phenotype changes through certain mechanisms without changing the DNA sequence. It mainly includes histone modification, DNA methylation, non-coding RNA and the latest research hotspot m6A RNA methylation. In the review, we comprehensively summarize the latest literature on the potential epigenetic regulations in various aspects of periodontitis.
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Affiliation(s)
- Jing Huang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan UniversityWuhan 430079, China
| | - Yi Zhou
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan UniversityWuhan 430079, China
- Department of Prosthodontics, Hospital of Stomatology, Wuhan UniversityWuhan 430079, China
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12
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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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13
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Hernández HG, Hernández-Castañeda AA, Pieschacón MP, Arboleda H. ZNF718, HOXA4, and ZFP57 are differentially methylated in periodontitis in comparison with periodontal health: Epigenome-wide DNA methylation pilot study. J Periodontal Res 2021; 56:710-725. [PMID: 33660869 DOI: 10.1111/jre.12868] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 02/07/2021] [Accepted: 02/14/2021] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To investigate the differences in the epigenomic patterns of DNA methylation in peripheral leukocytes between patients with periodontitis and gingivally healthy controls evaluating its functional meaning by functional enrichment analysis. BACKGROUND The DNA methylation profiling of peripheral leukocytes as immune-related tissue potentially relevant as a source of biomarkers between periodontitis patients and gingivally healthy subjects has not been investigated. METHODS A DNA methylation epigenome-wide study of peripheral leukocytes was conducted using the Illumina MethylationEPIC platform in sixteen subjects, eight diagnosed with periodontitis patients and eight age-matched and sex-matched periodontally healthy controls. A trained periodontist performed the clinical evaluation. Global DNA methylation was estimated using methylation-sensitive high-resolution melting in LINE1. Routine cell count cytometry and metabolic laboratory tests were also performed. The analysis of differentially methylated positions (DMPs) and differentially methylated regions (DMRs) was made using R/Bioconductor environment considering leukocyte populations assessed in both routine cell counts and using the FlowSorted.Blood.EPIC package. Finally, a DMP and DMR intersection analysis was performed. Functional enrichment analysis was carried out with the differentially methylated genes found in DMP. RESULTS DMP analysis identified 81 differentially hypermethylated genes and 21 differentially hypomethylated genes. Importantly, the intersection analysis showed that zinc finger protein 718 (ZNF718) and homeobox A4 (HOXA4) were differentially hypermethylated and zinc finger protein 57 (ZFP57) was differentially hypomethylated in periodontitis. The functional enrichment analysis found clearly immune-related ontologies such as "detection of bacterium" and "antigen processing and presentation." CONCLUSION The results of this study propose three new periodontitis-related genes: ZNF718, HOXA4, and ZFP57 but also evidence the suitability and relevance of studying leukocytes' DNA methylome for biological interpretation of systemic immune-related epigenetic patterns in periodontitis.
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Affiliation(s)
- Hernán G Hernández
- Faculty of Dentistry, Division of Health Sciences, Universidad Santo Tomás, Bucaramanga, Colombia
| | | | - Maria P Pieschacón
- Faculty of Dentistry, Division of Health Sciences, Universidad Santo Tomás, Bucaramanga, Colombia
| | - Humberto Arboleda
- Neurosciences Research Group, Faculty of Medicine and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
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14
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Jurdziński KT, Potempa J, Grabiec AM. Epigenetic regulation of inflammation in periodontitis: cellular mechanisms and therapeutic potential. Clin Epigenetics 2020; 12:186. [PMID: 33256844 PMCID: PMC7706209 DOI: 10.1186/s13148-020-00982-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
Epigenetic mechanisms, namely DNA and histone modifications, are critical regulators of immunity and inflammation which have emerged as potential targets for immunomodulating therapies. The prevalence and significant morbidity of periodontitis, in combination with accumulating evidence that genetic, environmental and lifestyle factors cannot fully explain the susceptibility of individuals to disease development, have driven interest in epigenetic regulation as an important factor in periodontitis pathogenesis. Aberrant promoter methylation profiles of genes involved in inflammatory activation, including TLR2, PTGS2, IFNG, IL6, IL8, and TNF, have been observed in the gingival tissue, peripheral blood or buccal mucosa from patients with periodontitis, correlating with changes in expression and disease severity. The expression of enzymes that regulate histone acetylation, in particular histone deacetylases (HDACs), is also dysregulated in periodontitis-affected gingival tissue. Infection of gingival epithelial cells, gingival fibroblasts and periodontal ligament cells with the oral pathogens Porphyromonas gingivalis or Treponema denticola induces alterations in expression and activity of chromatin-modifying enzymes, as well as site-specific and global changes in DNA methylation profiles and in histone acetylation and methylation marks. These epigenetic changes are associated with excessive production of inflammatory cytokines, chemokines, and matrix-degrading enzymes that can be suppressed by small molecule inhibitors of HDACs (HDACi) or DNA methyltransferases. HDACi and inhibitors of bromodomain-containing BET proteins ameliorate inflammation, osteoclastogenesis, and alveolar bone resorption in animal models of periodontitis, suggesting their clinical potential as host modulation therapeutic agents. However, broader application of epigenomic methods will be required to create a comprehensive map of epigenetic changes in periodontitis. The integration of functional studies with global analyses of the epigenetic landscape will provide critical information on the therapeutic and diagnostic potential of epigenetics in periodontal disease.
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Affiliation(s)
- Krzysztof T Jurdziński
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - 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, USA
| | - Aleksander M Grabiec
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
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15
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Jiang Y, Fu J, Du J, Luo Z, Guo L, Xu J, Liu Y. DNA methylation alterations and their potential influence on macrophage in periodontitis. Oral Dis 2020; 28:249-263. [PMID: 32989880 DOI: 10.1111/odi.13654] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/03/2020] [Accepted: 09/20/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVES To explore how various methylation mechanisms function and affect macrophages in periodontitis, with an aim of getting a comprehensive understanding of pathogenesis of the disease. SUBJECT Alterations in DNA methylation are associated with different periodontitis susceptible factors and disrupt immunity homeostasis. The host's immune response to stimulus plays a vital role in the progression of periodontitis. Macrophages are key immune cells of immune system. They act as critical regulators in maintaining issue homeostasis with their nature of high plasticity. The altered methylation status of genes may cause abnormal expression of proteins in the progress of periodontitis, thus, exert potential influence on macrophages. RESULTS Certain genes are selectively activated or silenced due to the changes in the methylation status, which causes the alteration of the expression level of cytokines/chemokines, signal molecules, extracellular matrix molecules, leads to the change in local microenvironment, affects activation states of immune cells including macrophages, thus influences the host immune response during periodontitis.. This results in differential susceptibility and therapeutic outcome. CONCLUSION DNA methylation alteration may cause aberrant expression level of genes associated with periodontal diseases, thus results in deregulation of macrophages, which supports the prospect of using DNA methylation-related parameter as a new biomarker for the diagnosis and treatment of periodontitis.
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Affiliation(s)
- Yiyang Jiang
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, PR China
| | - Jingfei Fu
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, PR China
| | - Juan Du
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, PR China
| | - Zhenhua Luo
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, PR China
| | - Lijia Guo
- Department of Orthodontics, School of Stomatology, Capital Medical University, Beijing, PR China
| | - Junji Xu
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, PR China
| | - Yi Liu
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, PR China
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16
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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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17
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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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Almiñana-Pastor PJ, Boronat-Catalá M, Micó-Martinez P, Bellot-Arcís C, Lopez-Roldan A, Alpiste-Illueca FM. Epigenetics and periodontics: A systematic review. Med Oral Patol Oral Cir Bucal 2019; 24:e659-e672. [PMID: 31433392 PMCID: PMC6764711 DOI: 10.4317/medoral.23008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023] Open
Abstract
Background Despite decades of research, our knowledge of several important aspects of periodontal pathogenesis remains incomplete. Epigenetics allows to perform dynamic analysis of different variations in gene expression, providing this great advantage to the static measurement provided by genetic markers. The aim of this systematic review is to analyze the possible relationships between different epigenetic mechanisms and periodontal diseases, and to assess their potential use as biomarkers of periodontitis. Material and Methods A systematic search was conducted in six databases using MeSH and non-MeSH terms. The review fulfilled PRISMA criteria (Preferred Reporting Items for Systematic reviews and Meta-analysis). Results 36 studies met the inclusion criteria. Due to the heterogeneity of the articles, it was not possible to conduct quantitative analysis. Regarding qualitative synthesis, however, it was found that epigenetic mechanisms may be used as biological markers of periodontal disease, as their dynamism and molecular stability makes them a valuable diagnostic tool. Conclusions Epigenetic markers alter gene expression, producing either silencing or over-expression of molecular transcription that respond to the demands of the cellular surroundings. Gingival crevicular fluid collection is a non-invasive and simple procedure, which makes it an ideal diagnostic medium for detection of both oral and systemic issues. Although further research is needed, this seems to be a promising field of research in the years to come. Key words:Epigenetics, periodontitis, DNA methylation, miRNA, epigenetic biomarker, periodontal diseases.
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19
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Daubert D, Pozhitkov A, Safioti L, Kotsakis G. Association of Global DNA Methylation to Titanium and Peri-Implantitis: A Case-Control Study. JDR Clin Trans Res 2019; 4:284-291. [DOI: 10.1177/2380084418822831] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- D.M. Daubert
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | - A.E. Pozhitkov
- Department of Restorative Dentistry, University of Washington, Seattle, WA, USA
| | - L.M. Safioti
- Department of Periodontics, University of Washington, Seattle, WA, USA
| | - G.A. Kotsakis
- Department of Periodontics, University of Washington, Seattle, WA, USA
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20
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Matsushita J, Okamura K, Nakabayashi K, Suzuki T, Horibe Y, Kawai T, Sakurai T, Yamashita S, Higami Y, Ichihara G, Hata K, Nohara K. The DNA methylation profile of liver tumors in C3H mice and identification of differentially methylated regions involved in the regulation of tumorigenic genes. BMC Cancer 2018; 18:317. [PMID: 29566670 PMCID: PMC5865360 DOI: 10.1186/s12885-018-4221-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/13/2018] [Indexed: 12/11/2022] Open
Abstract
Background C3H mice have been frequently used in cancer studies as animal models of spontaneous liver tumors and chemically induced hepatocellular carcinoma (HCC). Epigenetic modifications, including DNA methylation, are among pivotal control mechanisms of gene expression leading to carcinogenesis. Although information on somatic mutations in liver tumors of C3H mice is available, epigenetic aspects are yet to be clarified. Methods We performed next generation sequencing-based analysis of DNA methylation and microarray analysis of gene expression to explore genes regulated by DNA methylation in spontaneous liver tumors of C3H mice. Overlaying these data, we selected cancer-related genes whose expressions are inversely correlated with DNA methylation levels in the associated differentially methylated regions (DMRs) located around transcription start sites (TSSs) (promoter DMRs). We further assessed mutuality of the selected genes for expression and DNA methylation in human HCC using the Cancer Genome Atlas (TCGA) database. Results We obtained data on genome-wide DNA methylation profiles in the normal and tumor livers of C3H mice. We identified promoter DMRs of genes which are reported to be related to cancer and whose expressions are inversely correlated with the DNA methylation, including Mst1r, Slpi and Extl1. The association between DNA methylation and gene expression was confirmed using a DNA methylation inhibitor 5-aza-2′-deoxycytidine (5-aza-dC) in Hepa1c1c7 cells and Hepa1-6 cells. Overexpression of Mst1r in Hepa1c1c7 cells illuminated a novel downstream pathway via IL-33 upregulation. Database search indicated that gene expressions of Mst1r and Slpi are upregulated and the TSS upstream regions are hypomethylated also in human HCC. These results suggest that DMRs, including those of Mst1r and Slpi, are involved in liver tumorigenesis in C3H mice, and also possibly in human HCC. Conclusions Our study clarified genome wide DNA methylation landscape of C3H mice. The data provide useful information for further epigenetic studies of mice models of HCC. The present study particularly proposed novel DNA methylation-regulated pathways for Mst1r and Slpi, which may be applied not only to mouse HCC but also to human HCC. Electronic supplementary material The online version of this article (10.1186/s12885-018-4221-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junya Matsushita
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan.,Graduate School of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Kazuyuki Okamura
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, Tokyo, Japan
| | - Takehiro Suzuki
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan
| | - Yu Horibe
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, Tokyo, Japan
| | - Toshihiro Sakurai
- Graduate School of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | | | - Yoshikazu Higami
- Graduate School of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Gaku Ichihara
- Graduate School of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, Tokyo, Japan
| | - Keiko Nohara
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan.
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Li X, Lu J, Teng W, Zhao C, Ye X. Quantitative Evaluation of MMP-9 and TIMP-1 Promoter Methylation in Chronic Periodontitis. DNA Cell Biol 2018; 37:168-173. [PMID: 29298087 DOI: 10.1089/dna.2017.3948] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this study, we investigated the promoter DNA methylation (DNAm) status of the MMP-9 and TIMP-1 genes in patients with chronic periodontitis to evaluate disease progression. Using pyrosequencing technology, DNAm levels of MMP-9 and TIMP-1 CpG islands were measured in 88 chronic periodontitis patients and 15 healthy controls. We found a positive correlation between methylation levels of MMP-9 CpG islands and the severity of chronic periodontitis. Methylated CpG islands were also closely associated with the duration of chronic periodontitis. Moreover, female patients exhibited lower methylation levels of MMP-9 but higher methylation levels of TIMP-1 compared with male patients, and the methylation levels of TIMP-1 gradually decreased with age. The findings of gender disparity in the DNAm of MMP-9 and TIMP-1 genes provide novel insights into chronic periodontitis.
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Affiliation(s)
- Xiting Li
- 1 Department of Periodontology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University , Guangzhou, People's Republic of China .,2 Department of Regenerative Medicine, Guangdong Provincial Key Laboratory of Stomatology , Guangzhou, People's Republic of China
| | - Jiaxuan Lu
- 1 Department of Periodontology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University , Guangzhou, People's Republic of China .,2 Department of Regenerative Medicine, Guangdong Provincial Key Laboratory of Stomatology , Guangzhou, People's Republic of China
| | - Wei Teng
- 1 Department of Periodontology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University , Guangzhou, People's Republic of China .,2 Department of Regenerative Medicine, Guangdong Provincial Key Laboratory of Stomatology , Guangzhou, People's Republic of China
| | - Chuanjiang Zhao
- 1 Department of Periodontology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-Sen University , Guangzhou, People's Republic of China .,2 Department of Regenerative Medicine, Guangdong Provincial Key Laboratory of Stomatology , Guangzhou, People's Republic of China
| | - Xiaolei Ye
- 3 Department of Pharmacology, Ningbo Institute of Medical Sciences, Ningbo University , Ningbo, People's Republic of China
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Abstract
Purpose The focus of this review is to provide an overview of the recent findings on the role of epigenetic mechanisms in periodontal disease, including disease susceptibility, progression, and as potential treatment options. Recent Findings The findings on the influence of oral pathogens on epigenetic regulation of pathogen recognition receptors, such as Toll-like receptors, as well as pro-inflammatory cytokines suggest an important role for epigenetics in the regulation of the host immune response. Recent studies also show that the epigenetic pattern in periodontitis lesions differ from that of healthy and gingivitis tissue. In addition, these patterns differ between tissues in the same individual. Research is also indicating a role for both DNA methylation and histone acetylation on cells osteogenic differentiation and bone regeneration. Summary Knowledge of epigenetic pattern in periodontal diseases may add not only to the knowledge of susceptibility of the disease but may also be a diagnostic tool to identify patients at risk to develop the severe form of periodontitis. In addition, recent research within gene therapy and tissue engineering indicate a role for epigenetics also to improve regeneration of periodontal tissues.
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Affiliation(s)
- Lena Larsson
- Department of Periodontology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Box 450, SE-405 30 Gothenburg, Sweden
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23
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Cho YD, Kim PJ, Kim HG, Seol YJ, Lee YM, Ku Y, Rhyu IC, Ryoo HM. Transcriptomics and methylomics in chronic periodontitis with tobacco use: a pilot study. Clin Epigenetics 2017; 9:81. [PMID: 28811843 PMCID: PMC5553745 DOI: 10.1186/s13148-017-0381-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 08/03/2017] [Indexed: 12/17/2022] Open
Abstract
Background Accumulating evidence suggests that tobacco smoking affects the susceptibility to and severity of chronic periodontitis. Epigenetics may explain the role of smoking in the development and progress of periodontal disease. In this study, we performed transcriptomic and methylomic analyses of non-periodontitis and periodontitis-affected gingival tissues according to smoking status. Methods Human gingival tissues were obtained from 20 patients, including non-smokers with and without periodontitis (n = 5 per group) and smokers with and without periodontitis (n = 5 per group). Total RNA and genomic DNA were isolated, and their quality was validated according to strict standards. The Illumina NextSeq500 sequencing system was used to generate transcriptome and methylome datasets. Results Comprehensive analysis, including between-group correlation, differential gene expression, DNA methylation, gene set enrichment, and protein-protein interaction, indicated that smoking may change the transcription and methylation states of extracellular matrix (ECM) organization-related genes, which exacerbated the periodontal condition. Conclusions Our results suggest that smoking-related changes in DNA methylation patterns and subsequent alterations in the expression of genes coding for ECM components may be causally related to the increased susceptibility to periodontitis in smokers as they could influence ECM organization, which in turn may have an effect on disease characteristics. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0381-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Young-Dan Cho
- Department of Periodontology, School of Dentistry, Seoul National University, 101 Daehak-no, Jongno-gu, Seoul, 03080 South Korea.,Department of Molecular Genetics, School of Dentistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Pil-Jong Kim
- Department of Dental Services Management and Informatics, School of Dentistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Hong-Gee Kim
- Department of Dental Services Management and Informatics, School of Dentistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Yang-Jo Seol
- Department of Periodontology, School of Dentistry, Seoul National University, 101 Daehak-no, Jongno-gu, Seoul, 03080 South Korea
| | - Yong-Moo Lee
- Department of Periodontology, School of Dentistry, Seoul National University, 101 Daehak-no, Jongno-gu, Seoul, 03080 South Korea
| | - Young Ku
- Department of Periodontology, School of Dentistry, Seoul National University, 101 Daehak-no, Jongno-gu, Seoul, 03080 South Korea
| | - In-Chul Rhyu
- Department of Periodontology, School of Dentistry, Seoul National University, 101 Daehak-no, Jongno-gu, Seoul, 03080 South Korea
| | - Hyun-Mo Ryoo
- Department of Molecular Genetics, School of Dentistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
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Fipronil-induced enantioselective developmental toxicity to zebrafish embryo-larvae involves changes in DNA methylation. Sci Rep 2017; 7:2284. [PMID: 28536466 PMCID: PMC5442102 DOI: 10.1038/s41598-017-02255-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 03/28/2017] [Indexed: 01/01/2023] Open
Abstract
Enantioselectivity in the aquatic toxicity of chiral pesticides has been widely investigated, while the molecular mechanisms remain unclear. Thus far, few studies has focused on genomic expression related to selective toxicity in chiral pesticide, nor on epigenetic changes, such as DNA methylation. Here, we used fipronil, a broad-spectrum insecticide, as a model chemical to probe its enantioselective toxicity in embryo development. Our results showed that S-(+)-fipronil caused severer developmental toxicity in embryos. The MeDIP-Seq analysis demonstrated that S-(+)-fipronil dysregulated a higher level of genomic DNA methylation than R-(−)-fipronil. Gene Ontology analysis revealed that S-(+)-fipronil caused more differentially methylated genes that are involved in developmental processes. Compared with R-(−)-fipronil, S-(+)-fipronil significantly disrupted 7 signaling pathways (i.e., mitogen-activated protein kinases, tight junctions, focal adhesion, transforming growth factor-β, vascular smooth muscle contraction, and the hedgehog and Wnt signaling pathways) by hyper-methylation of developmentally related genes, which further induced the downregulation of those genes. Together, these data suggest that differences in DNA methylation may partly explain the enantioselectivity of fipronil to zebrafish embryos. The application of epigenetics to investigate the enantioselective toxicity mechanism of chiral chemicals would provide a further understanding of their stereoselectivity biological effects.
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Razzouk S. Regulatory elements and genetic variations in periodontal diseases. Arch Oral Biol 2016; 72:106-115. [PMID: 27569042 DOI: 10.1016/j.archoralbio.2016.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/11/2016] [Accepted: 08/16/2016] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Current evidence suggests that many GWAS and IL1 SNPs are associated with periodontal diseases but their functional role remains ambiguous. Therefore, it is imperative to elucidate the molecular pathways through which these SNPs might act on the development of the disease. The purpose of this review was to highlight the regulatory elements of noncoding regions of the genome and provide insights on the functional role of periodontitis-associated GWAS and IL1 SNPs. DESIGN A search was performed using ENCODE data available on different browsers. RESULTS GWAS and IL1 SNPs overlap DNase I hypersensitivity sites, histone modifications and transcription binding sites. Some of these noncoding variants influenced the transcription activity of inflammatory genes. CONCLUSION SNPs associated with periodontal diseases may contribute to the development of the disorder through their functional roles. Unraveling the character of genetic components might explain the diversity of clinical phenotypes among population groups as well as disease susceptibility.
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Affiliation(s)
- Sleiman Razzouk
- Adjunct faculty, Department of Periodontology and Implant Dentistry, New York University College of Dentistry, New York, United States; Private Practice, Beirut, Lebanon.
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Yin L, Zheng LJ, Jiang X, Liu WB, Han F, Cao J, Liu JY. Effects of Low-Dose Diethylstilbestrol Exposure on DNA Methylation in Mouse Spermatocytes. PLoS One 2015; 10:e0143143. [PMID: 26588706 PMCID: PMC4654501 DOI: 10.1371/journal.pone.0143143] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/30/2015] [Indexed: 12/31/2022] Open
Abstract
Evidence from previous studies suggests that the male reproductive system can be disrupted by fetal or neonatal exposure to diethylstilbestrol (DES). However, the molecular basis for this effect remains unclear. To evaluate the effects of DES on mouse spermatocytes and to explore its potential mechanism of action, the levels of DNA methyltransferases (DNMTs) and DNA methylation induced by DES were detected. The results showed that low doses of DES inhibited cell proliferation and cell cycle progression and induced apoptosis in GC-2 cells, an immortalized mouse pachytene spermatocyte-derived cell line, which reproduces primary cells responses to E2. Furthermore, global DNA methylation levels were increased and the expression levels of DNMTs were altered in DES-treated GC-2 cells. A total of 141 differentially methylated DNA sites were detected by microarray analysis. Rxra, an important component of the retinoic acid signaling pathway, and mybph, a RhoA pathway-related protein, were found to be hypermethylated, and Prkcd, an apoptosis-related protein, was hypomethylated. These results showed that low-dose DES was toxic to spermatocytes and that DNMT expression and DNA methylation were altered in DES-exposed cells. Taken together, these data demonstrate that DNA methylation likely plays an important role in mediating DES-induced spermatocyte toxicity in vitro.
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Affiliation(s)
- Li Yin
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Li-juan Zheng
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
- Gansu People’s Hospital, Lanzhou, China
| | - Xiao Jiang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Wen-bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
| | - Jin-yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, China
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