Class I and II histone deacetylase expression in human chronic periodontitis gingival tissue

Histone deacetylases and their inhibitors in inflammatory diseases

Despite considerable research efforts, inflammatory diseases remain a heavy burden on human health, causing significant economic losses annually. Histone deacetylases (HDACs) play a significant role in regulating inflammation (via histone and non-histone protein deacetylation) and chromatin structure and gene expression regulation. Herein, we present a detailed description of the different HDACs and their functions and analyze the role of HDACs in inflammatory diseases, including pro-inflammatory cytokine production reduction, immune cell function modulation, and anti-inflammatory cell activity enhancement. Although HDAC inhibitors have shown broad inflammatory disease treatment potentials, their clinical applicability remains limited because of their non-specific effects, adverse effects, and drug resistance. With further research and insight, these inhibitors are expected to become important tools for the treatment of a wide range of inflammatory diseases. This review aims to explore the mechanisms and application prospects of HDACs and their inhibitors in multiple inflammatory diseases.

Histone acetylation, BET proteins, and periodontal inflammation

Periodontitis is one of the most common inflammatory diseases in humans. The susceptibility to periodontitis is largely determined by the host response, and the severity of inflammation predicts disease progression. Upon microbial insults, host cells undergo massive changes in their transcription program to trigger an appropriate response (inflammation). It is not surprising that successful keystone pathogens have developed specific mechanisms to manipulate the gene expression network in host cells. Emerging data has indicated that epigenetic regulation plays a significant role in inflammation. Acetylation of lysine residues on histones is a major epigenetic modification of chromatin, highly associated with the accessibility of chromatin and activation of transcription. Specific histone acetylation patterns are observed in inflammatory diseases including periodontitis. Bromo- and extraterminal domain (BET) proteins recognize acetylated histones and then recruit transcription factors and transcription elongation complexes to chromatin. BET proteins are regulated in inflammatory diseases and small molecules blocking the function of BET proteins are promising "epi-drugs" for treating inflammatory diseases.

Effect of non-surgical periodontal therapy on salivary histone deacetylases expression: A prospective clinical study

AIM

To evaluate the effect of non-surgical periodontal therapy (NSPT) on salivary histone deacetylases (HDACs) gene expression in patients with Stage III-IV periodontitis at baseline and at 3 and 6 months post NSPT treatment.

MATERIALS AND METHODS

Twenty patients completed the study. Periodontitis (as well as the corresponding staging and grading) was diagnosed according to the 2017 World Workshop Classification. Clinical measures were recorded and whole unstimulated saliva was collected at baseline and at 3 and 6 months after NSPT. The expression of 11 HDACs was determined using reverse-transcription PCR, and the respective changes over time were evaluated.

RESULTS

Six months after NSPT, significant improvements in all clinical periodontal parameters were observed, concomitant with significant up-regulation of HDAC2, 4, 6, 8, 9 and 11 expressions. Subgroup analyses of non-responders and responders revealed no significant differences in HDACs mRNA expression between groups at any time point.

CONCLUSIONS

This prospective clinical study identified longitudinal changes in salivary HDACs expression in response to NSPT, which provides new insights into the epigenetic mechanisms underlying the pathobiology of periodontitis and creates avenues for the discovery of novel biomarkers.

Immunolocalization patterns of histone-deacetylases in salivary glands of mice during postnatal development

OBJECTIVE

Histone-deacetylases (HDACs) are epigenetic modulators involved in the control of gene expression. No data are available on the expression or subcellular localization of HDACs in salivary glands. The present study aims to examine the subcellular distribution of HDACs in salivary glands during postnatal development.

DESIGN

The major salivary glands of C57/BL6 mice were separately removed at 10, 25, 30,60 and 90 days after birth. Hematoxylin-eosin (H&E) and immunohistochemical staining were performed for HDACs. Gene Expression of HDACs in C57BL/6. NOD-Aec1Aec2 mice salivary glands during the development of Sjögren's syndrome-like illness were also analyzed by using the gene expression datasets (GSE 15640).

RESULTS

In the mice salivary gland, HDACs were found to have different localization patterns at various stages of development (10, 25, 30, 60, and 90 days). Apart from HDAC6, ductal cells of salivary glands were the primary sites for HDAC localization. HDAC2, 8, 5, 10 and 11 were expressed at high levels in the salivary gland after birth while HDAC6 showed no expression during postnatal development. This suggests that these HDAC subtypes may have different roles in salivary gland function. In the context of Sjögren's syndrome-like illness, HDAC 2, 8 and 10 showed low expression while HDAC1, 6,5,3 and 11 had relatively high expression in the salivary gland.

CONCLUSIONS

This study has provided an important reference for understanding the spatiotemporal-specific expression of HDACs in the salivary gland. These results offer new clues for the experimenters and hold promise for developing innovative therapeutic strategies for salivary gland-related diseases.

Role of histone deacetylase 9 in human periodontal ligament stem cells autophagy in a tumour necrosis factor α-induced inflammatory environment

Histone deacetylases (HDACs) play important roles in the post-translational modification of histones, which can affect the biological properties of cells, thereby altering disease progression and outcomes. However, it remains unclear how HDAC9, a class II HDAC, affects the autophagy of human periodontal ligament stem cells (hPDLSCs). We aimed to identify its role in autophagy in hPDLSCs in an inflammatory environment and to explore the potential regulatory mechanisms. A rat periodontitis model was induced by ligating the molars with silk thread. Expression of autophagy-related genes and TNF-α was elevated in this model. TNF-α was used to stimulate hPDLSCs to establish an inflammatory environment. In the TNF-α-stimulated hPDLSCs, the expression of ATG7, ATG12, Beclin-1, LC3 and HDAC9 was upregulated, and that of p62 was downregulated. When HDAC9 expression was inhibited, autophagy-related genes expression was downregulated, and p62 expression was upregulated in TNF-α-treated hPDLSCs, indicating that autophagy was inhibited under these conditions. ERK pathway inhibition significantly reduced HDAC9-mediated autophagy in TNF-α-treated hPDLSCs. These findings reveal that autophagy occurred in our rat periodontitis model and that HDAC9 regulated autophagy via ERK pathways in hPDLSCs in the inflammatory environment. HDAC9 is therefore a potential target for the treatment of periodontitis.

Salivary histone deacetylase in periodontal disease: A cross-sectional pilot study

OBJECTIVE

The objective of the study was to profile the expression level of histone deacetylase enzymes (HDACs) in human saliva in periodontal health, gingivitis and periodontitis.

BACKGROUND

HDACs are epigenetic modulators and a group of enzymes that catalyse the removal of acetyl functional groups from the lysine residues of both histone and nonhistone proteins. HDACs have been detected in gingival tissues and may provide valuable insight into the periodontal inflammatory response. However, no studies have investigated the expression of HDACs in saliva from periodontitis-affected individuals and their capacity for periodontal diagnostics and screening.

MATERIALS AND METHODS

Whole unstimulated saliva was collected from 53 participants (17 healthy, 14 gingivitis and 22 stages III/IV periodontitis). The expression of 11 HDACs in saliva samples was determined using RT-qPCR and diagnostic power was calculated using the receiver operating characteristic (ROC) curves and area under the ROC Curve (AUC).

RESULTS

Relative to health, the expression of HDAC4, 8 and 10 was downregulated in gingivitis, and the expression of HDAC4, 6, 8 and 9 was downregulated in periodontitis. Increased HDAC1 and decreased HDAC9 expression were observed in periodontitis compared to gingivitis. Higher HDAC1 and lower HDAC6 and 9 expression was observed in periodontitis compared to non-periodontitis (combining health and gingivitis). Expression of HDAC3, 4, 8, 9 and 10 was significantly decreased in periodontal disease (combining gingivitis and periodontitis) compared to health. HDAC4 and 8 exhibited an excellent diagnostic capacity for distinguishing gingivitis and periodontal disease from health (AUC 0.79-0.86). HDAC9 showed an acceptable power in discriminating periodontitis from health, gingivitis and non-periodontitis (AUC 0.76-0.80). Salivary HDAC enzyme activity showed no significant difference among the groups.

CONCLUSION

This pilot study has demonstrated the differential expression of HDACs in human saliva for the first time and identified HDAC4, 8 and 9 as potential biomarkers in periodontal diagnosis.

Influence of epigenetics on periodontitis and peri-implantitis pathogenesis

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.

Cellular expression of epigenetic markers and oxidative stress in periodontitis lesions of smokers and non-smokers

Objective

To evaluate differences in the cellular expression of epigenetic markers and oxidative stress in periodontitis lesions between current smokers and non‐smokers.

Background

Tobacco smoking is recognized as one of the major risk factors for periodontitis. However, the mechanisms by which smoking affects the progression of the disease remain to be determined.

Methods

Twenty‐five current smokers and 21 non‐smokers with generalized severe periodontitis were included. From each patient, one soft tissue biopsy from a periodontitis site was harvested and prepared for histological analysis. The infiltrated connective tissue (ICT) was selected as the region of interest to assess the cellular expression of epigenetic markers and reactive oxygen/nitrogen species (RONS) by immunohistochemistry.

Results

Although the ICT of smokers and non‐smokers did not differ in size or in the expression of markers for DNA damage or oxidative stress, current smokers presented with significantly lower area proportions and densities of cells positive for the epigenetic markers DNMT1 and AcH3. In addition, periodontitis lesions in current smokers presented with a diminished antimicrobial activity, as indicated by significantly lower densities and area proportions of NOX2‐ and iNOS‐positive cells.

Conclusions

Components of the host response and epigenetic mechanisms in periodontitis lesions in smokers are downregulated as opposed to lesions of non‐smokers.

Epigenetic regulation of inflammation in periodontitis: cellular mechanisms and therapeutic potential

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.

The Role of DNA Methylation and Histone Modification in Periodontal Disease: A Systematic Review

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.

From Gene to Protein-How Bacterial Virulence Factors Manipulate Host Gene Expression During Infection

Bacteria evolved many strategies to survive and persist within host cells. Secretion of bacterial effectors enables bacteria not only to enter the host cell but also to manipulate host gene expression to circumvent clearance by the host immune response. Some effectors were also shown to evade the nucleus to manipulate epigenetic processes as well as transcription and mRNA procession and are therefore classified as nucleomodulins. Others were shown to interfere downstream with gene expression at the level of mRNA stability, favoring either mRNA stabilization or mRNA degradation, translation or protein stability, including mechanisms of protein activation and degradation. Finally, manipulation of innate immune signaling and nutrient supply creates a replicative niche that enables bacterial intracellular persistence and survival. In this review, we want to highlight the divergent strategies applied by intracellular bacteria to evade host immune responses through subversion of host gene expression via bacterial effectors. Since these virulence proteins mimic host cell enzymes or own novel enzymatic functions, characterizing their properties could help to understand the complex interactions between host and pathogen during infections. Additionally, these insights could propose potential targets for medical therapy.

HDAC3 Regulates Gingival Fibroblast Inflammatory Responses in Periodontitis

Histone deacetylases (HDACs) are important regulators of gene expression that are aberrantly regulated in several inflammatory and infectious diseases. HDAC inhibitors (HDACi) suppress inflammatory activation of various cell types through epigenetic and non-epigenetic mechanisms, and ameliorate pathology in a mouse model of periodontitis. Activation of gingival fibroblasts (GFs) significantly contributes to the development of periodontitis and the anaerobic bacterium Porphyromonas gingivalis plays a key role in driving chronic inflammation. Here, we analyzed the role of HDACs in inflammatory responses of GFs. Pan-HDACi suberoylanilide hydroxamic acid (SAHA) and/or ITF2357 (givinostat) significantly reduced TNFα- and P. gingivalis–inducible expression and/or production of a cluster of inflammatory mediators in healthy donor GFs (IL1B, CCL2, CCL5, CXCL10, COX2, and MMP3) without affecting cell viability. Selective inhibition of HDAC3/6, but not specific HDAC1, HDAC6, or HDAC8 inhibition, reproduced the suppressive effects of pan-HDACi on the inflammatory gene expression profile induced by TNFα and P. gingivalis, suggesting a critical role for HDAC3 in GF inflammatory activation. Consistently, silencing of HDAC3 expression with siRNA largely recapitulated the effects of HDAC3/6i on mRNA levels of inflammatory mediators in P. gingivalis–infected GFs. In contrast, P. gingivalis internalization and intracellular survival in GFs remained unaffected by HDACi. Activation of mitogen-activated protein kinases and NFκB signaling was unaffected by global or HDAC3/6-selective HDACi, and new protein synthesis was not required for gene suppression by HDACi. Finally, pan-HDACi and HDAC3/6i suppressed P. gingivalis–induced expression of IL1B, CCL2, CCL5, CXCL10, MMP1, and MMP3 in GFs from patients with periodontitis. Our results identify HDAC3 as an important regulator of inflammatory gene expression in GFs and suggest that therapeutic targeting of HDAC activity, in particular HDAC3, may be clinically beneficial in suppressing inflammation in periodontal disease.

BET Bromodomain Inhibitors Suppress Inflammatory Activation of Gingival Fibroblasts and Epithelial Cells From Periodontitis Patients

BET bromodomain proteins are important epigenetic regulators of gene expression that bind acetylated histone tails and regulate the formation of acetylation-dependent chromatin complexes. BET inhibitors suppress inflammatory responses in multiple cell types and animal models, and protect against bone loss in experimental periodontitis in mice. Here, we analyzed the role of BET proteins in inflammatory activation of gingival fibroblasts (GFs) and gingival epithelial cells (GECs). We show that the BET inhibitors I-BET151 and JQ1 significantly reduced expression and/or production of distinct, but overlapping, profiles of cytokine-inducible mediators of inflammation and bone resorption in GFs from healthy donors (IL6, IL8, IL1B, CCL2, CCL5, COX2, and MMP3) and the GEC line TIGK (IL6, IL8, IL1B, CXCL10, MMP9) without affecting cell viability. Activation of mitogen-activated protein kinase and nuclear factor-κB pathways was unaffected by I-BET151, as was the histone acetylation status, and new protein synthesis was not required for the anti-inflammatory effects of BET inhibition. I-BET151 and JQ1 also suppressed expression of inflammatory cytokines, chemokines, and osteoclastogenic mediators in GFs and TIGKs infected with the key periodontal pathogen Porphyromonas gingivalis. Notably, P. gingivalis internalization and intracellular survival in GFs and TIGKs remained unaffected by BET inhibitors. Finally, inhibition of BET proteins significantly reduced P. gingivalis-induced inflammatory mediator expression in GECs and GFs from patients with periodontitis. Our results demonstrate that BET inhibitors may block the excessive inflammatory mediator production by resident cells of the gingival tissue and identify the BET family of epigenetic reader proteins as a potential therapeutic target in the treatment of periodontal disease.

Mutual inhibition between HDAC9 and miR-17 regulates osteogenesis of human periodontal ligament stem cells in inflammatory conditions

Histone deacetylases (HDAC) plays important roles in the post-translational modifications of histone cores as well as non-histone targets. Many of them are involved in key inflammatory processes. Despite their importance, whether and how HDAC9 is regulated under inflammatory conditions remains unclear. The aim of this study was to evaluate the effects of HDAC9 under chronic inflammation condition in human periodontal ligament stromal cell (PDLSCs) and to explore the underlying regulatory mechanism. PDLSCs from healthy or periodontitis human tissue was compared. The therapeutic effects of HDAC inhibitors was determined in PDLSC pellet transplanted nude mice and LPS-induced rat periodontitis. We report that HDAC9 was the most affected HDAC family member under inflammatory conditions in PDLSCs. HDAC9 impaired osteogenic differentiation capacity of PDLSCs under inflammatory conditions. Downregulation of HDAC9 by HDAC inhibitors or si-HDAC9 rescued the osteogenic differentiation capacity of inflammatory PDLSC to a similar level with the healthy PDLSC. In this context, HDAC9 and miR-17 formed an inhibitory loop. The inhibition of miR-17 aggravated loss of calcified nodules in inflamed PDLSCs and interrupted the effect of HDAC inhibitor in rescuing osteogenesis. In vivo experiments using nude mice and LPS-induced periodontitis model confirmed that HDAC inhibitors could improve new bone formation. We conclude that HDAC inhibitors improved osteogenesis of PDLSCs in vitro and periodontitis in vivo.

Current Concepts of Epigenetics and Its Role in Periodontitis

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.

Epigenetic regulation in bacterial infections: targeting histone deacetylases

Pathogens have developed sophisticated strategies to evade the immune response, among which manipulation of host cellular epigenetic mechanisms plays a prominent role. In the last decade, modulation of histone acetylation in host cells has emerged as an efficient strategy of bacterial immune evasion. Virulence factors and metabolic products of pathogenic microorganisms alter expression and activity of histone acetyltransferases (HATs) and histone deacetylases (HDACs) to suppress transcription of host defense genes through epigenetic changes in histone acetylation marks. This new avenue of pathogen-host interactions is particularly important in light of introduction of HDAC inhibitors into clinical practice. Considerable effort is currently being applied to better understand the effects of HDAC inhibitors on the quality of immune responses to pathogens and to characterize the therapeutic potential of these compounds in microbial infections. In this review, we will discuss the recently discovered mechanisms utilized by bacteria to facilitate their survival within infected hosts through subversion of the host acetylation system and the effects of acetylation modulators, including HDAC inhibitors and bromodomain-containing BET protein inhibitors, on innate immune responses against microbial pathogens. Integration of these two lines of experimental evidence provides critical information on the perspectives of epigenetic therapies targeting protein acetylation in infectious diseases.

Histone deacetylases (HDAC) in physiological and pathological bone remodelling

Histone deacetylases (HDACs)² play important roles in the epigenetic regulation of gene expression in cells and are emerging therapeutic targets for treating a wide range of diseases. HDAC inhibitors (HDACi)³ that act on multiple HDAC enzymes have been used clinically to treat a number of solid and hematological malignancies. HDACi are also currently being studied for their efficacy in non-malignant diseases, including pathologic bone loss, but this has necessitated a better understanding of the roles of individual HDAC enzymes, particularly the eleven zinc-containing isozymes. Selective isozyme-specific inhibitors currently being developed against class I HDACs (1, 2, 3 and 8) and class II HDACs (4, 5, 6, 7, 9 and 10) will be valuable tools for elucidating the roles played by individual HDACs in different physiological and pathological settings. Isozyme-specific HDACi promise to have greater efficacy and reduced side effects, as required for treating chronic disease over extended periods of time. This article reviews the current understanding of roles for individual HDAC isozymes and effects of HDACi on bone cells, (osteoblasts, osteoclasts and osteocytes), in relation to bone remodelling in conditions characterised by pathological bone loss, including periodontitis, rheumatoid arthritis and myeloma bone disease.

Role of epigenetics in modulation of immune response at the junction of host-pathogen interaction and danger molecule signaling

Epigenetic mechanisms have rapidly and controversially emerged as silent modulators of host defenses that can lead to a more prominent immune response and shape the course of inflammation in the host. Thus, the epigenetics can both drive the production of specific inflammatory mediators and control the magnitude of the host response. The epigenetic actions that are predominantly shown to modulate the host defense against microbial pathogens are DNA methylation, histone modification and the activity of non-coding RNAs. There is also growing evidence that opportunistic chronic pathogens, such as Porphyromonas gingivalis, as a microbial host subversion strategy, can epigenetically interfere with the host DNA machinery for successful colonization. Similarly, the novel involvement of small molecule 'danger signals', which are released by stressed or infected cells, at the center of host-pathogen interplay and epigenetics is developing. In this review, we systematically examine the latest knowledge within the field of epigenetics in the context of host-derived danger molecule and purinergic signaling, with a particular focus on host microbial defenses and infection-driven chronic inflammation.