DNA methylation profiles of immune response-related genes in apical periodontitis

Multi-omics study of key genes, metabolites, and pathways of periodontitis

OBJECTIVE

This study aimed to explore the key genes, metabolites, and pathways that influence periodontitis pathogenesis by integrating transcriptomic and metabolomic studies.

DESIGN

Gingival crevicular fluid samples from periodontitis patients and healthy controls were collected for liquid chromatography/tandem mass-based metabolomics. RNA-seq data for periodontitis and control samples were obtained from the GSE16134 dataset. Differential metabolites and differentially expressed genes (DEGs) between the two groups were then compared. Based on the protein-protein interaction (PPI) network module analysis, key module genes were selected from immune-related DEGs. Correlation and pathway enrichment analyses were performed for differential metabolites and key module genes. A multi-omics integrative analysis was performed using bioinformatic methods to construct a gene-metabolite-pathway network.

RESULTS

From the metabolomics study, 146 differential metabolites were identified, which were mainly enriched in the pathways of purine metabolism and Adenosine triphosphate binding cassette transporters (ABC transporters). The GSE16134 dataset revealed 102 immune-related DEGs (458 upregulated and 264 downregulated genes), 33 of which may play core roles in the key modules of the PPI network and are involved in cytokine-related regulatory pathways. Through a multi-omics integrative analysis, a gene-metabolite-pathway network was constructed, including 28 genes (such as platelet derived growth factor D (PDGFD), neurturin (NRTN), and interleukin 2 receptor, gamma (IL2RG)); 47 metabolites (such as deoxyinosine); and 8 pathways (such as ABC transporters).

CONCLUSION

PDGFD, NRTN, and IL2RG may be potential biomarkers of periodontitis and may affect disease progression by regulating deoxyinosine to participate in the ABC transporter pathway.

Interleukin 6 and Interleukin 1β hypomethylation and overexpression are common features of apical periodontitis: a case-control study with gingival tissue as control

OBJECTIVES

Apical periodontitis is a periradicular tissue disorder that usually arises from infection by microorganisms in the root canal system resulting in local bone resorption. This usually involves the dysregulation of inflammatory mediators, which can be mediated by epigenetic mechanisms. Thus, the objective of this study was to evaluate Interleukin 6 (IL6) and Interleukin 1β (IL1β) and DNA methylation and gene expression levels in apical periodontitis.

METHODS

Gene expression was analyzed in 60 participants using quantitative polymerase chain reaction, while the methylation levels of IL6 and IL1β promoters were analyzed in 72 patients using pyrosequencing. All statistical analyzes were performed using the GraphPad Prism software version 8.0. The p value was considered statistically significant when < 0.05.

RESULTS

A significantly higher IL6 and IL1β expression levels were observed in cases relative to controls (fold-changes of 27.4 and 11.43, respectively, and p < 0.0001). By comparing the same groups, lower promoter methylation levels were observed for both genes in cases (methylation percentage delta relative to controls of -24.57% and -16.02%, respectively, and p < 0.0001). A significant inverse correlation between gene expression and promoter methylation was observed for both IL6 (p = 0.0002) and IL1β (p = 0.001). Neither IL6 expression nor promoter methylation were significantly associated with cases' age, smoking history, alcohol consumption history or sex. For IL1β, alcoholic cases showed lower methylation level relative to non-alcoholic cases (p = 0.01), while females showed higher methylation levels relative to males (p = 0.03).

CONCLUSIONS

Our data suggest a role for DNA methylation in IL6 and IL1β upregulation in apical periodontitis.

Identification of prognostic biomarkers among ICAMs in the breast cancer microenvironment

BACKGROUND

Intercellular adhesion molecules (ICAMs) in the tumor microenvironment are closely related to immunity and affect the prognosis of cancer patients.

OBJECTIVE

The aim of our study is to explore the correlation between ICAM expression, mutation, methylation and immunity and their prognostic value in breast cancer (BC) is not clear.

METHODS

Online databases and tools such as UALCAN, COSMIC, cBioPortal, MethSurv, PrognoScan, Kaplan-Meier Plotter, GSCA and TIMER were utilized in this study.

RESULTS

We found that the mRNA and protein expression levels of ICAM1 were upregulated in triple-negative breast cancer (TNBC) compared with normal tissues, and TNBC patients with high expression of ICAM1 had better overall survival (OS) and recurrence-free survival (RFS). The main types of ICAM1 gene variants were missense mutation and amplification, and ICAM1 showed a lower level of methylation in TNBC cancer tissues than in normal tissues, which was contrary to the high expression levels of ICAM1 mRNA and protein. Next, the function of ICAM1 was mainly related to the activation of apoptosis, epithelial-mesenchymal transition (EMT) and inhibition of the androgen receptor (AR) and estrogen receptor (ER) pathways. Meanwhile, functional pathway enrichment results showed that ICAM1 was also involved in the immune regulation process of BC. Furthermore, the expression of ICAM1 was positively associated with 6 types of tumor-infiltrating immune cells (CD8+ T cells, CD4+ T cells, B cells, neutrophils, macrophages and dendritic cells) and was also positively related to the expression of programmed cell death-1 (PD-1), programmed cell death-ligand 1 (PD-L1) and cytotoxic T lymphocyte-associated antigen-4 (CTLA4).

CONCLUSIONS

Our research indicated that ICAM1 was likely to be a potential therapeutic target in TNBC.

FADD as a key molecular player in cancer progression

Cancer is a leading disease-related cause of death worldwide. Despite advances in therapeutic interventions, cancer remains a major global public health problem. Cancer pathogenesis is extremely intricate and largely unknown. Fas-associated protein with death domain (FADD) was initially identified as an adaptor protein for death receptor-mediated extrinsic apoptosis. Recent evidence suggests that FADD plays a vital role in non-apoptotic cellular processes, such as proliferation, autophagy, and necroptosis. FADD expression and activity of are modulated by a complicated network of processes, such as DNA methylation, non-coding RNA, and post-translational modification. FADD dysregulation has been shown to be closely associated with the pathogenesis of numerous types of cancer. However, the detailed mechanisms of FADD dysregulation involved in cancer progression are still not fully understood. This review mainly summarizes recent findings on the structure, functions, and regulatory mechanisms of FADD and focuses on its role in cancer progression. The clinical implications of FADD as a biomarker and therapeutic target for cancer patients are also discussed. The information reviewed herein may expand researchers’ understanding of FADD and contribute to the development of FADD-based therapeutic strategies for cancer patients.

Mechanisms of bone remodeling and therapeutic strategies in chronic apical periodontitis

Chronic periapical periodontitis (CAP) is a typical oral disease in which periodontal inflammation caused by an odontogenic infection eventually leads to bone loss. Uncontrolled infections often lead to extensive bone loss around the root tip, which ultimately leads to tooth loss. The main clinical issue in the treatment of periapical periodontitis is the repair of jawbone defects, and infection control is the first priority. However, the oral cavity is an open environment, and the distribution of microorganisms through the mouth in jawbone defects is inevitable. The subversion of host cell metabolism by oral microorganisms initiates disease. The presence of microorganisms stimulates a series of immune responses, which in turn stimulates bone healing. Given the above background, we intended to examine the paradoxes and connections between microorganisms and jaw defect repair in anticipation of new ideas for jaw defect repair. To this end, we reviewed the microbial factors, human signaling pathways, immune cells, and cytokines involved in the development of CAP, as well as concentrated growth factor (CGF) and stem cells in bone defect repair, with the aim of understanding the impact of microbial factors on host cell metabolism to inform the etiology and clinical management of CAP.

Comprehensive analysis of DNA methylation for periodontitis

Background

Periodontitis is an infectious disease, and a risk factor for peri-implantitis that could result in the implant loss. DNA methylation has an essential role in the etiology and pathogenesis of inflammatory disease. However, there is lack of study on methylation status of genes in periodontitis. This study sought to explore the gene methylation profiling microarray in periodontitis.

Methods

Through searching in the Gene Expression Omnibus database, a gene methylation profiling data set GSE173081 was identified, which included 12 periodontitis samples and 12 normal samples, respectively. Thereafter, the data of GSE173081 was downloaded and analyzed to determined differentially methylated genes (DMGs), which then were used to perform Gene Ontology analysis and pathway enrichment analyses through online database. In addition, the DMGs were applied to construct the protein–protein interaction (PPI) network information, predict the hub genes in pathology of periodontitis.

Results

In total 668 DMGs were sorted and identified from the data set, which included 621 hypo-methylated genes and 47 hyper-methylated genes. Through the function and ontology analysis, these 668 genes are mainly classified into intracellular signaling pathway, cell components, cell–cell interaction, and cellular behaviors. The pathway analysis showed that the hypo-methylated genes were mostly enriched in the pathway of cGMP–PKG signaling pathway; RAF/MAP kinase; PI3K–Akt signaling pathway, while hyper-methylated genes were mostly enriched in the pathway of bacterial invasion of epithelial cells; sphingolipid signaling pathway and DCC mediated attractive signaling. The PPI network contained 630 nodes and 1790 interactions. Moreover, further analysis identified top 10 hub genes (APP; PAX6; LPAR1; WNT3A; BMP2; PI3KR2; GATA4; PLCB1; GATA6; CXCL12) as central nodes that are involved in the immune system and the inflammatory response.

Conclusions

This study provides comprehensive information of methylation status of genes to the revelation of periodontitis pathogenesis that may contribute to future research on periodontitis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40729-022-00420-8.

Effect of TLR9 methylation on its transcription in apical inflammation

AIM

to explore the methylation pattern, its role on transcriptional regulation and potential modifiers of methylation of theTLR9 gene in chronic periapical inflammation.

METHODOLOGY

In this cross-sectional study, apical lesions of endodontic origin (ALEO, n=61) and healthy periodontal ligaments (HPL, n=15) were included. Products from bisulfited and PCR-amplified DNA were analyzed for their methylation profiles in the promoter region and at each CpG island. Additionally, TLR9 mRNA levels were quantified by qPCR and bivariate and multiple modelling were performed to better understand the influence of methylations on gene transcription.

RESULTS

TLR9 mRNA levels were upregulated in ALEO compared to HPL (p<0.001). TLR9 promoter CpG sites and CpG +2086 in the intragenic island 1 were demethylated in ALEO compared to HPL (p<0.05). Multivariate analysis, adjusted by smoking and gender, revealed that demethylation of TLR9 promoter sites enhanced transcriptional activity, specifically demethylated CpGs at positions -736 and -683, (p=0.02), which are close to CRE binding. Whereas ALEO reduced the global methylation of the gene-promoter and intragenic-island 2 (p<0.05) by -42.5 and -9.5 percentage points, respectively, age reduced the global methylation of intragenic-island 3 within the exon 2.

CONCLUSIONS

Demethylations of TLR9 promoter CpG sites, along with the intragenic DNA methylation status, were involved in higher transcription in ALEO. Hence, chronic periapical inflammation and aging modify the methylation status both in the gene promoter and in intragenic CpG islands.

Role of ascorbic acid in the regulation of epigenetic processes induced by Porphyromonas gingivalis in endothelial-committed oral stem cells

Periodontitis is a common inflammatory disease that affects the teeth-supporting tissue and causes bone and tooth loss. Moreover, in a worldwide population, periodontal disease is often associated with cardiovascular diseases. Emerging studies have reported that one of the major pathogens related to periodontitis is Porphyromonas gingivalis (P. gingivalis), which triggers the inflammatory intracellular cascade. Here, we hypothesized a possible protective effect of ascorbic acid (AA) in the restoration of the physiological molecular pathway after exposure to lipopolysaccharide derived from P. gingivalis (LPS-G). In particular, human gingiva-derived mesenchymal stem cells (hGMSCs) and endothelial-differentiated hGMSCs (e-hGMSCs) exposed to LPS-G showed upregulation of p300 and downregulation of DNA methyltransferase 1 (DNMT1), proteins associated with DNA methylation and histone acetylation. The co-treatment of AA and LPS-G showed a physiological expression of p300 and DNMT1 in hGMSCs and e-hGMSCs. Moreover, the inflammatory process triggered by LPS-G was demonstrated by evaluation of reactive oxygen species (ROS) and their intracellular localization. AA exposure re-established the physiological ROS levels. Despite the limitations of in vitro study, these findings collectively expand our knowledge regarding the molecular pathways involved in periodontal disease, and suggest the involvement of epigenetic modifications in the development of periodontitis.

Regulation of IL12B Expression in Human Macrophages by TALEN-mediated Epigenome Editing

Although the exact etiology of inflammatory bowel disease (IBD) remains unclear, exaggerated immune response in genetically predisposed individuals has been reported. Th1 and Th17 cells mediate IBD development. Macrophages produce IL-12 and IL-23 that share p40 subunit encoded by IL12B gene as heteromer partner to drive Th1 and Th17 differentiation. The available animal and human data strongly support the pathogenic role of IL-12/IL-23 in IBD development and suggest that blocking p40 might be the potential strategy for IBD treatment. Furthermore, aberrant alteration of some cytokines expression via epigenetic mechanisms is involved in pathogenesis of IBD. In this study, we analyzed core promoter region of IL12B gene and investigated whether IL12B expression could be regulated through targeted epigenetic modification with gene editing technology. Transcription activator-like effectors (TALEs) are widely used in the field of genome editing and can specifically target DNA sequence in the host genome. We synthesized the TALE DNA-binding domains that target the promoter of human IL12B gene and fused it with the functional catalytic domains of epigenetic enzymes. Transient expression of these engineered enzymes demonstrated that the TALE-DNMT3A targeted the selected IL12B promoter region, induced loci-specific DNA methylation, and down-regulated IL-12B expression in various human cell lines. Collectively, our data suggested that epigenetic editing of IL12B through methylating DNA on its promoter might be developed as a potential therapeutic strategy for IBD treatment.

DNA Methylation patterns of immune response-related genes in inflammatory external root resorption

Inflammatory external root resorption (IERR) is a pathological process defined by the progressive loss of dental hard tissue, dentin, and cementum, resulting from the combination of the loss of external root protective apparatus and root canal infection. It has been suggested that healing patterns after tooth replantation may be influenced by the genetic and immunological profiles of the patients. The purpose of the present investigation was to evaluate the DNA methylation patterns of 22 immune response-related genes in extracted human teeth presenting with IERR. Methylation assays were performed on samples of root fragments showing IERR and compared with healthy bone tissue collected during the surgical extraction of impacted teeth. The methylation patterns were quantified using EpiTect Methyl II Signature Human Cytokine Production PCR Array. The results revealed significantly higher hypermethylation of the FOXP3 gene promoter in IERR (65.95%) than in the bone group (23.43%) (p < 0.001). The ELANE gene was also highly methylated in the pooled IERR sample, although the difference was not statistically significant (p= 0.054). Our study suggests that the differential methylation patterns of immune response-related genes, such as FOXP3 and ELANE, may be involved in IERR modulation, and this could be related to the presence of root canal infection. However, further studies are needed to corroborate these findings to determine the functional relevance of these alterations and their role in the pathogenesis of IERR.

Long Term Delta-9-tetrahydrocannabinol Administration Inhibits Proinflammatory Responses in Minor Salivary Glands of Chronically Simian Immunodeficieny Virus Infected Rhesus Macaques

HIV/SIV-associated oral mucosal disease/dysfunction (HAOMD) (gingivitis/periodontitis/salivary adenitis) represents a major comorbidity affecting HIV patients on anti-retroviral therapy. Using a systems biology approach, we investigated molecular changes (mRNA/microRNA) underlying HAOMD and its modulation by phytocannabinoids (delta-9-tetrahydrocannabinol (∆⁹-THC)) in uninfected (n = 5) and SIV-infected rhesus macaques untreated (VEH-untreated/SIV; n = 7) or treated with vehicle (VEH/SIV; n = 3) or ∆⁹-THC (THC/SIV; n = 3). Relative to controls, fewer mRNAs were upregulated in THC/SIV compared to VEH-untreated/SIV macaques. Gene enrichment analysis showed differential enrichment of biological functions involved in anti-viral defense, Type-I interferon, Toll-like receptor, RIG-1 and IL1R signaling in VEH-untreated/SIV macaques. We focused on the anti-ER-stress anterior gradient-2 (AGR2), epithelial barrier protecting and anti-dysbiotic WAP Four-Disulfide Core Domain-2 (WFDC2) and glucocorticoid-induced anti-inflammatory TSC22D3 (TSC22-domain family member-3) that were significantly downregulated in oropharyngeal mucosa (OPM) of VEH-untreated/SIV macaques. All three proteins localized to minor salivary gland acini and secretory ducts and showed enhanced and reduced expression in OPM of THC/SIV and VEH/SIV macaques, respectively. Additionally, inflammation associated miR-21, miR-142-3p and miR-29b showed significantly higher expression in OPM of VEH-untreated/SIV macaques. TSC22D3 was validated as a target of miR-29b. These preliminary translational findings suggest that phytocannabinoids may safely and effectively reduce oral inflammatory responses in HIV/SIV and other (autoimmune) diseases.

Epigenetic regulation of TLR2-mediated periapical inflammation

AIM

To determine the methylation pattern of TLR2 gene promoter and its association with the transcriptional regulation of periapical inflammatory and angiogenic responses in symptomatic and asymptomatic forms of apical periodontitis.

METHODOLOGY

In this cross-sectional study, apical lesions were obtained from volunteers with asymptomatic apical periodontitis (AAP) (n = 17) and symptomatic apical periodontitis (SAP) (n = 17) scheduled for tooth extraction, and both total RNA and DNA were extracted. DNA was bisulfite-treated, a region of CpG island within the TLR2 gene was amplified by qPCR and the products were sequenced. Additionally, the mRNA expression of TLR2, TLR4, IL-6, IL-12, TNFalpha, IL-23, IL-10, TGFbeta, VEGFA and CDH5 was analysed by qPCR. The data were analysed with chi-square tests, Mann-Whitney or unpaired t-tests, and Spearman´s correlation; variable adjustments were performed using multiple linear regression (P < 0.05).

RESULTS

TLR2 depicted a hypomethylated DNA profile at the CpG island in SAP when compared with AAP, along with upregulated expression of TLR2, with pro-inflammatory cytokines IL-6 and IL-23, and the angiogenesis marker CDH5 (P < 0.05). TLR2 methylation percentage negatively correlated with mRNA levels of IL-23 and CDH5 in apical periodontitis. Lower methylation frequencies of single CpG dinucleotides -8 and -10 localized in close proximity to nuclear factor κB (NFκB) binding within the TLR2 promoter were identified in SAP versus AAP (P < 0.05). Finally, unmethylated -10 and -8 single sites demonstrated up-regulation of IL-23, IL-10 and CDH5 transcripts compared to their methylated counterparts (P < 0.05).

CONCLUSIONS

TLR2 gene promoter hypomethylation was linked to transcriptional activity of pro-inflammatory cytokines and angiogenic markers in exacerbated periapical inflammation. Moreover, unmethylated single sites in close proximity to NFκB binding were involved in active transcription of IL-23, IL-10 and CDH5.

Association of DNA sequence-independent genetic regulatory mechanisms with apical periodontitis: A scoping review

OBJECTIVE

Different studies in the last decade have proposed that gene expression alterations that are independent of the DNA sequence may also play an important role in periapical disease. The present study aimed to assess the available evidence supporting a relationship between these alterations and apical periodontitis through a scoping review.

DESIGN

Specific strategies were developed for different databases (MEDLINE via PubMed, Cochrane Library, Scopus, Web of Science, and Virtual Health Library) and a search performed by March 1st, 2019. The evidence sources were selected according to the eligibility criteria and underwent a critical appraisal of methodological quality.

RESULTS

The initial search retrieved 212 references, with eight eligible articles after the removal of replicates and application of exclusion criteria. Five studies identified altered DNA methylation on inflammatory response genes (FOXP3, CXCL3, FADD, MMP2, MMP9, IFNG, IL4, IL12) on AP patients. Three others identified the alterations on the expression of several microRNAs (miR-29b, 106b, 125b, 143, 146a, 155, 198) during AP. No evidence was identified regarding mechanisms of histone methylation, or of epigenetic heritability or stability.

CONCLUSIONS

There is available evidence for the involvement of different genetic regulatory mechanisms independent of changes in DNA sequence in the development or severity of apical periodontitis. However, due to methodological limitations, further research must be performed before novel therapies and diagnostic tools for AP may arise from these data.

FADD in Cancer: Mechanisms of Altered Expression and Function, and Clinical Implications

FADD was initially described as an adaptor molecule for death receptor-mediated apoptosis, but subsequently it has been implicated in nonapoptotic cellular processes such as proliferation and cell cycle control. During the last decade, FADD has been shown to play a pivotal role in most of the signalosome complexes, such as the necroptosome and the inflammasome. Interestingly, various mechanisms involved in regulating FADD functions have been identified, essentially posttranslational modifications and secretion. All these aspects have been thoroughly addressed in previous reviews. However, FADD implication in cancer is complex, due to pleiotropic effects. It has been reported either as anti- or protumorigenic, depending on the cell type. Regulation of FADD expression in cancer is a complex issue since both overexpression and downregulation have been reported, but the mechanisms underlying such alterations have not been fully unveiled. Posttranslational modifications also constitute a relevant mechanism controlling FADD levels and functions in tumor cells. In this review, we aim to provide detailed, updated information on alterations leading to changes in FADD expression and function in cancer. The participation of FADD in various biological processes is recapitulated, with a mention of interesting novel functions recently proposed for FADD, such as regulation of gene expression and control of metabolic pathways. Finally, we gather all the available evidence regarding the clinical implications of FADD alterations in cancer, especially as it has been proposed as a potential biomarker with prognostic value.

Methionine Attenuates Lipopolysaccharide-Induced Inflammatory Responses via DNA Methylation in Macrophages

Methionine (Met) is an essential and multifunctional nutrient in vertebrate diets. It is a precursor of S-adenosylmethionine (SAM), the methyl donor for DNA methylation, which has an important role in the inflammatory responses. However, whether Met exerts anti-inflammatory effects by altering DNA methylation in macrophages is unclear. In this study, Met was found to diminish the activation of the mitogen-activated protein kinase signaling pathway; decrease the production of tumor necrosis factor-α, interleukin-6, and interferon-β; and enhance the levels of intracellular SAM after lipopolysaccharide (LPS) treatment in macrophages. Similarly, SAM inhibited the LPS-induced inflammatory response, consistent with the result of Met treatment. Met-treated macrophages displayed increased global DNA methylation. The DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine partially blocked the anti-inflammatory effects of Met in macrophages, suggesting a mechanism involving DNA methylation. Collectively, the results indicated that Met inhibits the LPS-induced inflammatory response by altering DNA methylation in RAW 264.7 macrophages. The findings provide new insights into the interplay between nutrition and immunology, and highlight the regulatory effects of amino acids on the host immune system.