Development of an miRNA-Array-Based Diagnostic Signature for Periodontitis

MicroRNA-671-5p regulates the inflammatory response of periodontal ligament stem cells via the DUSP8/p38 MAPK pathway

BACKGROUND

MicroRNAs are differentially expressed in periodontitis tissues. They are involved in cellular responses to inflammation and can be used as markers for diagnosing periodontitis. Microarray analysis showed that the expression level of microRNA-671-5p in periodontal tissues of patients with periodontitis was increased. In this study, we investigated the mechanism of action of microRNA-671-5p in human periodontal ligament stem cells (hPDLSCs) under inflammatory conditions.

METHODS AND RESULTS

HPDLSCs were treated with lipopolysaccharide (LPS) to establish an inflammation model. The cell survival rate was determined using the cell counting kit-8 (CCK8). Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blot analyses were used to detect the expression of microRNA-671-5p and dual-specificity phosphatase (DUSP) 8 proteins, respectively, Interleukin (IL)-6, IL-1β, and tumor necrosis factor (TNF)-α were detected using qRT-PCR and Enzyme-linked immunosorbent assay (ELISA). A dual-luciferase reporter system was employed to determine the relationship between micoRNA-671-5p and DUSP8 expression. Activation of the p38 mitogen-activated protein kinase (MAPK) signaling pathway was confirmed using western blot analysis. Following the treatment of hPDLSCs with LPS, the expression levels of microRNA-671-5p in hPDLSCs were increased, cell viability decreased, and the expression of inflammatory factors displayed an increasing trend. MicroRNA-671-5p targets and binds to DUSP8. Silencing microRNA-671-5p or overexpressing DUSP8 can improve cell survival rate and reduce inflammatory responses. When DUSP8 was overexpressed, the expression of p-p38 was reduced.

CONCLUSIONS

microRNA-671-5p targets DUSP8/p38 MAPK pathway to regulate LPS-induced proliferation and inflammation in hPDLSCs.

Identifying genes for regulating osteogenic differentiation of human periodontal ligament stem cells in inflammatory environments by bioinformatics analysis

BACKGROUND AND OBJECTIVES

Periodontitis is an immuno-inflammatory disease caused by dental plaque biofilms and inflammations. The regeneration of bone tissue in inflammatory environment is of great significance for the treatment of periodontal disease, but the specific molecular mechanism of bone formation in periodontitis still needs further exploration. The objective of this study was to identify key osteogenesis-related genes (ORGs) in periodontitis.

METHODS

We used two datasets from the Gene Expression Omnibus (GEO) database to find differentially expressed mRNAs and miRNAs, further performed Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Then we predicted the downstream genes of the differentially expressed miRNAs (DEMs) by the TargetScan database and established a miRNA-mRNA regulatory network. Finally, the osteogenic mechanism of periodontitis was explored through quantitative real-time PCR (qRT-PCR) by inducing inflammatory environment and osteogenic differentiation of hPDLSCs.

RESULTS

Through differential expression analysis and prediction of downstream target genes of DEMs, we created a miRNA-mRNA regulatory network consisting of 29 DEMs and 11 differentially expressed osteogenesis-related genes (DEORGs). In addition, the qRT-PCR results demonstrated that BTBD3, PLAT, AKAP12, SGK1, and GLCE expression levels were significantly upregulated, while those of TIMP3, ZCCHC14, LIN7A, DNAH6, NNT, and ITGA6 were downregulated under the dual effects of inflammatory stimulation and osteogenic induction.

CONCLUSION

DEORGs might be important factors in the osteogenic phase of periodontitis, and the miRNA-mRNA network may shed light on the clarification of the role and mechanism of osteogenesis in periodontitis and contribute to the development of novel therapeutic strategies.

Osteoprotective Role of the Mir338 Cluster Ablation during Periodontitis

Periodontitis is a chronic inflammatory disease that compromises the integrity of the supporting tissues of the teeth and leads to the loss of the alveolar bone. The Mir338 cluster has been proven to be a potential target for the treatment of osteoporosis and is also enriched in gingival tissues with periodontitis; however, its role in periodontitis remains unknown. Here, we aimed to use periodontitis as a model to expand our understanding of the Mir338 cluster in osteoimmunology and propose a new target to protect against bone loss during periodontitis progression. Significant enrichment of the Mir338 cluster was validated in gingival tissues from patients with chronic periodontitis and a ligature-induced periodontitis mouse model. In vivo, attenuation of alveolar bone loss after 7 d of ligature was observed in the Mir338 cluster knockout (KO) mice. Interestingly, immunofluorescence and RNA sequencing showed that ablation of the Mir338 cluster reduced osteoclast formation and elevated the inflammatory response, with enrichment of IFN-γ and JAK-STAT signaling pathways. Ablation of the Mir338 cluster also skewed macrophages toward the M1 phenotype and inhibited osteoclastogenesis via Stat1 in vitro and in vivo. Furthermore, the local administration of miR-338-3p antagomir prevented alveolar bone loss from periodontitis. In conclusion, the Mir338 cluster balanced M1 macrophage polarization and osteoclastogenesis and could serve as a novel therapeutic target against periodontitis-related alveolar bone loss.

Immune infiltration and diagnostic value of immune-related genes in periodontitis using bioinformatics analysis

BACKGROUND AND OBJECTIVES

Periodontitis, which is a chronic inflammatory periodontal disease resulting in destroyed periodontal tissue, is the leading cause of tooth loss in adults. Many studies have found that inflammatory immune responses are involved in the risk of periodontal tissue damage. Therefore, we analyzed the association between immunity and periodontitis using bioinformatics methods to further understand this disease.

MATERIALS AND METHODS

First, the expression profiles of periodontitis and healthy samples were downloaded from the GEO database, including a training dataset GSE16134 and an external validation dataset GSE10334. Then, differentially expressed genes were identified using the limma package. Subsequently, immune cell infiltration was calculated by using the CIBERSORT algorithm. We further identified genes linking periodontitis and immunity from the ImmPort and DisGeNet databases. In addition, some of them were selected to construct a diagnostic model via a logistic stepwise regression analysis.

RESULTS AND CONCLUSIONS

Two hundred sixty differentially expressed genes were identified and found to be involved in responses to bacterial and immune-related processes. Subsequently, immune cell infiltration analysis demonstrates significant differences in the abundance of most immune cells between periodontitis and healthy samples, especially in plasma cells. These results suggested that immunity doses play a non-negligible role in periodontitis. Twenty-one genes linking periodontitis and immunity were further identified. And nine hub genes of them were identified that may be key genes involved in the development of periodontitis. Gene ontology analyses showed that these genes are involved in response to molecules of bacterial origin, cell chemotaxis, and response to chemokines. In addition, three genes of them were selected to construct a diagnostic model. And its good diagnostic performance was demonstrated by the receiver operating characteristic curves, with an area under the curve of 0.9424 for the training dataset and 0.9244 for the external validation dataset.

Anti-apoptosis and anti-inflammation activity of circ_0097010 downregulation in lipopolysaccharide-stimulated periodontal ligament cells by miR-769-5p/Krüppel like factor 6 axis

Background/purpose

Periodontitis is a prevalent infectious inflammatory disease. Growing evidence has revealed important roles for circular RNAs (circRNAs) and circRNA sponge activity in periodontitis. Here, we elucidated the precise part of circ_0097010 in periodontitis pathogenesis.

Materials and methods

Human periodontal ligament cells (hPDLCs) were exposed to lipopolysaccharide (LPS). Cell viability, proliferation and apoptosis were evaluated by CCK-8 assay, EdU incorporation assay and flow cytometry, respectively. Circ_0097010, microRNA (miR)-769-5p and Krüppel like factor 6 (KLF6) were quantified by qRT-PCR and Western blot. Interleukin 6 (IL-6) level, tumor necrosis factor-α (TNF-α) secretion, superoxide dismutase (SOD) activity and malondialdehyde (MDA) level were detected by enzyme-linked immunosorbent assay (ELISA). Dual-luciferase reporter, RNA immunoprecipitation (RIP) and RNA pull-down assays were used to confirm the direct relationship between miR-769-5p and circ_0097010 or KLF6.

Results

Our data showed that LPS repressed cell proliferation and induced cell apoptosis and inflammation in hPDLCs. Circ_0097010 was upregulated in periodontitis samples and LPS-exposed hPDLCs. Downregulation of circ_0097010 exerted anti-apoptosis and anti-inflammation functions in LPS-exposed hPDLCs. Mechanistically, circ_0097010 acted as a miR-769-5p sponge, and reduced abundance of miR-769-5p reversed the anti-apoptosis and anti-inflammation effects of circ_0097010 suppression. KLF6 was a direct miR-769-5p target, and miR-769-5p-mediated inhibition of KLF6 possessed anti-apoptosis and anti-inflammation functions in LPS-induced hPDLCs. Moreover, circ_0097010 controlled KLF6 expression by miR-769-5p.

Conclusion

These data identify circ_0097010 as a key regulator of LPS-induced inflammation and apoptosis in hPDLCs and highlight a novel mechanism of circ_0097010 regulation through miR-769-5p/KLF6 axis.

Identifying Common Genes and Pathways Associated with Periodontitis and Aging by Bioinformatics Analysis

BACKGROUND

This work used bioinformatic analysis to identify the relationship between periodontitis (PD) and aging, which could lead to new treatments for periodontal disease in the elderly.

METHOD

Four microarray datasets were obtained from the Gene Expression Omnibus (GEO) database and analyzed in R language to identify differentially expressed genes (DEGs). The common DEGs of PD and aging were evaluated as key genes in this investigation by a Venn diagram. These common DEGs were analyzed through additional experiments and analysis, such as pathway analysis and enrichment analysis, and a network of protein-protein interactions (PPIs) was constructed. Cytoscape was used to visualize hub genes and critical modules based on the PPI network. Interaction of TF-genes and miRNAs with hub genes is identified.

RESULT

84 common DEGs were found between PD and aging. Cytohubba was performed on the PPI network obtained from STRING tool, and the top 10 genes (MMP2, PDGFRB, CTGF, CD34, CXCL12, VIM, IL2RG, ACTA2, COL4A2, and TAGLN) were selected as hub genes. VIM may be a potential biomarker in the analysis of linked hub gene regulatory networks, and hsa-mir-21 and hsa-mir-125b are predicted to be associated in PD and aging.

CONCLUSION

This study investigated the key genes and pathways interactions between PD and aging, which may help reveal the correlation between PD and aging. The current research results are obtained by prediction, and follow-up biological experiments are required for further verification.

Construction of artificial neural network diagnostic model and analysis of immune infiltration for periodontitis

Background: Periodontitis is a chronic inflammatory disease leading to tooth loss in severe cases, and early diagnosis is essential for periodontitis prevention. This study aimed to construct a diagnostic model for periodontitis using a random forest algorithm and an artificial neural network (ANN). Methods: Gene expression data of two large cohorts of patients with periodontitis, GSE10334 and GSE16134, were downloaded from the Gene Expression Omnibus database. We screened for differentially expressed genes in the GSE10334 cohort, identified key periodontitis biomarkers using a Random Forest algorithm, and constructed a classification artificial neural network model, using receiver operating characteristic curves to evaluate its diagnostic utility. Furthermore, patients with periodontitis were classified using a consensus clustering algorithm. The immune infiltration landscape was assessed using CIBERSOFT and single-sample Gene Set Enrichment Analysis. Results: A total of 153 differentially expressed genes were identified, of which 42 were downregulated. We utilized 13 key biomarkers to establish a periodontitis diagnostic model. The model had good predictive performance, with an area under the receiver operative characteristic curve (AUC) of 0.945. The independent cohort (GSE16134) was used to further validate the model's accuracy, showing an area under the receiver operative characteristic curve of 0.900. The proportion of plasma cells was highest in samples from patients with period ontitis, and 13 biomarkers were closely related to immunity. Two molecular subgroups were defined in periodontitis, with one cluster suggesting elevated levels of immune infiltration and immune function. Conclusion: We successfully identified key biomarkers of periodontitis using machine learning and developed a satisfactory diagnostic model. Our model may provide a valuable reference for the prevention and early detection of periodontitis.

miR-141-3p Regulates EZH2 to Attenuate Porphyromonas gingivalis Lipopolysaccharide-Caused Inflammation and Inhibition of Osteogenic Differentiation in Human Periodontal Ligament Stem Cells

Objective

miR-141-3p has been demonstrated to be both anti-inflammatory and osteoprotective. This study is aimed at investigating the effect of miR-141-3p on osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs) stimulated by Porphyromonas gingivalis lipopolysaccharide (PgLPS) and its mechanism.

Methods

PgLPS was used to induce an inflammatory environment, and overexpression of miR-141-3p was done to assess its effect on hPDLSCs in an inflammatory environment. The level of miR-141-3p and EZH2 in hPDLSCs from each treatment group was detected via qRT-PCR, and the inflammatory factors IL-6 and IL-8 in the supernatant of each group were detected by ELISA. ALP staining and alizarin red staining were used to assess the effect of miR-141-3p on the osteogenic differentiation ability of hPDLSCs, and also, western blot was used to detect expression of osteogenic differentiation-related proteins. Further, dual-luciferase reporter assay examined whether miR-141-3p targeted EZH2.

Results

PgLPS led to a significant decrease of miR-141-3p in hPDLSCs. Overexpression of miR-141-3p could enhance ALP activity and alizarin red staining intensity and increase Runx2, OPN and OCN protein expression levels in PgLPS-treated hPDLSCs. Additionally, miR-141-3p could reduce IL-6 and IL-8. miR-141-3p could target and negatively regulate EZH2, and overexpression of EZH2 reversed the promoting effect of miR-141-3p on osteogenic differentiation.

Conclusion

miR-141-3p can attenuate PgLPS-induced inhibition of osteogenic differentiation and inflammation in hPDLSCs by negatively regulating EZH2.

Autophagy-Related Genes Predict the Progression of Periodontitis Through the ceRNA Network

Purpose

The goal of this study was to identify the crucial autophagy-related genes (ARGs) in periodontitis and construct mRNA-miRNA-lncRNA networks to further understand the pathogenesis of periodontitis.

Methods

We used the Gene Expression Omnibus (GEO) database and Human Autophagy Database (HADb) to identify differentially expressed mRNAs, miRNAs, and ARGs. These ARGs were subjected to Gene Ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, and PPI (protein–protein interaction) network analysis. Two databases (miRDB and StarBase v2.0) were used to reverse-predict miRNAs while the miRNA-lncRNA interaction was predicted using the StarBase v2.0 and LncBase Predicted v.2 databases. After excluding the lncRNAs only present in the nucleus, a competing endogenous RNA (ceRNA) network was built. Finally, we used quantitative real-time PCR (qRT-PCR) to confirm the levels of mRNA expression in the ceRNA network.

Results

The differential expression analysis revealed 10 upregulated and 10 downregulated differentially expressed ARGs. After intersecting the reverse-predicted miRNAs with the differentially expressed miRNAs, a ceRNA network consisting of 4 mRNAs (LAMP2, NFE2L2, NCKAP1, and EGFR), 3 miRNAs (hsa-miR-140-3p, hsa-miR-142-5p, and hsa-miR-671-5p), and 30 lncRNAs was constructed. In addition, qRT-PCR results revealed that EGFR expression was downregulated in diseased gingival tissue of periodontitis patients.

Conclusion

Four autophagy-related genes, especially EGFR, may play a key role in periodontitis progression. The novel ceRNA network may aid in elucidating the role and the mechanism of autophagy in periodontitis, which could be important in developing new therapeutic options.

Cannabinoid control of gingival immune activation in chronically SIV-infected rhesus macaques involves modulation of the indoleamine-2,3-dioxygenase-1 pathway and salivary microbiome

BACKGROUND

HIV/SIV-associated periodontal disease (gingivitis/periodontitis) (PD) represents a major comorbidity affecting people living with HIV (PLWH) on combination anti-retroviral therapy (cART). PD is characterized by chronic inflammation and dysbiosis. Nevertheless, the molecular mechanisms and use of feasible therapeutic strategies to reduce/reverse inflammation and dysbiosis remain understudied and unaddressed.

METHODS

Employing a systems biology approach, we report molecular, metabolome and microbiome changes underlying PD and its modulation by phytocannabinoids [delta-9-tetrahydrocannabinol (Δ9-THC)] in uninfected and SIV-infected rhesus macaques (RMs) untreated (VEH-untreated/SIV) or treated with vehicle (VEH/SIV) or Δ9-THC (THC/SIV).

FINDINGS

VEH- untreated/SIV but not THC/SIV RMs showed significant enrichment of genes linked to anti-viral defense, interferon-β, NFκB, RIG-1, and JAK-STAT signaling. We focused on the anti-microbial DUOX1 and immune activation marker IDO1 that were reciprocally regulated in the gingiva of VEH-untreated/SIV RMs. Both proteins localized to the gingival epithelium and CD163+ macrophages, and showed differential expression in the gingiva of THC/SIV and VEH/SIV RMs. Additionally, inflammation-associated miR-21, miR-142-3p, miR-223, and miR-125a-5p showed significantly higher expression in the gingiva of VEH/SIV RMs. In human primary gingival epithelial cells, miR-125a-5p post-transcriptionally downregulated DUOX1 and THC inhibited IDO1 protein expression through a cannabinoid receptor-2 mediated mechanism. Interestingly, THC/SIV RMs showed relatively reduced plasma levels of kynurenine, kynurenate, and the neurotoxic quinolinate compared to VEH/SIV RMs at 5 months post SIV infection (MPI). Most importantly, THC blocked HIV/SIV-induced depletion of Firmicutes and Bacteroidetes, and reduced Gammaproteobacteria abundance in saliva. Reduced IDO1 protein expression was associated with significantly (p<0.05) higher abundance of Prevotella, Lactobacillus (L. salivarius, L. buchneri, L. fermentum, L. paracasei, L. rhamnosus, L. johnsonii) and Bifidobacteria and reduced abundance of the pathogenic Porphyromonas cangingivalis and Porphyromonas macacae at 5MPI.

INTERPRETATION

The data provides deeper insights into the molecular mechanisms underlying HIV/SIV-induced PD and more importantly, the anti-inflammatory and anti-dysbiotic properties of THC in the oral cavity. Overall, these translational findings suggest that phytocannabinoids may help reduce gingival/systemic inflammation, salivary dysbiosis and potentially metabolic disease/syndrome in PLWH on cART and those with no access to cART or do not suppress the virus under cART.

FUNDING

Research reported in this publication was supported by the National Institutes of Health Award Numbers R01DA052845 (MM and SNB), R01DA050169 (MM and CO), R01DA042524 and R56DE026930 (MM), and P51OD011104 and P51OD011133. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

Early Biomarkers of Periodontitis: New Challenges for a Personalized Medicine Approach

Recently, the concept of precision medicine has attracted attention [...].

Ascorbic Acid: A New Player of Epigenetic Regulation in LPS-gingivalis Treated Human Periodontal Ligament Stem Cells

Periodontitis is usually sustained from microorganism of oral cavity, like Porphyromonas gingivalis (P. gingivalis). Periodontal disease is an infectious disease that afflicts a large number of people. Researches are investigating on the mesenchymal stem cells (MSCs) response to inflammatory events in combination with antioxidant substances. In particular, ascorbic acid (AA) increased cell proliferation, upregulated the cells pluripotency marker expression, provide a protection from inflammation, and induced the regeneration of periodontal ligament tissue. The purpose of the present research was to investigate the effects of AA in primary culture of human periodontal ligament stem cells (hPDLSCs) exposed to P. gingivalis lipopolysaccharide (LPS-G). The effect of AA on hPDLSCs exposed to LPS-G was determined through the cell proliferation assay. The molecules involved in the inflammatory pathway and epigenetic regulation have been identified using immunofluorescence and Western blot analyses. miR-210 level was quantified by qRT-PCR, and the ROS generation was finally studied. Cells co-treated with LPS-G and AA showed a restoration in terms of cell proliferation. The expression of NFκB, MyD88, and p300 was upregulated in LPS-G exposed cells, while the expression was attenuated in the co-treatment with AA. DNMT1 expression is attenuated in the cells exposed to the inflammatory stimulus. The level of miR-210 was reduced in stimulated cells, while the expression was evident in the hPDLSCs co-treated with LPS-G and AA. In conclusion, the AA could enhance a protective effect in in vitro periodontitis model, downregulating the inflammatory pathway and ROS generation and modulating the miR-210 level.