MicroRNAs: Harbingers and shapers of periodontal inflammation

PANoptosis: a new insight for oral diseases

PANoptosis, a burgeoning area of research, is a unique type of programmed cell death typified by pyroptosis, apoptosis, and necroptosis, yet it defies singular classification by any one mode of death. The assembly and activation of PANoptosomes are pivotal processes in PANoptosis, with several PANoptosomes already identified. Linkages between PANoptosis and the pathophysiology of various systemic illnesses are established, with increasing recognition of its association with oral ailments. This paper aims to deepen understanding by conducting a comprehensive analysis of the molecular pathways driving PANoptosis and exploring its potential implications in oral diseases.

Hsa-miR-342-3p and hsa-miR-360 may be the key molecules that promote periodontitis in type 2 diabetes mellitus

Background

Periodontitis (PD) has been acknowledged as a complication associated with type 2 diabetes mellitus (T2DM). However, the precise mechanism through which T2DM fosters the development of PD remains elusive. Our objective is to elucidate the connection between these two conditions by conducting bioinformatics analysis.

Methods

In this study, we analyzed miRNA datasets pertaining to T2DM and PD sourced from GEO. Through differential expression analysis, we identified common differentially expressed miRNAs (DE-miRNAs) and subsequently analyzed the functional enrichment of these common DE-miRNAs. We further leveraged the PD transcriptome database to select DE-miRNA-targeted mRNAs and examined their association with immune infiltration. Finally, machine learning was used to further screen hub DE-miRNA-targeted mRNAs and validate our data in external datasets.

Results

Two common DE-miRNAs, namely hsa-miR-342-3p and hsa-miR-360, were identified from the miRNA datasets of PD and T2DM. Functional enrichment analysis indicated that these two common DE-miRNAs predominantly participate in Ras, PI3K-Akt, p53, and MAPK signaling pathways. Integration of the PD transcriptome dataset revealed a total of 21 DE-miRNA-targeted mRNAs in PD, with strong correlations observed with plasma cells and dendritic cells. Finally, three hub DE-miRNA-targeted mRNAs (hsa-miR-342-3p-/hsa-miR-360-RASAL2, hsa-miR-360-ENTPD1/PLXDC2) were identified. ENTPD1 exhibited a robust positive correlation with plasma cells and a negative correlation with resting dendritic cells.

Conclusions

Therefore, hsa-miR-342-3p-/hsa-miR-360-RASAL2, as well as hsa-miR-360-ENTPD1/PLXDC2, may serve as diagnostic and therapeutic targets for T2DM-associated PD.

Could Periodontitis Increase the Risk of Suffering from Pancreatic Cancer?-A Systematic Review

(1) Background: The relationship between periodontitis and systemic pathologies continues to grow. Recently, the presence of periodontal pathogens has been linked to an increased risk of pancreatic cancer (PC) and its mortality. Thus, a systematic review is needed to identify whether an association between the two diseases can be established. The objective of this review is to elucidate the mechanisms responsible for this association. (2) Methods: A systematic review was carried out using three databases (PubMed, Embase and Scopus) with the following keywords "Periodontitis AND pancreatic cancer". A total of 653 articles were retrieved; before selection and screening, the inclusion and exclusion criteria were defined, resulting in a total of 13 articles being included in the review. (3) Results: The increase in low-grade systemic inflammation, pH changes, and the cytotoxicity of certain periodontopathogenic bacteria were found in the scientific literature reviewed as mechanisms linking periodontitis with the risk of PC. (4) Conclusions: Through this systematic review, we have seen how periodontitis can be related to PC and how it worsens its prognosis. Knowing the behavior of periodontopathogenic bacteria and the influence they have on our immune and inflammatory system may help to achieve an interdisciplinary approach to both pathologies.

Quercetin-loaded mesoporous nano-delivery system remodels osteoimmune microenvironment to regenerate alveolar bone in periodontitis via the miR-21a-5p/PDCD4/NF-κB pathway

BACKGROUND

Impaired osteo-/angiogenesis, excessive inflammation, and imbalance of the osteoimmune homeostasis are involved in the pathogenesis of the alveolar bone defect caused by periodontitis. Unfortunately, there is still a lack of ideal therapeutic strategies for periodontitis that can regenerate the alveolar bone while remodeling the osteoimmune microenvironment. Quercetin, as a monomeric flavonoid, has multiple pharmacological activities, such as pro-regenerative, anti-inflammatory, and immunomodulatory effects. Despite its vast spectrum of pharmacological activities, quercetin's clinical application is limited due to its poor water solubility and low bioavailability.

RESULTS

In this study, we fabricated a quercetin-loaded mesoporous bioactive glass (Quercetin/MBG) nano-delivery system with the function of continuously releasing quercetin, which could better promote the bone regeneration and regulate the immune microenvironment in the alveolar bone defect with periodontitis compared to pure MBG treatment. In particular, this nano-delivery system effectively decreased injection frequency of quercetin while yielding favorable therapeutic results. In view of the above excellent therapeutic effects achieved by the sustained release of quercetin, we further investigated its therapeutic mechanisms. Our findings indicated that under the periodontitis microenvironment, the intervention of quercetin could restore the osteo-/angiogenic capacity of periodontal ligament stem cells (PDLSCs), induce immune regulation of macrophages and exert an osteoimmunomodulatory effect. Furthermore, we also found that the above osteoimmunomodulatory effects of quercetin via macrophages could be partially blocked by the overexpression of a key microRNA--miR-21a-5p, which worked through inhibiting the expression of PDCD4 and activating the NF-κB signaling pathway.

CONCLUSION

In summary, our study shows that quercetin-loaded mesoporous nano-delivery system has the potential to be a therapeutic approach for reconstructing alveolar bone defects in periodontitis. Furthermore, it also offers a new perspective for treating alveolar bone defects in periodontitis by inhibiting the expression of miR-21a-5p in macrophages and thereby creating a favorable osteoimmune microenvironment.

MiR-103a-3p Promotes Tumorigenesis of Breast Cancer by Targeting ETNK1

Background

We aimed to elucidate the molecular mechanism of miR-103a-3p regulating breast cancer progression.

Methods

Firstly, clinical tissues was obtained from 2019-2023 at Yancheng Third People's Hospital, Yancheng, China. miR-103a-3p or ETNK1 expression in clinical tissues or breast cancer cell lines was analyzed with qRTPCR. MDA-MB-231 cells were performed with miR-103a-3p inhibitor or mimic, and OE-ETNK1. The proliferation and apoptosis ability were detected by CCK-8 and TUNEL assay. The xenograft models were established by inoculating transfected MDA-MB-231 cells to BALB/c mice.

Results

miR-103a-3p showed an overexpression and was related to poor prognosis in breast cancer. miR-103a-3p-deprived MDA-MB-231 cells displayed weaker levels of cell proliferation and higher rates of apoptosis. In contrast, ETNK1 was downregulated in breast cancer and proved to be a downstream target of miR-103a-3p. Xenograft models subjected to either miR-103a-3p antagomir treatment or ETNK1-knockdown resulted in tumor growth suppression.

Conclusion

miR-103a-3p might promote breast cancer progression by inhibiting ETNK1.

Unique miRomics Expression Profiles in Tannerella forsythia-Infected Mandibles during Periodontitis Using Machine Learning

T. forsythia is a subgingival periodontal bacterium constituting the subgingival pathogenic polymicrobial milieu during periodontitis (PD). miRNAs play a pivotal role in maintaining periodontal tissue homeostasis at the transcriptional, post-transcriptional, and epigenetic levels. The aim of this study was to characterize the global microRNAs (miRNA, miR) expression kinetics in 8- and 16-week-old T. forsythia-infected C57BL/6J mouse mandibles and to identify the miRNA bacterial biomarkers of disease process at specific time points. We examined the differential expression (DE) of miRNAs in mouse mandibles (n = 10) using high-throughput NanoString nCounter® miRNA expression panels, which provided significant advantages over specific candidate miRNA or pathway analyses. All the T. forsythia-infected mice at two specific time points showed bacterial colonization (100%) in the gingival surface, along with a significant increase in alveolar bone resorption (ABR) (p < 0.0001). We performed a NanoString analysis of specific miRNA signatures, miRNA target pathways, and gene network analysis. A total of 115 miRNAs were DE in the mandible tissue during 8 and 16 weeks The T. forsythia infection, compared with sham infection, and the majority (99) of DE miRNAs were downregulated. nCounter miRNA expression kinetics identified 67 downregulated miRNAs (e.g., miR-375, miR-200c, miR-200b, miR-34b-5p, miR-141) during an 8-week infection, whereas 16 upregulated miRNAs (e.g., miR-1902, miR-let-7c, miR-146a) and 32 downregulated miRNAs (e.g., miR-2135, miR-720, miR-376c) were identified during a 16-week infection. Two miRNAs, miR-375 and miR-200c, were highly downregulated with >twofold change during an 8-week infection. Six miRNAs in the 8-week infection (miR-200b, miR-141, miR-205, miR-423-3p, miR-141-3p, miR-34a-5p) and two miRNAs in the 16-week infection (miR-27a-3p, miR-15a-5p) that were downregulated have also been reported in the gingival tissue and saliva of periodontitis patients. This preclinical in vivo study identified T. forsythia-specific miRNAs (miR-let-7c, miR-210, miR-146a, miR-423-5p, miR-24, miR-218, miR-26b, miR-23a-3p) and these miRs have also been reported in the gingival tissues and saliva of periodontitis patients. Further, several DE miRNAs that are significantly upregulated (e.g., miR-101b, miR-218, miR-127, miR-24) are also associated with many systemic diseases such as atherosclerosis, Alzheimer's disease, rheumatoid arthritis, osteoarthritis, diabetes, obesity, and several cancers. In addition to DE analysis, we utilized the XGBoost (eXtreme Gradient boost) and Random Forest machine learning (ML) algorithms to assess the impact that the number of miRNA copies has on predicting whether a mouse is infected. XGBoost found that miR-339-5p was most predictive for mice infection at 16 weeks. miR-592-5p was most predictive for mice infection at 8 weeks and also when the 8-week and 16-week results were grouped together. Random Forest predicted miR-592 as most predictive at 8 weeks as well as the combined 8-week and 16-week results, but miR-423-5p was most predictive at 16 weeks. In conclusion, the expression levels of miR-375 and miR-200c family differed significantly during disease process, and these miRNAs establishes a link between T. forsythia and development of periodontitis genesis, offering new insights regarding the pathobiology of this bacterium.

MicroRNA-155 (miR-155) as an accurate biomarker of periodontal status and coronary heart disease severity: a case-control study

BACKGROUND

Increasing evidence supports associations between periodontal disease and coronary heart disease (CHD). This case-control study evaluated whether inflammatory regulator, microRNA-155 (miR-155), could be utilised as a biomarker of periodontitis and/or CHD.

METHODS

Of 120 participants, 30 patients had clinically healthy periodontium (controls, C), 30 patients had generalized periodontitis (P), 30 patients had CHD and clinically healthy periodontium (AS-C); and 30 patients had CHD with generalized periodontitis (AS-P). Patient demographic and periodontal characteristics (plaque index, bleeding on probing, probing pocket depth and clinical attachment loss), were collected. Patient whole blood and saliva levels of miR-155 and pro-inflammatory cytokine (interleukin-1β), were quantified by quantitative real time polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA). One-way ANOVA with post-hoc Tukey test was used to determine differences among the four groups. Chi Square test was used for participant gender comparisons. Pearson correlation tests and multiple linear regression analyses were used to assess associations between the demographic and clinical variables analysed, versus IL-1β and miR-155 levels. miR-155 and IL-1β accuracy in differentiating healthy versus other patient groups were analysed using receiver operating characteristic (ROC) curves, by calculating area under the curve (AUC) values and sensitivity and specificity cut-off points using Youden's index. Statistical tests of sensitivity and specificity were conducted using the McNemar test.

RESULTS

Whole blood miR-155 levels were elevated in periodontitis/non-periodontitis patients with CHD (AS-P, AS-C), and periodontitis patients alone (P) (p < 0.001). Receiver operating characteristic (ROC) and area under the curve (AUC) analyses confirmed miR-155 accuracy in discriminating P, AS-C and AS-P groups (AUC 0.6861-0.9944, p < 0.0001-0.05), coupled with high sensitivity (76.7-100.0%), specificity (53.3-96.7%) and cut-off points (> 0.955- > 2.915 a.u.; p < 0.0001). miR-155 levels further distinguished between CHD (AS-C, AS-P) and periodontitis (P) patients (AUC ≥ 0.8378, sensitivity ≥ 88.7%, specificity ≥ 73.3%, cut-off > 2.82 a.u; p < 0.0001), and between AS-C and AS-P patients (AUC 0.7578, sensitivity 80.0%, specificity 50.0%, cut-off > 7.065 a.u; p < 0.001). Subsequent analyses identified positive correlations between miR-155 and the various patient demographics, salivary interleukin-1β and periodontal parameters assessed.

CONCLUSIONS

This study advocates miR-155 as an accurate diagnostic/prognostic biomarker of periodontitis and/or CHD severity, thereby improving detection and treatment for both conditions.

Analysis of oral microbiome on temporary anchorage devices under different periodontal conditions

BACKGROUND

Temporary anchorage devices (TADs) are maximum anchorages that have been widely used in orthodontic treatment. The aim of the study was to uncover whether a history of periodontitis would influence microbiome colonization on the TAD surface.

RESULTS

Patients were grouped by periodontal evaluations before the orthodontic treatment. Patients with healthy periodontal conditions were classified as the healthy group, and patients diagnosed with periodontitis stage II or even worse were classified as the periodontitis group. Scanning electron microscopy (SEM) was used to analyze the existence of biofilm on the surface of 4 TADs from the healthy group and 4 TADs from the periodontitis group. Fifteen TADs from the healthy group and 12 TADs from the periodontitis group were collected. The microorganisms on the surface of TADs were harvested and analyzed by 16S rRNA gene sequencing. α-diversity indices and β-diversity indices were calculated. Wilcoxon's test was used to determine differences between genera, species as well as KEGG functions. SEM analysis revealed bacteria colonization on the surface of TADs from both groups. Principal coordinate analysis (PCoA) based on β diversity revealed differential sample clusters depending on periodontal conditions (P < 0.01). When comparing specific genera, Fusobacterium, Porphyromonas, Saccharibacteria_(TM7)_[G-1], Dialister, Parvimonas, Fretibacterium, Treponema were more enriched in TADs in the periodontitis group. In the KEGG analysis, TADs in the periodontitis group demonstrated enriched microbial activities involved with translation, genetic information processing, metabolism, and cell motility.

CONCLUSIONS

This analysis elucidated the difference in total composition and function of TADs oral microorganisms between patients periodontally healthy and with periodontitis.

MicroRNAs and Periodontal Disease: Helpful Therapeutic Targets?

Periodontal disease is the most common oral disease. This disease can be considered as an inflammatory disease. The immune response to bacteria accumulated in the gum line plays a key role in the pathogenesis of periodontal disease. In addition to immune cells, periodontal ligament cells and gingival epithelial cells are also involved in the pathogenesis of this disease. miRNAs which are small RNA molecules with around 22 nucleotides have a considerable relationship with the immune system affecting a wide range of immunological events. These small molecules are also in relation with periodontium tissues especially periodontal ligament cells. Extensive studies have been performed in recent years on the role of miRNAs in the pathogenesis of periodontal disease. In this review paper, we have reviewed the results of these studies and discussed the role of miRNAs in the immunopathogenesis of periodontal disease comprehensively. miRNAs play an important role in the pathogenesis of periodontal disease and maybe helpful therapeutic targets for the treatment of periodontal disease.

Long non‑coding RNA SNHG5 promotes osteogenic differentiation of human periodontal ligament stem cells via mediating miR‑23b‑3p/Runx2 axis

The treatment of bone loss due to periodontitis has posed a great challenge for physicians for decades. Therefore, it is of extraordinary significance to identify an effective regeneration scheme for alveolar bone. This study aimed to investigate long non-coding RNA (lncRNA) small nucleolar RNA host gene 5 (SNHG5) whether sponges microRNA-23b-3p (miR-23b-3p) to achieve the osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs). Results revealed that the expression of SNHG5 was upregulated whereas that of miR-23b-3p was downregulated in osteogenic hPDLSCs. Alizarin red staining assays and qRT-PCR demonstrated that SNHG5 silencing or miR-23b-3p overexpression inhibits hPDLSCs osteogenic differentiation and vice versa. In addition, miR-23b-3p partially abolished the promotive effect of SNHG5 on osteogenic differentiation of hPDLSCs. Dual luciferase report and RNA pulldown assay verified that miR-23b-3p is a regulatory target of SNHG5 and that Runx2 is a gene target of miR-23b-3p. In brief, the results demonstrate that SNHG5 promotes the osteogenic differentiation of hPDLSCs by regulating the miR-23b-3p/Runx2 axis. Our study provides novel mechanistic insights into the critical role of lncRNA SNHG5 as a miR-23b-3p sponge to regulate Runx2 expression in hPDLSCs and may serve as a potential therapeutics target for periodontitis.

Genetically engineered CXCR4-modified exosomes for delivery of miR-126 mimics to macrophages alleviate periodontitis

Biofilm-related diseases are a group of diseases that tolerate antimicrobial chemotherapies and therefore are refractory to treatment. Periodontitis, a non-device chronic biofilm disease induced by dental plaque, can serve as an excellent in vivo model to study the important effects of host factors on the biofilm microenvironment. Macrophage activity is one of the key factors that modulate the progression of inflammation-driven destruction in periodontitis; therefore it is an important host immunomodulatory factor. In this study, the reduction of microRNA-126 (miR-126) with the recruitment of macrophages in periodontitis was confirmed in clinical samples, and a strategy for targeted delivery of miR-126 to macrophages was explored. Exosomes overexpressing the C-X-C motif chemokine receptor 4 (CXCR4) loaded with miR-126 (CXCR4-miR126-Exo) was successfully constructed, which reduced off-target delivery to macrophages and regulated macrophages toward the anti-inflammatory phenotype. In vivo local injection of CXCR4-miR126-Exo into sites of periodontitis in rats effectively reduced bone resorption and osteoclastogenesis and inhibited the progression of periodontitis. These results provide new insights for designing novel immunomodulatory factor targeted delivery systems to treat periodontitis and other biofilm-related diseases.

Novel long non-coding RNAs associated with inflammation and macrophage activation in human

Inflammation plays a central role in immune response and macrophage activation. Emerging studies demonstrate that along with proteins and genomic factors, noncoding RNA are potentially involved in regulation of immune response and inflammation. Our recent study demonstrated that lncRNA HOTAIR plays key roles in cytokine expression and inflammation in macrophages. The primary goal of this study is to discover novel lncRNAs that are crucial players in inflammation, macrophage activation, and immune response in humans. Towards this, we have stimulated THP1-derived macrophages (THP1-MΦ) with lipopolysaccharides (LPS) and performed the whole transcriptome RNA-seq analysis. Based on this analysis, we discovered that along with well-known marker for inflammation (such as cytokines), a series of long noncoding RNAs (lncRNAs) expression were highly induced upon LPS-stimulation of macrophages, suggesting their potential roles in inflammation and macrophage activation. We termed these family of lncRNAs as Long-noncoding Inflammation Associated RNA (LinfRNA). Dose and time dependent analysis demonstrated that many human LinfRNA (hLinfRNAs) expressions follow similar patterns as cytokine expressions. Inhibition of NF-κB suppressed the expression of most hLinfRNAs suggesting their potential regulation via NF-κB activation during inflammation and macrophage activation. Antisense-mediated knockdown of hLinfRNA1 suppressed the LPS-induced expression of cytokines and pro-inflammatory genes such as IL6, IL1β, and TNFα expression, suggesting potential functionality of the hLinfRNAs in cytokine regulation and inflammation. Overall, we discovered a series of novel hLinfRNAs that are potential regulators of inflammation and macrophage activation and may be linked to inflammatory and metabolic diseases.

Identification of a miRNA Panel with a Potential Determinant Role in Patients Suffering from Periodontitis

In recent years, the role of microRNA (miRNA) in post-transcriptional gene regulation has advanced and supports strong evidence related to their important role in the regulation of a wide range of fundamental biological processes. Our study focuses on identifying specific alterations of miRNA patterns in periodontitis compared with healthy subjects. In the present study, we mapped the major miRNAs altered in patients with periodontitis (n = 3) compared with healthy subjects (n = 5), using microarray technology followed by a validation step by qRT-PCR and Ingenuity Pathways Analysis. Compared to healthy subjects, 159 differentially expressed miRNAs were identified among periodontitis patients, of which 89 were downregulated, and 70 were upregulated, considering a fold change of ±1.5 as the cut-off value and p ≤ 0.05. Key angiogenic miRNAs (miR-191-3p, miR-221-3p, miR-224-5p, miR-1228-3p) were further validated on a separate cohort of patients with periodontitis versus healthy controls by qRT-PCR, confirming the microarray data. Our findings indicate a periodontitis-specific miRNA expression pattern representing an essential issue for testing new potential diagnostic or prognostic biomarkers for periodontal disease. The identified miRNA profile in periodontal gingival tissue was linked to angiogenesis, with an important molecular mechanism that orchestrates cell fate.

microRNA-142-3p regulates osteogenic differentiation of human periodontal ligament stem cells via mediating SGK1

OBJECTIVE

Human periodontal ligament stem cells (hPDLSCs) refer to one kind of somatic stem cells that are capable of differentiating into multiple cell kinds and undergoing robust clonal self-renewal. This work was unearthed to elucidate the possible molecular mechanism of miR-142-3p in mediating osteogenic differentiation of hPDLSCs by targeting SGK1.

METHODS

The hPDLSCs were isolated, cultured, and identified. hPDLSCs were identified by immunofluorescence staining and multiple differentiation ability detection. Cell proliferation ability was assessed by CCK-8 assay. hPDLSCs were induced using osteogenic differentiation medium. ALP activity was detected by alkaline phosphatase (ALP) staining  and ALP activity assay, and mineralized nodule formation was determined by alizarin red staining. The expression levels of osteogenic differentiation marker proteins ALP, RUNX2, and OCN were measured by RT-qPCR. miR-142-3p candidate targets were obtained through bioinformatics analysis. The relationship between miR-142-3p and SKG1 was verified.

RESULTS

miR-142-3p in hPDLSCs after osteogenic induction was down-regulated. Elevated miR-142-3p restricted hPDLSCs proliferation, and diminished ALP activity and mineralized nodule formation, as well as the expression of ALP, RUNX2, and OCN, while miR-142-3p inhibition led to inverse results. miR-142-3p inhibited SKG1 expression. SKG1 overexpression promoted hPDLSC proliferation and osteogenic differentiation, and reversed the inhibitory function of miR-142-3p on hPDLSCs.

CONCLUSION

This study highlights that miR-142-3p represses osteogenic differentiation of hPDLSCs by reducing SGK1 expression.

Exploring craniofacial and dental development with microRNAs

microRNAs (miRs) are small RNA molecules that regulate many cellular and developmental processes. They control gene expression pathways during specific developmental time points and are required for tissue homeostasis and stem cell maintenance. miRs as therapeutic reagents in tissue regeneration and repair hold great promise and new technologies are currently being designed to facilitate their expression or inhibition. Due to the large amount of miR research in cells and cancer many cellular processes and gene networks have been delineated however, their in vivo response can be different in complex tissues and organs. Specifically, this report will discuss animal developmental models to understand the role of miRs as well as xenograft, disease, and injury models. We will discuss the role of miRs in clinical studies including their diagnostic function, as well as their potential ability to correct craniofacial diseases.

Research progress in endothelial cell injury and repair

Endothelial cells, which are important metabolic and endocrine cells, play an important role in regulating vascular function. The occurrence and development of various cardiovascular and cerebrovascular diseases are associated with endothelial dysfunction. However, the underlying mechanism of vascular endothelial injury is not fully understood. It has been reported that the mechanism of endothelial injury mainly involves inflammation and oxidative stress. Moreover, endothelial progenitor cells are regarded as important contributors in repairing damaged endothelium. Multiple interventions (including chemical drugs and traditional Chinese medicines) exert endothelial protection by decreasing the release of inducing factors, suppressing inflammation and oxidative stress, and preventing endothelial cell senescence.

MicroRNA sequence and function analysis in peri-implantitis and periodontitis: An animal study

OBJECTIVE

To compare miRNA expression levels and predict relevant target genes and signaling pathways in peri-implantitis and periodontitis.

BACKGROUND

There are many differences between periodontitis and peri-implantitis. An understanding of the similarities and differences in the transcriptional patterns of these diseases, as well as the molecular mechanisms, is beneficial for the development of management strategies.

MATERIALS AND METHODS

Rat models of periodontitis (PD, n = 6) and peri-implantitis (PI, n = 5) were established by ligation. Implantation without ligation (PIC, n = 5) and normal rats (PDC, n = 6) were used as controls. Micro-CT was used to confirm the successful establishment of the model. Gingiva was harvested for miRNA transcriptome sequencing, and the results were confirmed by qRT-PCR. miRNA target genes were predicted with miRTarBase. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed.

RESULTS

Sixty-nine miRNAs were differentially expressed in PI vs. PD, 105 were differentially expressed in PI vs. PIC, and 70 were differentially expressed in PD vs. PDC (log₂ FC ≥1 and padj <0.05). The upregulated genes in all three comparisons were mostly involved in the biological process response to stimulus, whereas most of the downregulated genes were involved in nervous system development (p < .01). The upregulated genes in PI vs. PD and PI vs. PIC were involved in Toll-like receptor signaling and RIG-I-like signaling. The upregulated genes in PI vs. PD were involved in T- and B-cell receptor signaling, apoptosis, and osteoclast differentiation. Focal adhesion was downregulated in all three comparisons, and adherens junction was downregulated in PI vs. PD and PD vs. PDC (p < .1).

CONCLUSION

This study showed differences in the miRNA expression profiles between peri-implantitis and periodontitis and annotated the possible target genes and molecular mechanisms; this study could lay a foundation for the development of management strategies.

Identification of microRNA-mRNA-TF regulatory networks in periodontitis by bioinformatics analysis

BACKGROUND

Periodontitis is a complex infectious disease with various causes and contributing factors. The aim of this study was to identify key genes, microRNAs (miRNAs) and transcription factors (TFs) and construct a miRNA-mRNA-TF regulatory networks to investigate the underlying molecular mechanism in periodontitis.

METHODS

The GSE54710 miRNA microarray dataset and the gene expression microarray dataset GSE16134 were downloaded from the Gene Expression Omnibus database. The differentially expressed miRNAs (DEMis) and mRNAs (DEMs) were screened using the "limma" package in R. The intersection of the target genes of candidate DEMis and DEMs were considered significant DEMs in the regulatory network. Next, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. Subsequently, DEMs were uploaded to the STRING database, a protein-protein interaction (PPI) network was established, and the cytoHubba and MCODE plugins were used to screen out key hub mRNAs and significant modules. Ultimately, to investigate the regulatory network underlying periodontitis, a global triple network including miRNAs, mRNAs, and TFs was constructed using Cytoscape software.

RESULTS

8 DEMis and 121 DEMs were found between the periodontal and control groups. GO analysis showed that mRNAs were most significantly enriched in positive regulation of the cell cycle, and KEGG pathway analysis showed that mRNAs in the regulatory network were mainly involved in the IL-17 signalling pathway. A PPI network was constructed including 81 nodes and 414 edges. Furthermore, 12 hub genes ranked by the top 10% genes with high degree connectivity and five TFs, including SRF, CNOT4, SIX6, SRRM3, NELFA, and ONECUT3, were identified and might play crucial roles in the molecular pathogenesis of periodontitis. Additionally, a miRNA-mRNA-TF coregulatory network was established.

CONCLUSION

In this study, we performed an integrated analysis based on public databases to identify specific TFs, miRNAs, and mRNAs that may play a pivotal role in periodontitis. On this basis, a TF-miRNA-mRNA network was established to provide a comprehensive perspective of the regulatory mechanism networks of periodontitis.