LncRNA-mediated ceRNA network was identified as a crucial determinant of differential effects in periodontitis and periimplantitis by high-throughput sequencing

A Modified Ligature-Induced Peri-Implantitis Murine Model and RNA Sequencing Analysis Compared With Human Subjects

AIM

To propose a modified method for establishing a peri-implantitis murine model, assess the gene expression profile and immune cell infiltration of the gingiva and alveolar bone, and evaluate the transcriptomic similarity between patients with peri-implantitis and the corresponding murine model.

MATERIALS AND METHODS

A ligature-induced peri-implantitis murine model was established using an immediate implant placement approach. RNA sequencing was performed to determine the transcriptomic profiles of peri-implant tissues from mice, patients with peri-implantitis and healthy individuals. Histopathological and bioinformatics analyses were performed to measure immune cell infiltration, bone remodelling, and inflammatory reactions.

RESULTS

Mouse gingival tissue showed strong immune and inflammatory responses, especially macrophage functions; these responses were weaker in the alveolar bone. Humans and mice showed similar gene expression patterns in the gingiva, with greater infiltration of macrophages and neutrophils.

CONCLUSIONS

During peri-implantitis progression, mouse gingival tissue exhibited increased immune-related functions and inflammation compared with the alveolar bone. Patients with peri-implantitis and the murine model displayed transcriptomic similarities within the gingiva. We propose that the modified ligature-induced peri-implantitis murine model is suitable for investigating peri-implantitis pathogenesis, with macrophages and neutrophils potentially being critical in its development.

CircRNA-mediated heterogeneous ceRNA regulation mechanism in periodontitis and peri-implantitis

BACKGROUND

Performing a comprehensive study on the differential expression of mRNAs, miRNAs, and circRNAs in the context of peri-implantitis and periodontitis has beneficial advantages to identify unique molecular signatures and pathways that may contribute to our understanding of these conditions.

METHODS

Gingival tissues from healthy individuals and peri-implantitis and periodontitis patients were obtained to identify differential expression genes (DEG) by Illumina HiSeq 2500 instrument. Differential expression analysis was conducted using R statistical software, with significance set at P < 0.05 and fold greater than 2. Functional enrichment analysis of the DEGs was conducted using the Reactome, Gene ontology and KEGG databases.

RESULTS

Significant differences in mRNA, miRNA, and circRNA profiles were identified between healthy gingival tissues. The top DEGs comprising 6 circRNAs, 2 miRNAs, and 4 mRNAs were identified and the constructed ceRNA network, elucidates their involvement in key signaling pathways such as ErbB, Wnt, and mTOR, which are crucial for understanding the inflammatory progression of these conditions.

CONCLUSIONS

This study highlights a heterogeneous circRNA-mediated ceRNA regulatory mechanism in peri-implantitis and periodontitis, activating signaling pathways and regulating gene expression. Key findings including a detailed analysis of the transcriptional landscape and identification of unique molecular signatures, pathways and cellular components in gingival tissues, offering insights into the molecular differences between peri-implantitis and periodontitis. The study may contribute to the understanding of the pathological mechanisms of these diseases and may aid in the development of targeted therapies.

Paired transcriptional analysis of periodontitis and peri-implantitis within same host: A pilot study

BACKGROUND

Peri-implantitis, a plaque-associated pathological condition, has been on the rise with the increasing prevalence of dental implants. Despite its similarities to periodontitis, peri‑implantitis is difficult to control completely and has high relapse rates. This has sparked interest in exploring the pathogenic differences between the two conditions.

METHODS

This cross-sectional study involved 10 participants to concurrently examine periodontitis and peri‑implantitis within the same patients, thereby minimizing inter-individual variation. Gingival tissue samples were collected from each participant, comprising 10 periodontitis and 10 peri‑implantitis tissues, and RNAs were extracted. Using RNA sequencing and bioinformatics analysis, we investigated complex gene interactions, immune responses, and the role of the extracellular matrix in both conditions. We identified hub genes in each enhanced Protein-Protein Interaction network, providing crucial insights into these diseases' pathogenesis.

RESULTS

Our findings highlighted the potential involvement of activated fibroblasts in the pathogenesis of peri‑implantitis, identifying three marker genes (ACTA2, FAP, and PDGFRβ) overexpressed in peri‑implantitis, thus highlighting their potential as disease-specific biomarkers.

CONCLUSIONS

Our study uncovered a novel connection between peri‑implantitis and activated fibroblasts, examining specific markers and microbial differences between periodontitis and peri‑implantitis. These insights improve our understanding of peri‑implantitis pathogenesis, encouraging future research for better management and prevention strategies.

CLINICAL SIGNIFICANCE

This study identifies key insights into the pathogenesis of peri‑implantitis compared to periodontitis. These findings promise to advance clinical approaches for better managing and preventing peri‑implantitis, addressing its complexities and high relapse rates effectively.

Diagnostic significance of LncRNA MIAT in periodontitis and the molecular mechanisms influencing periodontal ligament fibroblasts via the miR-204-5p/DKK1 axis

OBJECTIVE

This study investigated the clinical importance of long noncoding RNA myocardial infarction-associated transcript (MIAT) in periodontitis and its impact on the functional regulation of human periodontal ligament fibroblasts (hPDLFs).

METHODS

Ninety-eight periodontitis patients and 74 healthy controls were enrolled. In vitro cellular models were created using Porphyromonas gingivalis lipopolysaccharide (Pg-LPS) to stimulate hPDLFs. Real-time quantitative polymerase chain reaction was used to measure mRNA levels of MIAT and osteogenic factors. Inflammation factor concentration was assessed using an enzyme-linked immunosorbent assay. Cell viability and apoptosis were examined by cell counting kit -8 and flow cytometry assay. The targeting relationship was verified by the dual-luciferase reporter and RNA Immunoprecipitation assay.

RESULTS

Highly expressed MIAT and Dicckopf-1 (DDK1), and lowly expressed miR-204-5p were found in the gingival crevicular fluid of periodontitis patients and Pg-LPS induced hPDLFs. MIAT has a sensitivity of 76.53 % and a specificity of 86.49 % for identifying patients with periodontitis among healthy individuals. MIAT acts as a sponge for miR-204-5p and upregulates DDK1 mRNA expression. Silencing of MIAT diminished the promotion of apoptosis and inflammation in hPDLFs by Pg-LPS and enhanced osteogenic differentiation. However, a miR-204-5p inhibitor significantly reversed the effect of silenced MIAT.

CONCLUSIONS

MIAT may act as a promising biomarker for periodontitis. It modulates apoptosis, inflammation, and osteogenic differentiation of PDLFs by focusing on the miR-204-5p/DKK1 axis, indicating its potential as a new therapeutic target for treating periodontitis.

Bioinformatics investigation of adaptive immune-related genes in peri-implantitis and periodontitis: Characteristics and diagnostic values

BACKGROUND

Peri-implantitis and periodontitis have similar immunological bioprocesses and inflammatory phenotypes. In the inflammatory process, the adaptive immune cells can drive the development of disease. This research investigated the differences and diagnostic significance of peri-implantitis and periodontitis in adaptive immune responses.

METHODS

We acquired four GEO datasets of gene expressions in surrounding tissues in healthy person, healthy implant, periodontitis, and peri-implantitis patients. The structural characteristics and enrichment analyses of differential expression genes were examined. The adaptive immune landscapes in peri-implantitis and periodontitis were then evaluated using single sample gene set enrichment analysis. The STRING database and Cytoscape were used to identify adaptive hub genes, and the ROC curve was used to verify them. Finally, qRT-PCR method was used to verify the expression level of Hub gene in activated T cells on the titanium-containing or titanium-free culture plates.

RESULTS

At the transcriptome level, the data of healthy implant, peri-implantitis and periodontitis were highly dissimilar. The peri-implantitis and periodontitis both exhibited adaptive immune response. Except for the activated CD4+T cells, there was no significant difference in other adaptive immune cells between peri-implantitis and periodontitis. In addition, correlation analysis showed that CD53, CYBB, and PLEK were significantly positively linked with activated CD4+T cells in the immune microenvironment of peri-implantitis, making them effective biomarkers to differentiate it from periodontitis.

CONCLUSIONS

Peri-implantitis has a uniquely immunogenomic landscape that differs from periodontitis. This study provides new insights and ideas into the activated CD4+T cells and hub genes that underpin the immunological bioprocess of peri-implantitis.

Dental implant material related changes in molecular signatures in peri-implantitis - A systematic review of omics in-vivo studies

OBJECTIVE

Titanium particles have been shown in in-vitro studies to lead to the activation of specific pathways, this work aims to systematically review in- vivo studies examining peri-implant and periodontal tissues at the transcriptome, proteome, epigenome and genome level to reveal implant material-related processes favoring peri-implantitis development investigated in animal and human trials.

METHODS

Inquiring three literature databases (Medline, Embase, Cochrane) a systematic search based on a priori defined PICOs was conducted: '-omics' studies comparing molecular signatures in healthy and infected peri-implant sites and/or healthy and periodontitis-affected teeth in animals/humans. After risk of bias assessments, lists of differentially expressed genes and results of functional enrichment analyses were compiled whenever possible.

RESULTS

Out of 2187 screened articles 9 publications were deemed eligible. Both healthy and inflamed peri-implant tissues showed distinct gene expression patterns compared to healthy/diseased periodontal tissues in animal (n = 4) or human studies (n = 5), with immune response, bone metabolism and oxidative stress being affected the most. Due to the lack of available re-analyzable data and inconsistency in methodology of the eligible studies, integrative analyses on differential gene expression were not applicable CONCLUSION: The differences of transcriptomic signatures in between peri-implant lesions compared to periodontal tissue might be related to titanium particles arising from dental implants and are in line with the in-vitro data recently published by our group. Nevertheless, limitations emerge from small sample sizes of included studies and insufficient publication of re-analyzable data.

Revealing a potential necroptosis-related axis (RP11-138A9.1/hsa-miR-98-5p/ZBP1) in periodontitis by construction of the ceRNA network

BACKGROUND AND OBJECTIVES

Periodontitis, a prevalent chronic inflammatory condition, poses a significant risk of tooth loosening and subsequent tooth loss. Within the realm of programmed cell death, a recently recognized process known as necroptosis has garnered attention for its involvement in numerous inflammatory diseases. Nevertheless, its correlation with periodontitis is indistinct. Our study aimed to identify necroptosis-related lncRNAs and crucial lncRNA-miRNA-mRNA regulatory axes in periodontitis to further understand the pathogenesis of periodontitis.

MATERIALS AND METHODS

Gene expression profiles in gingival tissues were acquired from the Gene Expression Omnibus (GEO) database. Selecting hub necroptosis-related lncRNA and extracting the key lncRNA-miRNA-mRNA axes based on the ceRNA network by adding novel machine-learning models based on conventional analysis and combining qRT-PCR validation. Then, an artificial neural network (ANN) model was constructed for lncRNA in regulatory axes, and the accuracy of the model was validated by receiver operating characteristic (ROC) curve analysis. The clinical effect of the model was evaluated by decision curve analysis (DCA). Weighted correlation network analysis (WGCNA) and single-sample gene set enrichment analysis (ssGSEA) was performed to explore how these lncRNAs work in periodontitis.

RESULTS

Seven hub necroptosis-related lncRNAs and three lncRNA-miRNA-mRNA regulatory axes (RP11-138A9.1/hsa-miR-98-5p/ZBP1 axis, RP11-96D1.11/hsa-miR-185-5p/EZH2 axis, and RP4-773 N10.4/hsa-miR-21-5p/TLR3 axis) were predicted. WGCNA revealed that RP11-138A9.1 was significantly correlated with the "purple module". Functional enrichment analysis and ssGSEA demonstrated that the RP11-138A9.1/hsa-miR-98-5p/ZBP1 axis is closely related to the inflammation and immune processes in periodontitis.

CONCLUSION

Our study predicted a crucial necroptosis-related regulatory axis (RP11-138A9.1/hsa-miR-98-5p/ZBP1) based on the ceRNA network, which may aid in elucidating the role and mechanism of necroptosis in periodontitis.

Decoding the role of long non-coding RNAs in periodontitis: A comprehensive review

Periodontitis is an inflammatory disease characterized by the pathological loss of alveolar bone and the adjacent periodontal ligament. It is considered a disease that imposes a substantial health burden, with an incidence rate of 20-50%. The etiology of periodontitis is multifactorial, with genetic factors accounting for approximately half of severe cases. Studies have revealed that long non-coding RNAs (lncRNAs) play a pivotal role in periodontitis pathogenesis. Accumulating evidence suggests that lncRNAs have distinct regulatory mechanisms, enabling them to control numerous vital processes in periodontal cells, including osteogenic differentiation, inflammation, proliferation, apoptosis, and autophagy. In this review, we summarize the diverse roles of lncRNAs in the pathogenesis of periodontitis, shedding light on the underlying mechanisms of disease development. By highlighting the potential of lncRNAs as biomarkers and therapeutic targets, this review offers a new perspective on the diagnosis and treatment of periodontitis, paving the way for further investigation into the field of lncRNA-based therapeutics.

Development of Ferroptosis-Associated ceRNA Network in Periodontitis

OBJECTIVES

Periodontitis is a chronic inflammatory illness that may lead to tooth loosening and even loss, and its pathogenesis is not fully understood. Ferroptosis is an iron-dependent, regulated cell death. The present study aims to find the key ferroptosis-related genes (FRGs) in periodontitis and develop an mRNA-miRNA-lncRNA network to deeply explore the pathogenesis of periodontitis.

METHODS

Data from the Gene Expression Omnibus (GEO) database and FerrDb database were downloaded to discover the differentially expressed mRNA, miRNA, and FRGs. Functional enrichment analysis was conducted for the differentially expressed FRGs (DE-FRGs), including gene ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein-protein interaction (PPI) network analysis. Targetscan and miRtarbase were used to estimate the miRNAs that DE-FRGs may interact with, whilst StarBase v3.0 was used for lncRNA-miRNA interaction.

RESULTS

Seven DE-FRGs were identified through differential expression analysis. Interleukin 1 beta (IL1B) interacted with XBP1 and MMP13 in the PPI network. After taking the intersection between DE-miRNAs and predicted miRNAs, a ceRNA network containing IL1B, has-miR-185, has-miR-204, has-miR-211, has-miR-4306, and 28 lncRNAs was established.

CONCLUSIONS

Seven FRGs in periodontitis were identified, which might promote deeper understanding of ferroptosis in periodontitis.

Common Genetic Factors and Pathways in Alzheimer's Disease and Ischemic Stroke: Evidences from GWAS

Alzheimer's disease (AD) and ischemic stroke (IS) are common neurological disorders, and the comorbidity of these two brain diseases is often seen. Although AD and IS were regarded as two distinct disease entities, in terms of different etiologies and clinical presentation, recent genome-wide association studies (GWASs) revealed that there were common risk genes between AD and IS, indicating common molecular pathways and their common pathophysiology. In this review, we summarize AD and IS risk single nucleotide polymorphisms (SNPs) and their representative genes from the GWAS Catalog database, and find thirteen common risk genes, but no common risk SNPs. Furthermore, the common molecular pathways associated with these risk gene products are summarized from the GeneCards database and clustered into inflammation and immunity, G protein-coupled receptor, and signal transduction. At least seven of these thirteen genes can be regulated by 23 microRNAs identified from the TargetScan database. Taken together, the imbalance of these molecular pathways may give rise to these two common brain disorders. This review sheds light on the pathogenesis of comorbidity of AD and IS, and provides molecular targets for disease prevention, manipulation, and brain health maintenance.

Dental implant material related changes in molecular signatures in peri-implantitis - A systematic review and integrative analysis of omics in-vitro studies

OBJECTIVE

Since peri-implantitis differs clinically and histopathologically from periodontitis, implant wear debris is considered to play a role in the destructive processes. This work aims to systematically review if titanium particles affect oral-related cells through changes in molecular signatures (e.g., transcriptome, proteome, epigenome), thereby promoting peri-implantitis.

METHODS

Leveraging three literature databases (Medline, Embase, Cochrane) a systematic search based on a priori defined PICOs was conducted: '-omics' studies examining titanium exposure in oral-related cells. After risk of bias assessments, lists of differentially expressed genes, proteins, and results of functional enrichment analyses were compiled. The significance of overlapping genes across multiple studies was assessed via Monte Carlo simulation and their ranking was verified using rank aggregation.

RESULTS

Out of 2104 screened articles we found 12 eligible publications. A significant overlap of gene expression in oral-related cells exposed to titanium particles was found in four studies. Furthermore, changes in biological processes like immune/inflammatory or stress response as well as toll-like receptor (TLR) and mitogen-activated protein kinase (MAPK) signaling pathways were linked to titanium in transcriptome and proteome studies. Epigenetic changes caused by titanium were detected but inconsistent.

CONCLUSION

An influence of titanium implant wear debris on the development and progression of peri-implantitis is plausible but needs to be proven in further studies. Limitations arise from small sample sizes of included studies and insufficient publication of re-analyzable data.

CCK regulates osteogenic differentiation through TNFα/NF-κB in peri-implantitis

OBJECTIVE

Peri-implantitis is characterized by peri-implant mucositis and alveolar bone resorption. This study investigated cholecystokinin (CCK) expression and the mechanism underlying its involvement in peri-implantitis.

METHODS

mRNA sequencing was performed using the Gene Expression Omnibus database GSE106090. Human bone marrow mesenchymal stem cells (hBMSCs) were pretreated with various concentrations of CCK (0, 10, 30, or 100 nM) for 1 hour before induction in osteogenic differentiation medium for 2 weeks. Alkaline phosphatase (ALP) activity was determined, and the cells were stained with alizarin red. The expression levels of TNFα and the osteogenic markers ALP, RUNX2, and OCN were measured using quantitative real-time PCR. TNFα, phosphorylated P65, and total P65 levels were determined by western blot.

RESULTS

Compared with healthy individuals, 262 and 215 genes were up- and down-regulated, respectively, in the periodontal tissues of patients with peri-implantitis. CCK expression was significantly upregulated in patients with peri-implantitis. CCK reduced ALP activity, osteogenic differentiation, and levels of the osteogenic markers ALP, RUNX2, and OCN. Moreover, CCK promoted levels of TNFα and phosphorylated P65, which is a marker of activation for the NF-κB inflammatory pathway.

CONCLUSIONS

CCK regulates osteogenic differentiation through the TNFα/NF-κB axis in peri-implantitis.

Exploration of cross-talk and pyroptosis-related gene signatures and molecular mechanisms between periodontitis and diabetes mellitus via peripheral blood mononuclear cell microarray data analysis

OBJECTIVES

This bioinformatics study is aimed at identifying cross-talk genes, pyroptosis-related genes, and related pathways between periodontitis (PD) and diabetes mellitus (DM), which includes type 1 diabetes (T1DM) and type 2 diabetes (T2DM).

METHODS

GEO datasets containing peripheral blood mononuclear cell (PBMC) data of PD and DM were acquired. After batch correction and normalization, differential expression analysis was performed to identify the differentially expressed genes (DEGs). And cross-talk genes in the PD-T1DM pair and the PD-T2DM pair were identified by overlapping DEGs with the same trend in each pair. The weighted gene coexpression network analysis (WGCNA) algorithm helped locate the pyroptosis-related genes that are related to cross-talk genes. Receiver-operating characteristic (ROC) curve analysis confirmed the predictive accuracy of these hub genes in diagnosing PD and DM. The correlation between hub genes and the immune microenvironment of PBMC in these diseases was investigated by Spearman correlation analysis. The experimentally validated protein-protein interaction (PPI) and gene-pathway network were constructed. Subnetwork analysis helped identify the key pathway connecting DM and PD.

RESULTS

Hub genes in the PD-T1DM pair (HBD, NLRC4, AIM2, NLRP2) and in the PD-T2DM pair (HBD, IL-1Β, AIM2, NLRP2) were identified. The similarity and difference in the immunocytes infiltration levels and immune pathway scores of PD and DM were observed. ROC analysis showed that AIM2 and HBD exhibited pleasant discrimination ability in all diseases, and the subnetwork of these genes indicated that the NOD-like receptor signaling pathway is the most potentially relevant pathway linking PD and DM.

CONCLUSION

HBD and AIM2 could be the most relevant potential cross-talk and pyroptosis-related genes, and the NOD-like receptor signaling pathway could be the top candidate molecular mechanism linking PD and DM, supporting a potential pathophysiological relationship between PD and DM.

Whole-transcriptome analysis of periodontal tissue and construction of immune-related competitive endogenous RNA network

Background

In periodontitis, noncoding RNAs may play a regulatory role in the immune microenvironment through competitive endogenous RNA. We aimed to profile noncoding RNA expression and construct immune-related ceRNA network in periodontitis.

Methods

Five inflamed periodontal tissue and five healthy gingivae were collected for whole-transcriptome sequencing. Differential gene, functional enrichment, and protein–protein interaction network analysis were performed to explore the function of differentially expressed genes. CIBERSORTx was used to analyze level of immune cell infiltration in the periodontal tissue. An immune-related competitive endogenous RNA network was constructed and expression of key regulators in the network was validated.

Results

Compared with healthy gingiva, 200 mRNAs, 90 long noncoding RNAs, 65 microRNAs, and 518 circular RNAs were differentially expressed, and cell chemotaxis was significantly enhanced in inflamed periodontal tissue. Immune cell infiltration analysis showed that neutrophils, macrophages M1, T follicular helper cells, and naive B cells were significantly increased in periodontitis. Key regulators including JUN, FOS, THBS1, KLF2, WIF1, were identified and their expression was then validated.

Conclusion

We constructed an immune-related competitive endogenous RNA network in periodontal tissue, which provided new insights into immune homeostasis in periodontitis and laid a foundation for further study of noncoding RNAs. Key regulators in this network may be promising targets for future periodontitis treatment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-022-02401-0.

Long non-coding RNA SNHG5 mediates periodontal inflammation through the NF-κB signaling pathway

AIM

We investigated the role of the long non-coding RNA (lncRNA), small nucleolar RNA host gene 5 (SNHG5), in the pathogenesis of periodontitis.

MATERIALS AND METHODS

A ligature-induced periodontitis mouse model was established, and gingival tissues from patients with periodontitis and healthy controls were collected. Inflammatory cytokines were detected using qRT-PCR and western blotting analyses. Direct interactions between SNHG5 and p65 were detected by RNA pull-down and RNA immunoprecipitation assays. Micro-computed tomography, hematoxylin and eosin staining, and immunohistochemical staining were used to measure periodontal bone loss.

RESULTS

SNHG5 expression was downregulated in human and mouse periodontal tissues compared to that in the healthy controls. In vitro experiments demonstrated that SNHG5 significantly ameliorated tumor necrosis factor-α (TNFα)-induced inflammation. Mechanistically, SNHG5 directly binds to the nuclear factor-kappa B (NF-κB) p65 subunit and inhibits its translocation, thereby suppressing the NF-κB signaling pathway activation and reducing the nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing 3 inflammasome expression. Locally injecting si-SNHG5 aggravated the periodontal destruction.

CONCLUSION

This study revealed that SNHG5 mediates periodontal inflammation through the NF-κB signaling pathway, providing a potential therapeutic target for periodontitis treatment. This article is protected by copyright. All rights reserved.

Long non-coding RNA ZFY-AS1 represses periodontitis tissue inflammation and oxidative damage via modulating microRNA-129-5p/DEAD-Box helicase 3 X-linked axis

A large number of studies have manifested long non-coding RNA (lncRNA) is involved in the modulation of the development of periodontitis, but the specific mechanism has not been fully elucidated. The purpose of this study was to explore the biological function and latent molecular mechanism of lncZFY-AS1 in periodontitis. The results clarified lncZFY-AS1 and DEAD-Box Helicase 3 X-Linked (DDX3X) were up-regulated, but microRNA (miR)-129-5p was down-regulated in periodontitis. Knockdown of lncZFY-AS2 or overexpression of miR-129-5p decreased macrophage infiltration and periodontal membrane cell apoptosis, increased cell viability, repressed inflammatory factors and nuclear factor kappa B activation, reduced oxidative stress, but promoted nuclear factor-E2-related factor 2/heme oxygenase 1 expression. LncZFY-AS1 elevation further aggravated periodontitis inflammation, oxidative stress, and apoptosis. LncZFY competitively adsorbed miR-129-5p to mediate DDX3X expression. Knockdown lncZFY’s improvement effect on periodontitis was reversed by depressive miR-129-5p or enhancive DDX3X. In conclusion, these data suggest lncZFY-AS1 promotes inflammatory injury and oxidative stress in periodontitis by competitively binding to miR-129-5p and mediating DDX3X expression. LncZFY-AS1/miR-129-5p/DDX3X may serve as a novel molecular target for treatment of periodontitis in the future.

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.

LncRNA OIP5-AS1 inhibits the lipopolysaccharide-induced inflammatory response and promotes osteogenic differentiation of human periodontal ligament cells by sponging miR-92a-3p

Periodontitis is a chronic infectious disease that affects the oral health of adults. Long non-coding RNA OIP5 antisense RNA 1 (OIP5-AS1) has been reported to downregulated in the periodontal tissue of patients with periodontitis. Therefore, the study sought to look at the possible functions of OIP5-AS1 in periodontitis and the associated underlying mechanisms. In the present study, the expression level of OIP5-AS1 and microRNA-92a-3p were analyzed using reverse transcription-quantitative PCR. The levels of osteogenic proteins were determined using western blotting and inflammatory cytokines and oxidative stress were also examined. The proliferation of human periodontal ligament stem cells (hPDLSCs) was evaluated using MTT assays. Assay of osteogenic differentiation was undertaken by means of Alkaline phosphatase staining. The possible association between OIP5-AS1 and miR-92a-3p was determined applying dual-luciferase reporter assays and verified by RNA immunoprecipitation assay. We found that OIP5-AS1 was expressed at low levels in lipopolysaccharide (LPS)-stimulated hPDLSCs. OIP5-AS1 overexpression promoted proliferation and osteogenic differentiation ability and reduced LPS-induced inflammation in hPDLSCs. Furthermore, OIP5-AS1 directly targeted and reduced miR-92a-3p expression. The overexpression of miR-92a-3p partly abolished the effects of OIP5-AS1 on LPS-induced cell proliferation and osteogenic differentiation as well as inflammation in hPDLSCs. Collectively, the results indicated that OIP5-AS1 overexpression inhibited the LPS-induced inflammatory response and promoted the osteogenic differentiation of hPDLSCs by sponging miR-92a-3p. Thus, OIP5-AS1 is probably an essential objective for research during periodontitis treatment.

Long Noncoding RNA Metastasis-Associated Lung Adenocarcinoma Transcript 1 Promotes the Osteoblast Differentiation of Human Bone Marrow-Derived Mesenchymal Stem Cells by Targeting the microRNA-96/Osterix Axis

OBJECTIVES

To investigate whether and how the long noncoding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) sponges microRNA-96 (miR-96) to achieve the osteogenic differentiation of human bone marrow-derived mesenchymal stem cells (hBMSCs).

METHODS

Protein levels were detected by Western blot. Mineralized bone matrix formation was studied by alizarin red staining. Metastasis-associated lung adenocarcinoma transcript 1, miR-96, and osteogenesis-related Messenger RNA expression was assessed by Quantitative Real-time Polymerase Chain Reaction (qRT-PCR). The interactions between miR-96 and osterix (Osx), MALAT1, and miR-96 were determined by luciferase reporter assay.

RESULTS

The expression of MALAT1 was upregulated whereas that of miR-96 was downregulated in osteogenic hBMSCs. In addition, the expression of MALAT1 significantly decreased whereas that of miR-96 increased in the hBMSCs of osteoporosis (OP) patients. qRT-PCR and alizarin red staining assays showed that MALAT1 silencing or miR-96 overexpression inhibits hBMSC osteogenic differentiation and vice versa. overexpression of miR-96 reversed the promotive effect of MALAT1 on the osteogenic differentiation of hBMSCs. Dual luciferase report assay verified that miR-96 is a regulatory target of MALAT1 and that Osx is a gene target of miR-96.

CONCLUSIONS

Taken together, the results demonstrate that MALAT1 promotes the osteogenic differentiation of hBMSCs by regulating the miR-96/Osx axis. Our study provides novel mechanistic insights into the critical role of lncRNA MALAT1 as a microRNA sponge in OP patients and sheds new light on lncRNA-directed diagnostics and therapeutics in OP.

Systems Biology in Periodontitis

Systems biology is a promising scientific discipline that allows an integrated investigation of host factors, microbial composition, biomarkers, immune response and inflammatory mediators in many conditions such as chronic diseases, cancer, neurological disorders, and periodontitis. This concept utilizes genetic decoding, bioinformatic, flux-balance analysis in a comprehensive approach. The aim of this review is to better understand the current literature on systems biology and identify a clear applicability of it to periodontitis. We will mostly focus on the association between this condition and topics such as genomics, transcriptomics, proteomics, metabolomics, as well as contextualize delivery systems for periodontitis treatment, biomarker detection in oral fluids and associated systemic conditions.

Association between Maternal Periodontitis and Development of Systematic Diseases in Offspring

Periodontal disease (PD) is one of the most common oral conditions affecting both youths and adults. There are some research works suggesting a high incidence of PD in pregnant women. As an inflammatory disease of bacterial origin, PD may result in the activation of the pathways affecting the course and the pregnancy outcome. The authors, based on the literature review, try to answer the PICO question: Does maternal periodontitis (exposure) influence the incidence of complications rates in pregnancy and the development of systemic diseases in childhood and adult offspring (outcome) in the humans of any race (population) compared to the offspring of mothers with healthy periodontium (comparison)? The authors try to describe the molecular pathways and mechanisms of these interdependencies. There is some evidence that maternal periodontitis may affect the pregnancy course and outcome, resulting in preeclampsia, preterm delivery, vulvovaginitis and low birth weight. It can be suggested that maternal periodontitis may affect offspring epigenome and result in some health consequences in their adult life.

Proteomic and phosphorylated proteomic landscape of injured lung in juvenile septic rats with therapeutic application of umbilical cord mesenchymal stem cells

Acute lung injury (ALI) is the most common complication of sepsis. Intravenous injection of HUMSCs can regulate the level of circulating endothelial cytokines and alleviate lung injury in juvenile septic rats. In this study, we performed proteomic and phosphorylated proteomic analysis of lung tissue of juvenile septic rats after Human Umbilical Cord Mesenchymal Stem Cells (HUMSCs) intervention for the first time, and screened the potential proteins and pathways of HUMSCs for therapeutic effect. The 4D proteome quantitative technique was used to quantitatively analyze the lung tissues of septic rats 24 hours (3 biological samples) and 24 hours after HUMSCs intervention (3 biological samples). A total of 213 proteins were identified as differentially expressed proteins, and 971 phosphorylation sites changed significantly. Based on the public database, we analyzed the functional enrichment of these proteins and phosphorylated proteins. In addition, Tenascin-C may be the key differential protein and ECM receptor interaction pathway may be the main signal pathway by using various algorithms to analyze the protein-protein interaction network. Phosphorylation analysis showed that tight junction pathway was closely related to immune inflammatory reaction, and EGFR interacted most, which may be the key differential phosphorylated protein. Finally, 123 conserved motifs of serine phosphorylation site (pS) and 17 conserved motifs of threonine (pT) phosphorylation sites were identified by motif analysis of phosphorylation sites. Results from proteomics and phosphorylated proteomics, the potential new therapeutic targets of HUMSCs in alleviating lung injury in juvenile septic rats were revealed.

OUP accepted manuscript

Radioresistance is one of the key obstacles that may lead to the failure of cancer treatment. The underlying mechanisms of radioresistance remain largely unknown; however, increasing evidence has shown that long noncoding RNAs (lncRNAs) are involved in radiotherapy resistance of several cancers. In the present study, we demonstrated that radiation-elevated transcript (RET), a newly identified lnRNA, was highly expressed in cancer cells. Knockdown of RET significantly inhibited the proliferation and colony formation of cancer cells and markedly inhibited apoptosis. Furthermore, downregulation of RET in cancer cells significantly inhibited cell growth, decreased colony survival fractions, and promoted apoptosis in response to radiation treatment, indicating a role in radiation resistance. Moreover, RET knockdown significantly increased the expression of γ-H2AX, an indicator of DNA double strand damage, and reversed radiation-induced EMT, both of which contributed to its radiation resistance. In addition, a negative correlation was found between the expression of RET and PTEN. Rescue assays confirmed RET knockdown enhanced radiosensitivity of cancer cells by upregulating the expression of PTEN. Mechanistically, RET positively regulated Slug, a repressor of PTEN transcription, by acting as a molecular sponge of miR-3179. Our present study showed that RET conferred radioresistance by regulating miR-3179/Slug/PTEN axis, indicating that RET may be a potential target for the clinical application in cancer patients with radioresistance.

Development of an immune-related lncRNA-miRNA-mRNA network based on competing endogenous RNA in periodontitis

AIM

To explore the relationship between long non-coding RNAs (lncRNAs) and immune response and to construct an immune-related competing endogenous RNA (ceRNA) network in periodontitis.

MATERIALS AND METHODS

Gene expression profiles in gingival tissues were acquired from the Gene Expression Omnibus database. Bioinformatic analysis was performed to establish an immune-related ceRNA network. Subsequently, functional enrichment analysis was performed to detect the biological processes in which the ceRNA network might be involved.

RESULTS

A combined classification model involving seven lncRNAs was constructed. Receiver operating characteristic curve analysis showed satisfactory classification ability of the established model. Further analysis revealed that the screened lncRNAs were significantly correlated with patient immunity. Finally, an immune-related ceRNA network was constructed based on the lncRNA MIAT, miR-1246, miR-1260b, miR-3652, miR-4286, and 27 mRNAs. Accordingly, functional enrichment analysis demonstrated that this network is closely related to the proliferation, differentiation, and activation of B cells.

CONCLUSIONS

The lncRNA MIAT and the MIAT-based ceRNA network may be instrumental in regulating the immune response, especially of B cells, during the progression of periodontitis.

Using Tumor-Infiltrating Immune Cells and a ceRNA Network Model to Construct a Prognostic Analysis Model of Thyroid Carcinoma

Thyroid carcinoma is a solid malignant tumor that has had a fast-growing incidence in recent years. Our research used thyroid carcinoma gene expression profiling from TCGA (The Cancer Genome Atlas) database to identify differentially expressed ceRNAs. Using the gene expression profiling from 502 carcinoma thyroid tissues and 58 normal thyroid tissues from the TCGA database, we established the thyroid carcinoma-specific competitive endogenous RNA (ceRNA) network and found nine overall survival (OS)-associated genes (PRDM1, TGFBR3, E2F1, FGF1, ADAM12, ALPL, RET, AL928654.2, AC128688.2). We quantified the proportions of immune cells using the algorithm “CIBERSORT”, found three OS-associated immune cells (memory B cells, M0 macrophages, and activated dendritic cells), and established a thyroid carcinoma-specific immune cell network based on that. The good reliabilities AUC (area under the curve) of 10-year survival (0.955, 0.944, respectively) were accessed from the nomograms of genes and immune cells. Subsequently, by conducting co-expression analyses, we found a potential regulation network among ceRNAs and immune cells. Besides, we found that ALPL (alkaline phosphatase) and hsa-miR-204-5p were significantly correlated and that ALPL was related to activated dendritic cells. We took advantage of multi-dimensional databases to verify our discovery. Besides, immunohistochemistry (IHC) assays were conducted to detect the expression of a dendritic cell marker (CD11c) and ALPL in thyroid carcinoma (TC) and paracancerous tissues. In summary, our study found a potential mechanism in which hsa-miR-204-5p regulated ALPL in activated dendritic cells, which may allow them to play a critical role in thyroid carcinoma. These findings provide potential prognostic biomarkers and therapeutic targets for thyroid carcinoma.

The Role of Noncoding RNAs in Osteogenic Differentiation of Human Periodontal Ligament Stem Cells

Chronic inflammatory diseases, including periodontitis, are the most common causes of bone tissue destruction. Periodontitis often leads to loss of connective tissue homeostasis and reduced alveolar bone levels. Human periodontal ligament stem cells (PDLSCs), a population of multipotent stem cells derived from periodontal ligament tissues, are considered as candidate cells for the regeneration of alveolar bone and periodontal tissues. Periodontitis impairs the osteogenic differentiation of human PDLSCs. Noncoding RNAs (ncRNAs), including long noncoding RNA (lncRNA), microRNA (miRNA), and circular RNA (circRNA), have been proposed as vital regulators influencing several differentiation processes including bone regeneration. Still, the molecular mechanisms of ncRNAs regulating osteogenic differentiation of human PDLSCs remain poorly understood. Exploring the influence of ncRNAs in the process of osteogenic differentiation of human PDLSCs may provide novel therapeutic strategies for tissue regeneration as the regeneration of the lost periodontium is the ultimate goal of periodontal therapy.

Knockdown of MALAT1 Inhibits the Progression of Chronic Periodontitis via Targeting miR-769-5p/HIF3A Axis

Purpose

Chronic periodontitis (CP) is a long-lasting inflammatory disease that seriously affects oral health. This study is aimed at investigating the regulatory mechanism of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) in CP.

Methods

Primary human periodontal ligament cells (PDLCs) were treated with P. gingivalis lipopolysaccharide (LPS) to establish a CP model. Quantitative real-time PCR (qRT-PCR) was used to measure the expression of MALAT1 and miR-769-5p in gingival tissues of patients with CP and LPS-treated PDLCs. Cell viability was detected by 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) assay. Enzyme-linked immunosorbent assay (ELISA) was used to measure the levels of inflammatory cytokines. The protein levels of caspase-3, Bax, Bcl-2, and hypoxia-inducible factor (HIF) 3A were determined by western blot assay. Dual-luciferase reporter (DLR) assay was applied to validate the target relationships between miR-769-5p and MALAT1/HIF3A.

Results

The expression of MALAT1 and HIF3A was enhanced, and the expression of miR-769-5p was reduced in gingival tissues of patients with CP and LPS-treated PDLCs. MALAT1 knockdown promoted cell viability and inhibited inflammation and cell apoptosis in LPS-treated PDLCs. MALAT1 targeted miR-769-5p and negatively regulated miR-769-5p expression. miR-769-5p overexpression promoted cell viability and inhibited inflammation and cell apoptosis in LPS-treated PDLCs. Besides, miR-769-5p targeted HIF3A and negatively modulated HIF3A expression. Both miR-769-5p inhibition and HIF3A overexpression reversed the inhibitory effects of MALAT1 silencing on LPS-induced PDLC injury in vitro.

Conclusion

MALAT1 knockdown attenuated LPS-induced PDLC injury via regulating the miR-769-5p/HIF3A axis, which may supply a new target for CP treatment.

Long Noncoding RNA H19 Induces Neuropathic Pain by Upregulating Cyclin-Dependent Kinase 5-Mediated Phosphorylation of cAMP Response Element Binding Protein

Objective

Neuropathic pain (NP) is a debilitating condition caused by nervous system injury and chronic diseases. LncRNA H19 is upregulated in many human diseases, including NP. Cyclin-dependent kinase 5 (CDK5) aggressively worsens inflammatory action and nerve damage to cause severe NP. Phosphorylated cAMP response element binding protein (CREB) is detrimental to nerves and promotes NP progression. Herein, aim of our study was to assess the mechanism of lncRNA H19.

Methods

The NP rat model was established using chronic constriction injury (CCI). Paw withdrawal threshold (PWT) tests and paw withdrawal latency (PWL) tests were performed. Then, small interfering (si)RNA against H19 was intrathecally injected into rats to suppress H19 expression. Schwann cells were isolated from NP rats and transfected with siRNA-H19 or a lentivirus (LV)-based vector expressing H19. Inflammatory factors and glial fibrillary acidic protein (GFAP) were detected. Western blot analysis was conducted to detect CDK5/p35 and p-CREB expression. Finally, H19, CDK5 and CREB phosphorylation were tested with the combination of the CDK5 inhibitor roscovitine and transfection of LV-H19 and siRNA-H19. Finally, we investigated the binding relationships between H19 and miR-196a-5p and between miR-196a-5p and CDK5 and detected the mRNA expression of miR-196a-5p and CDK5 in rats with H19 knockdown and in Schwann cells with H19 knockdown.

Results

Highly expressed H19, CDK5/p-35 and p-CREB were observed in NP rats, accompanied by obviously decreased PWT and PWL, upregulated inflammatory factors and GFAP levels, and reduced 5-HT_2A and GABA_B2 expression. siRNA-H19 restored NP-related indexes and downregulated CDK5/p35 and p-CREB phosphorylation. siRNA-H19, together with the CDK5 inhibitor roscovitine, reduced CDK5 and p-CREB expression in Schwann cells isolated from NP rats. Binding sites between H19 and miR-196a-5p and between miR-196a-5p and CDK5 were identified. Silencing H19 upregulated miR-196a-5p expression and downregulated CDK5 levels.

Conclusion

Our study demonstrated that silencing H19 inhibited NP by suppressing CDK5/p35 and p-CREB phosphorylation via the miR-196a-5p/CDK5 axis, which may provide new insight into NP treatment.

Emerging role of long non-coding RNAs in the pathogenesis of periodontitis

Periodontitis is a bacteria-related chronic immune-associated condition that destructs bone and connective tissues around teeth. With a high incidence rate, it is regarded as a condition that impose substantial health burden. About half of the variance in the severity of periodontitis is attributed to genetic factors. Long non-coding RNAs (lncRNAs) have crucial roles in the development of several disorders such as periodontitis. A number of studies have reported dysregulation of lncRNAs such as UCA1, ANRIL, FGD5-AS1, NEAT1, FAS-AS1, Linc-RAM and NKILA in gingival tissues or blood samples of patients with periodontitis in comparison with healthy subjects. Moreover, several single nucleotide polymorphisms within lncRNAs have been associated with the susceptibility to this disorder. In the current review, we discuss the most recent articles about the role of lncRNAs in the pathogenesis of periodontitis.