Impact of root canal disinfection on the bacteriome present in primary endodontic infection: A next generation sequencing study.

AIM: To investigate the bacteriome present in teeth with primary endodontic infection (PEI) and apical periodontitis (AP) and to determine quantitatively and qualitatively the impact of chemomechanical preparation (CMP) using 2.5% sodium hypochlorite NAOCl on the bacteriome found in PEI with AP using the Illumina MiSeq platform. METHODOLOGY: Thirty-six paired samples from 18 patients were successfully sequenced and analysed. Samples were collected at two sampling times: before (s1) and after (s2) CMP using 2.5% NaOCl. The DNA was extracted from s1 and s2 samples and quantified using quantitative PCR (qPCR). All 36 samples were sequenced using the Illumina MiSeq platform. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants (ASVs). Alpha diversity metrics representing abundance (Chao1) and diversity and evenness (Shannon, Simpson) were computed. The paired-sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2. The PERMANOVA method (with 999 permutations) was applied to compare community composition between sample types (s1 versus s2) and between patient IDs. ALDEx2 (ANOVA-like differential expression tool for high-throughput sequencing data) to investigate differentially abundant taxa between s1 and s2. A paired-sample Wilcoxon's test was used to compare alpha diversity metrics and qPCR counts between s1 and s2. RESULTS: The qPCR counts were significantly higher in s1 compared to s2 (p = .0007). The Chao1 index indicated no difference in alpha diversity (p < .7019); whereas Shannon (p = .0056) and Simpson (p = .02685) indexes showed higher values in s2. The PERMANOVA test using Adonis2 showed a significant effect of sample time on community composition (R2 = .0630, p = .012). Patient ID also showed a significant effect on community composition (R2 = .6961, p = .001). At the genus level, Dialister, Mogibacterium, Prevotella, and Olsenella were differentially enriched at s1, while Actinomyces, Stenotrophomonas_unclassified, Enterococcus_unclassified, and Actinomyces_unclassified were differentially enriched in s2. CONCLUSION: The bacteriome present in teeth with PEI with AP is complex and diverse. CMP using 2.5% NaOCl showed a high quantitatively and qualitatively disinfectant impact on the bacteriome present in PEI with AP.

The antitumor effects of herbal medicine Triphala on oral cancer by inactivating PI3K/Akt signaling pathway: based on the network pharmacology, molecular docking, in vitro and in vivo experimental validation.

BACKGROUND: This research aimed to investigate the anti-tumor effects and underlying genetic mechanisms of herbal medicine Triphala (TRP) in oral squamous cell carcinoma (OSCC). METHODS: The target genes of Triphala (TRP) in oral squamous cell carcinoma (OSCC) were identified, and subsequent functional enrichment analysis was conducted to determine the enriched signaling pathways. Based on these genes, a protein-protein interaction network was constructed to identify the top 10 genes with the highest degree. Genes deregulated in OSCC tumor samples were identified to be hub genes among the top 10 genes. In vitro experiments were performed to investigate the influence of TRP extracts on the cell metabolic activity, migration, invasion, apoptosis, and proliferation of two OSCC cell lines (CAL-27 and SCC-9). The functional rescue assay was conducted to investigate the effect of applying the inhibitor and activator of an enriched pathway on the phenotypes of cancer cells. In addition, the zebrafish xenograft tumor model was established to investigate the influence of TRP extracts on tumor growth and metastasis in vivo. RESULTS: The target genes of TRP in OSCC were prominently enriched in the PI3K-Akt signaling pathway, with the identification of five hub genes (JUN, EGFR, ESR1, RELA, and AKT1). TRP extracts significantly inhibited cell metabolic activity, migration, invasion, and proliferation and promoted cell apoptosis in OSCC cells. Notably, the application of TRP extracts exhibited the capacity to downregulate mRNA and phosphorylated protein levels of AKT1 and ESR1, while concomitantly inducing upregulation of mRNA and phosphorylated protein levels in the remaining three hub genes (EGFR, JUN, and RELA). The functional rescue assay demonstrated that the co-administration of TRP and the PI3K activator 740Y-P effectively reversed the impact of TRP on the phenotypes of OSCC cells. Conversely, the combination of TRP and the PI3K inhibitor LY294002 further enhanced the effect of TRP on the phenotypes of OSCC cells. Remarkably, treatment with TRP in zebrafish xenograft models demonstrated a significant reduction in both tumor growth and metastatic spread. CONCLUSIONS: Triphala exerted significant inhibitory effects on cell metabolic activity, migration, invasion, and proliferation in OSCC cell lines, accompanied by the induction of apoptosis, which was mediated through the inactivation of the PI3K/Akt pathway.

Surgical interventions for implant placement in the anterior maxilla: A systematic scoping review with evidence mapping.

OBJECTIVES: Simplification and standardization of interventions are critical challenges to improving performance in implant dentistry. This study aimed to systematically identify and schematically present the evidence base of the implant dentistry surgical interventions for the anterior maxilla as a basis for further development and standardization. METHODS: Electronic searches were conducted in PubMed, Embase and Cochrane CENTRAL. Primary clinical studies reporting surgical interventions in the anterior maxilla, with a sample size of at least ten patients, were included. Bibliometric information and study details were extracted. Descriptive analysis and a mind map approach were used to describe the documentation of different surgical interventions. RESULTS: Two hundred and seventy-two studies reporting on 9001 patients were included. Within the past two decades, the number of literatures on implant placement in the anterior maxilla has increased dramatically (7 studies before 2005, 151 studies after 2016). Overall, the evidence map identified six primary operations and 33 variations. For hopeless tooth extraction, immediate implant placement was the most frequently reported (141 studies, 4670 patients); flapless implant placement with hard tissue augmentation and immediate provisionalization was the most commonly reported variation (33 studies, 987 patients). Type 3/4 implant placement (62 studies, 1902 patients) and implant site augmentation (33 studies, 788 patients) were frequently reported for missing teeth. Geographical differences were observed, with type 2 placement studies almost exclusively from Europe. CONCLUSIONS: Research on immediate implant placement was the most reported surgical intervention in the anterior maxilla. Hard tissue augmentation was frequently reported simultaneously with or before implant placement. Immediate provisionalization was mainly used for type 1 implant placement. The finding that six primary operations with 33 variations have been reported indicates the need for additional research to simplify and consolidate the surgical approach.

Sponsorship Bias in Clinical Trials in the Dental Application of Probiotics: A Meta-Epidemiological Study.

Many experimental and clinical trials have investigated the dental application of probiotics, although the evidence concerning the effects of probiotic supplements is conflicting. We aimed to examine whether sponsorship in trials about dental applications of probiotics is associated with biased estimates of treatment effects. Overall, 13 meta-analyses involving 48 randomized controlled trials (23 with high risk of sponsorship bias, 25 with low risk) with continuous outcomes were included. Effect sizes were calculated from differences in means of first reported continuous outcomes, divided by the pooled standard deviation. For each meta-analysis, the difference in standardized mean differences between high-risk and low-risk trials was estimated by random effects meta-regression. Differences in standardized mean differences (DSMDs) were then calculated via meta-analyses in a random effects meta-analysis model. A combined DSMD of greater than zero indicated that high-risk trials showed more significant treatment effects than low-risk trials. The results show that trials with a high risk of sponsorship bias showed more significant intervention effects than did low-risk trials (combined DSMD, 0.06; 95% confidence interval, 0.3 to 0.9; p < 0.001), with low heterogeneity among meta-analyses (I2 = 0%; between-meta-analyses variance τ2 = 0.00). Based on our study, high-risk clinical trials with continuous outcomes reported more favorable intervention effects than did low-risk trials in general.

Identification of Key Pyroptosis-Related Genes and Distinct Pyroptosis-Related Clusters in Periodontitis.

Aim: This study aims to identify pyroptosis-related genes (PRGs), their functional immune characteristics, and distinct pyroptosis-related clusters in periodontitis. Methods: Differentially expressed (DE)-PRGs were determined by merging the expression profiles of GSE10334, GSE16134, and PRGs obtained from previous literatures and Molecular Signatures Database (MSigDB). Least absolute shrinkage and selection operator (LASSO) regression was applied to screen the prognostic PRGs and develop a prognostic model. Consensus clustering was applied to determine the pyroptosis-related clusters. Functional analysis and single-sample gene set enrichment analysis (ssGSEA) were performed to explore the biological characteristics and immune activities of the clusters. The hub pyroptosis-related modules were defined using weighted correlation network analysis (WGCNA). Results: Of the 26 periodontitis-related DE-PRGs, the highest positive relevance was for High-Mobility Group Box 1 (HMGB1) and SR-Related CTD Associated Factor 11 (SCAF11). A 14-PRG-based signature was developed through the LASSO model. In addition, three pyroptosis-related clusters were obtained based on the 14 prognostic PRGs. Caspase 3 (CASP3), Granzyme B (GZMB), Interleukin 1 Alpha (IL1A), IL1Beta (B), IL6, Phospholipase C Gamma 1 (PLCG1) and PYD And CARD Domain Containing (PYCARD) were dysregulated in the three clusters. Distinct biological functions and immune activities, including human leukocyte antigen (HLA) gene expression, immune cell infiltration, and immune pathway activities, were identified in the three pyroptosis-related clusters of periodontitis. Furthermore, the pink module associated with endoplasmic stress-related functions was found to be correlated with cluster 2 and was suggested as the hub pyroptosis-related module. Conclusion: The study identified 14 key pyroptosis-related genes, three distinct pyroptosis-related clusters, and one pyroptosis-related gene module describing several molecular aspects of pyroptosis in the pathogenesis and immune micro-environment regulation of periodontitis and also highlighted functional heterogeneity in pyroptosis-related mechanisms.

The effectiveness of adjunctive measures in managing peri-implant mucositis: an umbrella review.

OBJECTIVES: The purpose of this umbrella review was to gather and summarize the data from published systematic reviews (SRs) that compared non-surgical mechanical debridement (NSMD) with and without the use of adjunctive treatments on the management of peri-implant mucositis (PIM). MATERIALS AND METHODS: A protocol was developed and registered in PROSPERO (CRD42021254350) before the systematic search for the SRs. Seven electronic databases, including Cochrane Library, Embase (via Ovid), MEDLINE (via Pubmed), Proquest, Prospero, Scopus and Web of Science, were searched for published reviews. The search for unpublished and informally published reviews was further attempted in the last four databases. The methodological quality of the included reviews was assessed using AMSTAR 2. RESULTS: Twelve included SRs assessed clinical studies published between 2014 and 2020, including a total of seventeen primary clinical trials. All SRs summarized data from individual studies and provided a narrative conclusion regarding the effectiveness of the adjunctive treatments. Only six SRs performed a meta-analysis (MA) of additional benefits of the adjunctive therapy for PIM, with results indicating no significant difference between the different treatment modalities. The overall confidence was adjudged ranging from critically low to low using AMSTAR 2 and significant additional benefits of any adjunctive treatments in comparison with NSMD were not apparent. CONCLUSION: Overall, the reviewed evidence did not support the use of adjunctive treatments for improvement of clinical outcomes in PM management as compared to NSMD alone.

Comparison between Conventional Modality Versus Cone-Beam Computer Tomography on the Assessment of Vertical Furcation in Molars.

This study aimed to assess the accuracy of diagnosis of vertical furcation subclass in molars using periapical radiographs (PAs) and clinical chartings compared against cone-beam computer tomography (CBCT) as the gold standard. The protocol involved examiners with different levels of experience. This retrospective radiographic study retrieved 40 molar teeth with full periodontal chartings, PAs, and CBCT records. Fifteen examiners with different levels of experience evaluated the PAs and periodontal chartings to assess the vertical depth of furcation and, thus, the vertical subclassification. CBCT was used as the gold standard for comparison. The accuracy of vertical furcal depth measured was assessed together with the accuracy of vertical subclassification assignment. The reliability of the conventional diagnostic modality among the examiners was also evaluated. A linear mixed model adjusted for the CBCT vertical furcal depth measurement was constructed to determine if tooth position, horizontal furcation distribution, and examiner experience level affect the bias in the vertical depth of furcation measurement. The reliability of the conventional periodontal diagnostic method in measuring vertical furcal depth was found to be fair, while vertical subclass assignment was moderate. Significantly better reliability during subclass assignment was found with mandibular molars (p < 0.001) and in maxillary molars with isolated buccal class II furcation. Within the study's limitations, conventional periodontal diagnostics based on periapical radiographs and clinical periodontal chartings appear to be in poor to fair agreement with CBCT (gold standard) when measuring the vertical depth of furcation. Examiners with the least experience were more prone to bias when estimating the vertical furcal depth.

Shared Molecular Mechanisms between Atherosclerosis and Periodontitis by Analyzing the Transcriptomic Alterations of Peripheral Blood Monocytes.

OBJECTIVE: This study investigated the nature of shared transcriptomic alterations in PBMs from periodontitis and atherosclerosis to unravel molecular mechanisms underpinning their association. METHODS: Gene expression data from PBMs from patients with periodontitis and those with atherosclerosis were each downloaded from the GEO database. Differentially expressed genes (DEGs) in periodontitis and atherosclerosis were identified through differential gene expression analysis. The disease-related known genes related to periodontitis and atherosclerosis each were downloaded from the DisGeNET database. A Venn diagram was constructed to identify crosstalk genes from four categories: DEGs expressed in periodontitis, periodontitis-related known genes, DEGs expressed in atherosclerosis, and atherosclerosis-related known genes. A weighted gene coexpression network analysis (WGCNA) was performed to identify significant coexpression modules, and then, coexpressed gene interaction networks belonging to each significant module were constructed to identify the core crosstalk genes. RESULTS: Functional enrichment analysis of significant modules obtained by WGCNA analysis showed that several pathways might play the critical crosstalk role in linking both diseases, including bacterial invasion of epithelial cells, platelet activation, and Mitogen-Activated Protein Kinases (MAPK) signaling. By constructing the gene interaction network of significant modules, the core crosstalk genes in each module were identified and included: for GSE23746 dataset, RASGRP2 in the blue module and VAMP7 and SNX3 in the green module, as well as HMGB1 and SUMO1 in the turquoise module were identified; for GSE61490 dataset, SEC61G, PSMB2, SELPLG, and FIBP in the turquoise module were identified. CONCLUSION: Exploration of available transcriptomic datasets revealed core crosstalk genes (RASGRP2, VAMP7, SNX3, HMGB1, SUMO1, SEC61G, PSMB2, SELPLG, and FIBP) and significant pathways (bacterial invasion of epithelial cells, platelet activation, and MAPK signaling) as top candidate molecular linkage mechanisms between atherosclerosis and periodontitis.

Impact of design elements of the implant supracrestal complex (ISC) on the risk of peri-implant mucositis and peri-implantitis: A critical review.

OBJECTIVE: The aim of this review was to investigate the evidence correlating the emergence profile (EP) and emergence angle (EA), peri-implant tissue height, implant neck design, abutment and/or prosthesis material, retention and connection types with risk of peri-implant mucositis and peri-implantitis. METHODS: Seven focus questions were identified, and seven electronic search queries were conducted in PubMed. Human studies reporting on bleeding on probing, probing depth or case definitions of peri-implant mucositis and peri-implantitis were included. RESULTS: Emerging evidence with bone-level implants suggests a link between EA combined with convex EP and peri-implantitis. Depth of the peri-implant sulcus of ≥3 mm is shown to be reducing the effectiveness of treatment of established peri-implant mucositis. Modification of the prosthesis contour is shown to be an effective supplement of the anti-infective treatment of peri-implant mucositis. Limited evidence points to no difference with regard to the risk for peri-implant mucositis between tissue- and bone-level implants, as well as the material of the abutment or the prosthesis. Limited evidence suggests the use or not of prosthetic abutments in external connections and does not change the risk for peri-implantitis. Literature with regard to prosthesis retention type and risk for peri-implantitis is inconclusive. CONCLUSIONS: Limited evidence indicates the involvement of EA, EP, sulcus depth and restricted accessibility to oral hygiene in the manifestation and/or management of peri-implant mucositis/peri-implantitis. Conclusions are limited by the lack of consensus definitions and validated outcomes measures, as well as diverse methodological approaches. Purpose-designed studies are required to clarify current observations.

Molecular Subtypes of Oral Squamous Cell Carcinoma Based on Immunosuppression Genes Using a Deep Learning Approach.

Background: The mechanisms through which immunosuppressed patients bear increased risk and worse survival in oral squamous cell carcinoma (OSCC) are unclear. Here, we used deep learning to investigate the genetic mechanisms underlying immunosuppression in the survival of OSCC patients, especially from the aspect of various survival-related subtypes. Materials and methods: OSCC samples data were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and OSCC-related genetic datasets with survival data in the National Center for Biotechnology Information (NCBI). Immunosuppression genes (ISGs) were obtained from the HisgAtlas and DisGeNET databases. Survival analyses were performed to identify the ISGs with significant prognostic values in OSCC. A deep learning (DL)-based model was established for robustly differentiating the survival subpopulations of OSCC samples. In order to understand the characteristics of the different survival-risk subtypes of OSCC samples, differential expression analysis and functional enrichment analysis were performed. Results: A total of 317 OSCC samples were divided into one inferring cohort (TCGA) and four confirmation cohorts (ICGC set, GSE41613, GSE42743, and GSE75538). Eleven ISGs (i.e., BGLAP, CALCA, CTLA4, CXCL8, FGFR3, HPRT1, IL22, ORMDL3, TLR3, SPHK1, and INHBB) showed prognostic value in OSCC. The DL-based model provided two optimal subgroups of TCGA-OSCC samples with significant differences (p = 4.91E-22) and good model fitness [concordance index (C-index) = 0.77]. The DL model was validated by using four external confirmation cohorts: ICGC cohort (n = 40, C-index = 0.39), GSE41613 dataset (n = 97, C-index = 0.86), GSE42743 dataset (n = 71, C-index = 0.87), and GSE75538 dataset (n = 14, C-index = 0.48). Importantly, subtype Sub1 demonstrated a lower probability of survival and thus a more aggressive nature compared with subtype Sub2. ISGs in subtype Sub1 were enriched in the tumor-infiltrating immune cells-related pathways and cancer progression-related pathways, while those in subtype Sub2 were enriched in the metabolism-related pathways. Conclusion: The two survival subtypes of OSCC identified by deep learning can benefit clinical practitioners to divide immunocompromised patients with oral cancer into two subpopulations and give them target drugs and thus might be helpful for improving the survival of these patients and providing novel therapeutic strategies in the precision medicine area.

Shared Molecular Mechanisms between Alzheimer's Disease and Periodontitis Revealed by Transcriptomic Analysis.

OBJECTIVE: To investigate the genetic crosstalk mechanisms that link periodontitis and Alzheimer's disease (AD). BACKGROUND: Periodontitis, a common oral infectious disease, is associated with Alzheimer's disease (AD) and considered a putative contributory factor to its progression. However, a comprehensive investigation of potential shared genetic mechanisms between these diseases has not yet been reported. METHODS: Gene expression datasets related to periodontitis were downloaded from the Gene Expression Omnibus (GEO) database, and differential expression analysis was performed to identify differentially expressed genes (DEGs). Genes associated with AD were downloaded from the DisGeNET database. Overlapping genes among the DEGs in periodontitis and the AD-related genes were defined as crosstalk genes between periodontitis and AD. The Boruta algorithm was applied to perform feature selection from these crosstalk genes, and representative crosstalk genes were thus obtained. In addition, a support vector machine (SVM) model was constructed by using the scikit-learn algorithm in Python. Next, the crosstalk gene-TF network and crosstalk gene-DEP (differentially expressed pathway) network were each constructed. As a final step, shared genes among the crosstalk genes and periodontitis-related genes in DisGeNET were identified and denoted as the core crosstalk genes. RESULTS: Four datasets (GSE23586, GSE16134, GSE10334, and GSE79705) pertaining to periodontitis were included in the analysis. A total of 48 representative crosstalk genes were identified by using the Boruta algorithm. Three TFs (FOS, MEF2C, and USF2) and several pathways (i.e., JAK-STAT, MAPK, NF-kappa B, and natural killer cell-mediated cytotoxicity) were identified as regulators of these crosstalk genes. Among these 48 crosstalk genes and the chronic periodontitis-related genes in DisGeNET, C4A, C4B, CXCL12, FCGR3A, IL1B, and MMP3 were shared and identified as the most pivotal candidate links between periodontitis and AD. CONCLUSIONS: Exploration of available transcriptomic datasets revealed C4A, C4B, CXCL12, FCGR3A, IL1B, and MMP3 as the top candidate molecular linkage genes between periodontitis and AD.

Deep Learning Reveals Key Immunosuppression Genes and Distinct Immunotypes in Periodontitis.

BACKGROUND: Periodontitis is a chronic immuno-inflammatory disease characterized by inflammatory destruction of tooth-supporting tissues. Its pathogenesis involves a dysregulated local host immune response that is ineffective in combating microbial challenges. An integrated investigation of genes involved in mediating immune response suppression in periodontitis, based on multiple studies, can reveal genes pivotal to periodontitis pathogenesis. Here, we aimed to apply a deep learning (DL)-based autoencoder (AE) for predicting immunosuppression genes involved in periodontitis by integrating multiples omics datasets. METHODS: Two periodontitis-related GEO transcriptomic datasets (GSE16134 and GSE10334) and immunosuppression genes identified from DisGeNET and HisgAtlas were included. Immunosuppression genes related to periodontitis in GSE16134 were used as input to build an AE, to identify the top disease-representative immunosuppression gene features. Using K-means clustering and ANOVA, immune subtype labels were assigned to disease samples and a support vector machine (SVM) classifier was constructed. This classifier was applied to a validation set (Immunosuppression genes related to periodontitis in GSE10334) for predicting sample labels, evaluating the accuracy of the AE. In addition, differentially expressed genes (DEGs), signaling pathways, and transcription factors (TFs) involved in immunosuppression and periodontitis were determined with an array of bioinformatics analysis. Shared DEGs common to DEGs differentiating periodontitis from controls and those differentiating the immune subtypes were considered as the key immunosuppression genes in periodontitis. RESULTS: We produced representative molecular features and identified two immune subtypes in periodontitis using an AE. Two subtypes were also predicted in the validation set with the SVM classifier. Three "master" immunosuppression genes, PECAM1, FCGR3A, and FOS were identified as candidates pivotal to immunosuppressive mechanisms in periodontitis. Six transcription factors, NFKB1, FOS, JUN, HIF1A, STAT5B, and STAT4, were identified as central to the TFs-DEGs interaction network. The two immune subtypes were distinct in terms of their regulating pathways. CONCLUSION: This study applied a DL-based AE for the first time to identify immune subtypes of periodontitis and pivotal immunosuppression genes that discriminated periodontitis from the healthy. Key signaling pathways and TF-target DEGs that putatively mediate immune suppression in periodontitis were identified. PECAM1, FCGR3A, and FOS emerged as high-value biomarkers and candidate therapeutic targets for periodontitis.

Oral Health-Related Quality of Life in Patients With Chronic Respiratory Diseases-Results of a Systematic Review.

Background: This systematic review evaluates the oral health-related quality of life (OHRQoL) of patients with chronic respiratory diseases. Methods: A systematic literature search was performed based on the PubMed, Medline, Web of Science, and Scopus, using the search terms: "oral health-related quality of life" and "respiratory disease" or "lung" and "oral health-related quality of life." Full-text articles published until June 30, 2021 and reporting any OHRQoL measurement in children or adults with a chronic respiratory disease or condition were included and analyzed qualitatively. Results: A total of seven out of 44 studies were included, of which four studies examined adults and three studies investigated children. The respective diseases were chronic obstructive pulmonary disease (COPD) (n = 2), sleep apnea (n = 2), severe asthma (n = 1), cystic fibrosis (n = 1), and lung transplantation (n = 1). Four studies confirmed a worse OHRQoL in the respiratory diseased group compared to healthy controls. The overall OHRQoL was reduced in the included studies. Oral health, health-related quality of life, and disease-related parameters were rarely examined with regard to OHRQoL. Conclusion: Patients with chronic respiratory diseases show a reduced OHRQoL. Oral health should be fostered in these individuals to support their OHRQoL.

Immune Checkpoint Gene Expression Profiling Identifies Programmed Cell Death Ligand-1 Centered Immunologic Subtypes of Oral and Squamous Cell Carcinoma With Favorable Survival.

OBJECTIVE: This study aimed to identify the programmed death ligand-1 (PDL1, also termed as CD274) and its positively correlated immune checkpoint genes (ICGs) and to determine the immune subtypes of CD274-centered ICG combinations in oral and squamous cell carcinoma (OSCC). MATERIALS AND METHODS: Firstly, the 95 ICGs obtained via literature reviews were identified in the Cancer Genome Atlas (TCGA) database in relation to OSCC, and such 88 ICG expression profiles were extracted. ICGs positively correlated with CD274 were utilized for subsequent analysis. The relationship between ICGs positively correlated with CD274 and immunotherapy biomarkers (tumor mutation burden (TMB), and adaptive immune resistance pathway genes) was investigated, and the relationships of these genes with OSCC clinical features were explored. The prognostic values of CD274 and its positively correlated ICGs and also their associated gene pairs were revealed using the survival analysis. RESULTS: Eight ICGs, including CTLA4, ICOS, TNFRSF4, CD27, B- and T-lymphocyte attenuator (BTLA), ADORA2A, CD40LG, and CD28, were found to be positively correlated with CD274. Among the eight ICGs, seven ICGs (CTLA4, ICOS, TNFRSF4, CD27, BTLA, CD40LG, and CD28) were significantly negatively correlated with TMB. The majority of the adaptive immune resistance pathway genes were positively correlated with ICGs positively correlated with CD274. The survival analysis utilizing the TCGA-OSCC data showed that, although CD274 was not significantly associated with overall survival (OS), the majority of ICGs positively correlated with CD274 (BTLA, CD27, CTLA4, CD40LG, CD28, ICOS, and TNFRSF4) were significantly correlated with OS, whereby their low-expression predicted a favorable prognosis. The survival analysis based on the gene pair subtypes showed that the combination subtypes of CD274_low/BTLA_low, CD274_low/CD27_low, CD274_low/CTLA4_low, CD8A_high/BTLA_low, CD8A_high/CD27_low, and CD8A_high/CTLA4_low predicted favorable OS. CONCLUSION: The results in this study provide a theoretical basis for prognostic immune subtyping of OSCC and highlight the importance of developing future immunotherapeutic strategies for treating oral cancer.

Identification of miRNAs as the Crosstalk in the Interaction between Neural Stem/Progenitor Cells and Endothelial Cells.

AIM: This study is aimed at identifying genetic and epigenetic crosstalk molecules and their target drugs involved in the interaction between neural stem/progenitor cells (NSPCs) and endothelial cells (ECs). MATERIALS AND METHODS: Datasets pertaining to reciprocal mRNA and noncoding RNA changes induced by the interaction between NSPCs and ECs were obtained from the GEO database. Differential expression analysis (DEA) was applied to identify NSPC-induced EC alterations by comparing the expression profiles between monoculture of ECs and ECs grown in EC/NSPC cocultures. DEA was also utilized to identify EC-induced NSPC alterations by comparing the expression profiles between monoculture of NSPCs and NSPCs grown in EC/NSPC cocultures. The DEGs and DEmiRNAs shared by NSPC-induced EC alterations and EC-induced NSPC alterations were then identified. Furthermore, miRNA crosstalk analysis and functional enrichment analysis were performed, and the relationship between DEmiRNAs and small molecular drug targets/environment chemical compounds was investigated. RESULTS: One dataset (GSE29759) was included and analyzed in this study. Six genes (i.e., MMP14, TIMP3, LOXL1, CCK, SMAD6, and HSPA2), three miRNAs (i.e., miR-210, miR-230a, and miR-23b), and three pathways (i.e., Akt, ERK1/2, and BMPs) were identified as crosstalk molecules. Six small molecular drugs (i.e., deptropine, fluphenazine, lycorine, quinostatin, resveratrol, and thiamazole) and seven environmental chemical compounds (i.e., folic acid, dexamethasone, choline, doxorubicin, thalidomide, bisphenol A, and titanium dioxide) were identified to be potential target drugs of the identified DEmiRNAs. CONCLUSION: To conclude, three miRNAs (i.e., miR-210, miR-230a, and miR-23b) were identified to be crosstalks linking the interaction between ECs and NSPCs by implicating in both angiogenesis and neurogenesis. These crosstalk molecules might provide a basis for devising novel strategies for fabricating neurovascular models in stem cell tissue engineering.

Effects of adjunctive probiotic L. reuteri lozenges on S/RSD outcomes at molar sites with deep pockets.

AIM: To evaluate effects of probiotic Lactobacillus reuteri (L. reuteri) lozenges as an S/RSD adjunct on site-level changes at molars with deep pockets. MATERIALS AND METHODS: 447 molar sites with pockets ≥ 5 mm from a previous randomized clinical trial of adjunctive L. reuteri lozenges for 28 days were analyzed. Multilevel mixed-effect models (MLM) were constructed to analyze site-level outcomes "change in CAL" and "pocket closure" (residual PPD < 5 mm) in placebo and probiotic groups at 90 and 180 days. Possible patient-, tooth-, and site-level predictors were analyzed as fixed-effects. RESULTS: Estimated change in CAL in probiotic (90 day: 0.87 mm, 180 day: 0.68 mm) was greater than placebo treated molar sites (90 day: 0.73 mm, 180 day: 0.66 mm) and the relative risk (RR) of pocket closure in the probiotic group (90 day: 1.7, 180 day: 1.6) was higher as compared to placebo. Furcation involvement and BOP at site predicted significantly worse treatment outcomes. CONCLUSION: As compared to S/RSD with placebo, a 28-day course of adjunctive probiotic L. reuteri lozenges improved CAL change at molar sites with ≥ 5 mm deep pockets and conferred a higher probability of shallow residual pocket depth. Presence of furcation-involvement and bleeding on probing worsened treatment outcomes.

A Systematic Review and Meta-analysis of Clinical, Immunological, and Microbiological Shift in Periodontitis After Nonsurgical Periodontal Therapy With Adjunctive Use of Probiotics.

OBJECTIVES: There is a lack of evidence regarding long-term effects of probiotics as adjuncts to nonsurgical periodontal therapy (NSPT) in the management of periodontitis. Therefore, this systematic review aimed to evaluate the clinical, microbiological, and immunological outcomes of probiotics applied as an adjunct to NSPT with at least 3 months of follow-up. METHODS: Electronic searches of 5 databases were performed. Clinical trials that compared the adjunctive use of probiotics in NSPT with NSPT alone, reporting clinical or immunological or microbiological outcomes, were selected. The primary clinical outcome variables were clinical attachment level (CAL) and probing pocket depth (PPD). Meta-analyses were conducted to evaluate the efficacy of probiotics over different longitudinal intervals. RESULTS: Ten randomized controlled trials were included, and high heterogeneity in methods was noted. Meta-analysis revealed CAL gain, and PPD reduction in the probiotics group was significant at 3 months and 12 months, but no significant difference was noted at 6 months and 9 months. There was no significant difference in periodontal pathogen levels between groups at 3 months. Immunological data were not sufficient for quantitative analysis. Ancillary sensitivity analysis indicated a subset of studies with severe mean baseline PPD (≥5 mm) at baseline showed significant and more CAL gain and PPD reduction at 3 months, with probiotics administration of 2-4 weeks. CONCLUSION: Heterogenous evidence implied a long-term clinical benefit of probiotics as an adjunct to NSPT. Outcomes may be impacted by baseline disease severity. Limited microbiological and immunological data precluded any conclusive findings. Current evidence is insufficient to formulate clinical recommendations.

Long non-coding RNA and mRNA expression profiles in peri-implantitis vs periodontitis.

BACKGROUND AND OBJECTIVE: Peri-implantitis is a biofilm-mediated infectious disease that results in progressive loss of implant-supporting bone. As compared to its analogue periodontitis, peri-implantitis is generally known to be more aggressive, with comparatively rapid progression and less predictable treatment outcomes, especially when advanced. An understanding of molecular mechanisms underpinning the similarities and differences between peri-implantitis and periodontitis is essential to develop novel management strategies. This study aimed to compare long non-coding RNAs (lncRNAs) and messenger RNA (mRNA) expression profiles between peri-implantitis and periodontitis. METHODS: Inflamed soft tissue from peri-implantitis and periodontitis lesions, and healthy gingival tissue controls were analyzed by microarray. Cluster graphs, gene ontology (GO) analysis, and pathway analysis were performed. Quantitative real-time PCR was employed to verify microarray results. The expression levels of RANKL and OPG in the three tissue types were also evaluated, using qRT-PCR. Coding non-coding (CNC) network analyses were performed. RESULTS: Microarray analyses revealed 1079 lncRNAs and 1003 mRNAs as differentially expressed in peri-implantitis when compared to periodontitis. The cyclooxygenase-2 pathway was the most up-regulated biological process in peri-implantitis as compared to periodontitis, whereas hemidesmosome assembly was the most down-regulated pathway. Osteoclast differentiation was relatively up-regulated, and RANKL/OPG ratio was higher in peri-implantitis than in periodontitis. CONCLUSIONS: The study demonstrated that peri-implantitis and periodontitis exhibit significantly different lncRNA and mRNA expression profiles, suggesting that osteoclast differentiation-related pathways are comparatively more active in peri-implantitis. These data highlight potential molecular targets for periodontitis and peri-implantitis therapy development.

Species-Level Salivary Microbial Indicators of Well-Resolved Periodontitis: A Preliminary Investigation.

Objective: To profile the salivary microbiomes of a Hong Kong Chinese cohort at a species-level resolution and determine species that discriminated clinically resolved periodontitis from periodontally healthy cases. Methods: Salivary microbiomes of 35 Hong Kong Chinese subjects' under routine supportive dental care were analyzed. All subjects had been treated for any dental caries or periodontal disease with all restorative treatment completed at least 1 year ago and had ≤3 residual pockets. They were categorized based on a past diagnosis of chronic periodontitis into "healthy" (H) or "periodontitis" (P) categories. Unstimulated whole saliva was collected, genomic DNA was isolated, and high throughput Illumina MiSeq sequencing of 16S rRNA (V3-V4) gene amplicons was performed. The sequences were assigned taxonomy at the species level by using a BLASTN based algorithm that used a combined reference database of HOMD RefSeqV14.51, HOMD RefSeqExtended V1.1 and GreenGeneGold. Species-level OTUs were subjected to downstream analysis in QIIME and R. For P and H group comparisons, community diversity measures were compared, differentially abundant species were determined using DESeq2, and disease indicator species were determined using multi-level pattern analysis within the R package "indicspecies." Results: P subjects were significantly older than H subjects (p = 0.003) but not significantly different in their BOP scores (p = 0.82). No significant differences were noted in alpha diversity measures after adjusting for age, gender, and BOP or in the beta diversity estimates. Four species; Treponema sp. oral taxon 237, TM7 sp. Oral Taxon A56, Prevotella sp. oral taxon 314, Prevotella sp. oral taxon 304, and Capnocytophaga leadbetteri were significantly more abundant in P than in the H group. Indicator species analysis showed 7 significant indicators species of P group. Fusobacterium sp oral taxon 370 was the sole positive indicator of P group (positive predictive value = 0.9, p = 0.04). Significant indicators of the H category were Leptotrichia buccalis, Corynebacterium matruchotii, Leptotrichia hofstadii, and Streptococcus intermedius. Conclusion: This exploratory study showed salivary microbial species could discriminate treated, well-maintained chronic periodontitis from healthy controls with similar gingival inflammation levels. The findings suggest that certain salivary microbiome features may identify periodontitis-susceptible individuals despite clinical disease resolution.

A double-blind, paralleled-arm, placebo-controlled and randomized clinical trial of the effectiveness of probiotics as an adjunct in periodontal care.

AIM: This study aimed to evaluate the clinical effectiveness of the probiotic Lactobacillus reuteri as an adjunct to non-surgical periodontal therapy (NSPT). MATERIALS AND METHODS: A double-blind, paralleled-arm, placebo-controlled and randomized clinical trial was conducted. Probiotics L. reuteri or placebo lozenges were randomly prescribed for use twice-daily for 28 days. Primary outcomes were clinical attachment levels (CAL) and probing pocket depths (PPD). All participants underwent NSPT, and follow-up clinical assessments were performed at day 90 and day 180. RESULTS: The trial response rate was 69.5% (41 out of 59). Among the test and control groups, there were significant intra-group differences in primary outcomes: CAL (both, p < .001) and PPD (both, p < .001); and in secondary outcomes: percentage of sites with 'bleeding on probing' (both, p < .001) and visible plaque (both, p < .001). There were no statistically significant inter-group differences in any outcomes at any time points (all, p > .05) nor in the changes in outcomes (∆) with time (all, p > .05). There was a trend of a greater magnitude of statistical change occurring among the test group compared to the control group. CONCLUSION: The adjunctive use of probiotics with NSPT did not show any additional clinical effectiveness when compared to NSPT alone in the management of periodontitis (ChiCTR-IOR-17010526).