Development of an immunogenomic landscape for the competing endogenous RNAs network of peri-implantitis

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.

Th-Cell Subsets of Submandibular Lymph Nodes in Peri-Implantitis

BACKGROUND

Implant surgery is a popular operation in craniomaxillofacial surgery, but the occurrence of peri-implantitis affects the success and survival rate of the implant. Research has found that Th-cell-related cytokines are associated with peri-implantitis. However, the distribution and proportions of Th-cell subsets in submandibular lymph nodes' immune environments during the progression of peri-implantitis remain unclear.

METHODS

Forty-eight rats were randomly divided into 4 groups: the control group, the 1-week ligation peri-implantitis induction (Lig 1w) group, the Lig 2w group, and the Lig 4w group (n=12). Ligation was maintained for different times to induce peri-implantitis 4 weeks after implantation. Inflammation and bone resorption were examined by clinical probing and micro-CT. The submandibular lymph nodes were harvested for quantitative real-time polymerase chain reaction and flow cytometry to obtain the Th-cell profiles.

RESULTS

With increasing ligation time, more redness and swelling in the gingiva and more bone resorption around the implant were observed (P<0.05). The proportions of Th1 and Th17 cells increased, the proportion of Th2 cells decreased, and the proportion of Treg cells first increased and then decreased in the lymph nodes (P<0.05).

CONCLUSIONS

This study provided a preliminary characterization of the temporal distribution of Th cells in lymph nodes of peri-implantitis. Persistent elevation of Th1 and Th17 proportions and decrease of Treg proportion may be the cause of bone resorption in peri-implantitis. Lymphatic drainage may be a bridge between craniomaxillofacial diseases and systemic diseases. Early immune support against T cells may be a potential therapeutic idea for the prevention of implant failure and the potential risk of systemic disease.

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.

Current Molecular, Cellular and Genetic Aspects of Peri-Implantitis Disease: A Narrative Review

(1) Background: Peri-implantitis is a multi-factorial disease with an inflammatory background that occurs in both soft and hard tissues surrounding implants. In recent years, the understanding of the cellular, molecular and genetic background of peri-implantitis has broadened. This study aims to summarize the currently available articles on the subject and highlight the most recent advances over the last 20 years. (2) Methods: For this study, the Embase and PubMed libraries were searched using the keywords: ("peri-implantitis" AND "cytokine" OR "genetics" OR "cellular") and ("peri-implantitis" AND "cytokine" OR "genetics" OR "cellular" AND "risk factors"). The search revealed a total of 3013 articles (992 from PubMed, 2021 from Embase). Following screening of the titles and abstracts and full-text reads, 55 articles were included. (3) Results: In peri-implantitis IL-6, IL-1β, TNF-α, MMP-8 and their genetic variations appear to be the most important cytokines in relation to not only pathogenesis, but also their potential diagnostic capabilities. Epithelial and inflammatory cells, along with those of the bone lineage, are prime cellular elements found in peri-implantitis. (4) Conclusions: A wide array of cells stand behind peri-implantitis, as well as cytokines and their genetic variations that take part in the process. However, the growing interest in this topic has led to the introduction of specific new diagnostic tools to enable a better understanding of patients' responses to treatment and, in turn, to even enable prediction of the risk of developing peri-implant disease.

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.

Gene Correlation Network Analysis to Identify Biomarkers of Peri-Implantitis

Background and Objectives: The histopathological and clinical conditions for transforming peri-implant mucositis into peri-implantitis (PI) are not fully clarified. We aim to uncover molecular mechanisms and new potential biomarkers of PI. Materials and Methods: Raw GSE33774 and GSE57631 datasets were obtained from the Gene Expression Omnibus (GEO) database. The linear models for microarray data (LIMMA) package in R software completes differentially expressed genes (DEGs). We conducted a weighted gene co-expression network analysis (WGCNA) on the top 25% of altered genes and identified the key modules associated with the clinical features of PI. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using the R software. We constructed a protein–protein interaction (PPI) network through the STRING database. After that we used Cytohubba plug-ins of Cytoscape to screen out the potential hub genes, which were subsequently verified via receiver operating characteristic (ROC) curves in another dataset, GSE178351, and revalidation of genes through the DisGeNET database. Results: We discovered 632 DEGs (570 upregulated genes and 62 downregulated genes). A total of eight modules were screened by WGCNA, among which the turquoise module was most correlated with PI. The Cytohubba plug-ins were used for filtering hub genes, which are highly linked with PI development, from the candidate genes in the protein–protein interaction (PPI) network. Conclusions: We found five key genes from PI using WGCNA. Among them, ICAM1, CXCL1, and JUN are worthy of further study of new target genes, providing the theoretical basis for further exploration of the occurrence and development mechanism of PI.

Investigation of the lncRNA THOR in Mice Highlights the Importance of Noncoding RNAs in Mammalian Male Reproduction

THOR is a highly conserved testis-specific long noncoding RNA (lncRNA). The interaction between THOR and the development of the male reproductive system remains unclear. Herein, CRISPR/Cas9 technology was used to establish a stable THOR-deficient mouse model, and the relationship between THOR and the fertility of adult male mice was investigated. The male mice in which THOR was deleted were smaller than the WT male mice. Moreover, their survival rate was reduced by 60%, their fertility was reduced by 50%, their testicular size and sperm motility were reduced by 50%, their testicular cell apoptosis was increased by 7-fold, and their ratio of female-to-male offspring was imbalanced (approximately 1:3). Furthermore, to elucidate the mechanisms of male reproductive system development, the mRNA levels of THOR targets were measured by qRT-PCR. Compared with WT mice, the THOR-deficient mice exhibited significantly decreased mRNA levels of IGF2BP1, c-MYC, IGF1, and IGF2. MEK-ERK signaling pathway expression was downregulated as determined by Western blot. We found that THOR targeted the MER-ERK signaling pathway downstream of IGF2 by binding to IGF2BP1 and affected testicular and sperm development in male mice. These results may also provide perspectives for exploring the roles of lncRNAs in human reproductive development and the pathogenesis and potential therapeutic targets of infertility.

MiR-1297 attenuates high glucose-induced injury in HK-2 cells via targeting COL1A2

BACKGROUND

In this study, we aimed to explore whether COL1A2 and miR-1297 participated in the progression of diabetic nephropathy (DN) in vitro and classified the underlying mechanisms.

METHODS

d-Glucose (30 mM; high glucose, HG)-stimulated HK-2 cells were used to mimic DN condition. RNA and non-coding RNA profiles were from Gene Expression Omnibus (GEO) database. The interaction between miR-1297 and COL1A2 was measured by dual-luciferase reporter assay. Gene Set Enrichment Analysis (GSEA) method was conducted to analyse COL1A2-associated signalling pathways. The role of miR-1297/COL1A2 in biological behaviours of HG-induced HK-2 cells were analysed by cell counting kit-8 and apoptosis assays.

RESULTS

Bioinformatics analysis revealed that COL1A2 was up-regulated in DN tissues. We predicted and verified miR-1297 as the regulatory miRNA of COL1A2, and the expression of miR-1297 was decreased in DN tissues and HG-stimulated HK-2 cells. Overexpression of miR-1297 could promote cell proliferation and inhibit apoptosis to protect HK-2 cells from HG-induced damage. And knockdown of COL1A2 enhanced the protective effects of miR-1297 on HG-stimulated HK-2 cells. GSEA results revealed that several inflammatory pathways were enriched in COL1A2 high-expression group. Meanwhile, transfection of miR-1297 reduced the phosphorylation of NFκB and expression of three important pro-inflammatory genes including cytokine CCL5, adhesion molecules ICAM1 and VCAM1 via targeting COL1A2. These results suggested that miR-1297 protected HG-treated HK-2 cells probably through suppressing inflammation via targeting COL1A2.

CONCLUSION

This study sheds a light on the role miR-1297/COL1A2 in DN progression and provides a novel promising therapy strategy for suppressing DN progression.