Identification of key genes and pathways for peri-implantitis through the analysis of gene expression data

Protein profile at newly restored implants compared to contralateral teeth over 12-months: a pilot study

OBJECTIVES

To determine crevicular fluid alterations in protein expression of newly restored implants during their first year of function and associate them with those of contralateral teeth.

MATERIALS AND METHODS

In ten non-smokers, successfully treated for periodontitis, one newly restored implant (baseline-T0) and one corresponding tooth were followed for 12-months (T1). Oral hygiene was monitored during the study. Periodontal clinical indices and crevicular fluid were collected from an implant-site (PICF) and a tooth-site (GCF). Total proteomic profiles of PICF and GCF were investigated using label-free quantitative proteomics.

RESULTS

Clinical recordings remained stable at 12-months on the tooth-/implant-site basis. The comparative analysis of protein enrichment between teeth and implants at T0 revealed 664 human proteins, with 93 found only in teeth and 217 exclusively in implants. Among the 354 overlapping proteins, 46 were upregulated (log2FC > 1) in teeth, while 61 in implants. At T1, 569 human proteins were exclusively identified, with 67 found only in teeth and 193 exclusively in implants. Of the 309 overlapping proteins, 22 were upregulated in teeth, while 48 were in implants. The over-representation enrichment analysis identified "interferon-alpha response" and "allograft rejection" pathways, as significantly regulated categories at T0, with the latter being over-represented at T1.

CONCLUSIONS

Peri-implant tissue maturation was evident during the study. Proteins expressed in crevicular fluid reflected unique patterns between implants and teeth that are worth studying.

CLINICAL RELEVANCE

Different proteomic patterns were observed at the implant-site compared to the contralateral tooth-site towards inflammatory processes that prevail within otherwise clinically healthy peri-implant tissues.

CLINICAL TRIAL REGISTRATION NUMBER

ClinicalTrials.gov ID: NCT06379022.

Anti-inflammatory effects of Chrozophora plicata uncovered using network pharmacology and in-vivo carrageenan paw edema model

Chrozophora plicata has been extensively utilized in India for the management of numerous disorders. The effective Phytoconstituents derived from the Ethyl Acetate Fraction of Chrozophora plicata [EAFCP] have been identified as Camptothecin Agathisflavone, Rutin, Procynidine B, and Apigenin. These Phytoconstituents have been detected in the EAFCP through qualitative analysis using LC-Q-TOF-MS/MS. The anti-inflammatory properties of Chrozophora plicata are yet to be determined. Therefore, the aim of this study was to utilize a network pharmacology-based methodology to predict potential therapeutic targets of EAFCP in the setting of inflammation. The identification of inflammation targets was followed by the acquisition of verified targets of EAFCP. The key therapeutic targets of EAFCP against inflammation were found by creating a target-functional PPI network, GO studies were conducted on the core therapeutic targets in order to assess the essential signalling pathways involved in the anti-inflammatory effects of EAFCP. A total of 38 significant hub targets associated with EAFCP's anti-inflammatory effects were identified. The key proteins were retrieved for the docking investigation based on the findings, which aided in anticipating the potential interaction between components and targets. The in vivo study revealed that EAFCP had a notable efficiency in decreasing paw edema induced by carrageenan in rats. The evidence we have gathered collectively offers clarification about the anti-inflammatory activity of EAFCP, which is predominantly linked to the suppression of the Cox 1, 2 pathway. The aforementioned findings highlight potential therapeutic targets that could be utilized for the anti-inflammatory activity of EAFCP.

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.

HSP90AA1 promotes the inflammation in human gingival fibroblasts induced by Porphyromonas gingivalis lipopolysaccharide via regulating of autophagy

BACKGROUND

Peri-implantitis of tooth seriously affects the life quality of patients. This study aimed to investigate the role of HSP90AA1 in the inflammatory of human gingival fibroblasts (HGFs) induced by porphyromonas gingivalis lipopolysaccharide (Pg-LPS), and to provide a potential therapeutic target for clinical treatment of peri-implantitis.

METHODS

Pg-LPS (0.1, 1, 10 μg/mL) was used to construct the inflammatory model of HGFs to evaluate the effect of Pg-LPS on HGFs. Then HSP90AA1-siRNA was transfected to construct HSP90AA1 low expression HGFs cell line, and 3-MA was also added. After that, cell viability, apoptosis, the contents of inflammatory cytokines were detected by CCK-8, flow cytometry and ELISA assay, respectively. Intracellular ROS, the expressions of HSP90α, HSP90β were detected by immunofluorescence. The levels of HSP90AA1, p-NF-κB p65/NF-κB p65, LC3 II/I, ATG5, Beclin-1 and TLR protein were detected by western blot.

RESULTS

Pg-LPS treatment didn't affect the viability of HGFs cells, but induced the cell apoptosis and ROS generation, increased the contents of IL-1β, IL-6, TNF-α, and the protein expressions of HSP90AA1, p-NF-κBp65/NF-κBp65, LC3II/I, ATG5, and Beclin-1 in HGFs. While HSP90AA1-siRNA transfected into Pg-LPS induced HGFs significantly reduced the HSP90AA1, HSP90α, HSP90β expression, decreased the inflammatory factors, ROS generation, cell apoptosis rate, and autophagy-related proteins and TLR2/4 protein levels. What's more, the addition of autophagy inhibitor 3-MA further promote the effect of HSP90AA1-siRNA on Pg-LPS treated HGFs.

CONCLUSIONS

This study showed that HSP90AA1 promoted the inflammatory response of Pg-LPS induced HGFs by regulating autophagy. The addition of 3-MA further confirmed that autophagy may mediate siHSP90AA1 to enhance the inflammatory response.

Expression Analysis of Long Non-Coding RNAs Related With FOXM1, GATA3, FOXA1 and ESR1 in Breast Tissues

Breast cancer is the most common neoplasm among females. Estrogen receptor (ESR) signaling has a prominent impact in the pathogenesis of breast cancer. Among the transcription factors associated with ESR signaling, FOXM1, GATA3, FOXA1 and ESR1 have been suggested as a candidate in the pathogenesis of this neoplasm. In the current project, we have designed an in silico approach to find long non-coding RNAs (lncRNAs) that regulate these transcription factors. Then, we used clinical samples to carry out validation of our in silico findings. Our systems biology method led to the identification of APTR, AC144450.1, linc00663, ZNF337.AS1, and RAMP2.AS1 lncRNAs. Subsequently, we assessed the expression of these genes in breast cancer tissues compared with the adjacent non-cancerous tissues (ANCTs). Expression of GATA3 was significantly higher in breast cancer tissues compared with ANCTs (Ratio of mean expressions (RME) = 4.99, P value = 3.12E−04). Moreover, expression levels of APTR, AC144450.1, and ZNF337.AS1 were elevated in breast cancer tissues compared with control tissues (RME = 2.27, P value = 5.40E−03; Ratio of mean expressions = 615.95, P value = 7.39E−19 and RME = 1.78, P value = 3.40E−02, respectively). On the other hand, the expression of RAMP2.AS1 was lower in breast cancer tissues than controls (RME = 0.31, P value = 1.87E−03). Expression levels of FOXA1, ESR1, and FOXM1 and linc00663 were not significantly different between the two sets of samples. Expression of GATA3 was significantly associated with stage (P value = 4.77E−02). Moreover, expressions of FOXA1 and RAMP2.AS1 were associated with the mitotic rate (P values = 2.18E−02 and 1.77E−02, respectively). Finally, expressions of FOXM1 and ZNF337.AS1 were associated with breastfeeding duration (P values = 3.88E−02 and 4.33E−02, respectively). Based on the area under receiver operating characteristics curves, AC144450.1 had the optimal diagnostic power in differentiating between cancerous and non-cancerous tissues (AUC = 0.95, Sensitivity = 0.90, Specificity = 0.96). The combination of expression levels of all genes slightly increased the diagnostic power (AUC = 0.96). While there were several significant pairwise correlations between expression levels of genes in non-tumoral tissues, the most robust correlation was identified between linc00663 and RAMP2.AS1 (r = 0.61, P value = 3.08E−8). In the breast cancer tissues, the strongest correlations were reported between FOXM1/ZNF337.AS1 and FOXM1/RAMP2.AS1 pairs (r = 0.51, P value = 4.79E−5 and r = 0.51, P value = 6.39E−5, respectively). The current investigation suggests future assessment of the functional role of APTR, AC144450.1 and ZNF337.AS1 in the development of breast neoplasms.

Current Concepts on the Pathogenesis of Peri-implantitis: A Narrative Review

As implant treatment has been integrated in contemporary dental practice, complications with the forms of peri-implant mucositis and peri-implantitis have also increased in prevalence. Peri-implantitis is the more severe biological complication and is defined as an inflammatory disease affecting peri-implant tissues resulting in bone and eventually implant loss. In addition, the treatment of peri-implantitis has currently become a substantial global economic burden. In the current study, a search was conducted in several electronic databases using specific keywords relevant to the article's main topic. An increasing number of scientific reports have investigated the etiopathology of peri-implant diseases, focusing mainly on peri-implantitis. Microbial biofilm consists an important etiological factor of peri-implant pathology analogous to periodontal diseases. Although several data confirm that peri-implant infections are dominated by gram-negative bacteria, similar to periodontal infections, there is evidence that some cases may harbor a distinct microbiota, including opportunistic microorganisms and/or uncultivable species. Additionally, data support that several parameters, such as genetic predisposition of individual patients, occlusal overload, and local factors such as titanium particles and excess cement, may be implicated in peri-implantitis pathogenesis. Simultaneously, the release of titanium metal particles and their biological consequences or the presence of excess cement in the adjacent peri-implant tissues have also been suggested as factors that contribute to peri-implant pathology. A specific line of research also indicates the role of foreign body response to implant installation. This narrative review aims to discuss the current concepts of etiopathogenetic factors implicated in peri-implantitis.

Levels of Gene Expression of Immunological Biomarkers in Peri-Implant and Periodontal Tissues

This study compared the gene expression of the immunoinflammatory markers interleukin (IL)-6, IL-1ß, and tumor necrosis factor alpha (TNF-α), the matrix metalloproteinases (MMP)-1, -2, -8, and -9, and the tissue inhibitors of matrix metalloproteases (TIMP)-1 and -2 in the gingival tissue of individuals with periodontal and peri-implant disease. The study population included individuals with four periodontal statuses: periodontal health (PH group, n = 20); periodontitis (P group, n = 20); peri-implant health (PIH group, n = 20), and peri-implantitis (PI group, n = 20). Gingival biopsies were collected from one tooth per patient according to the inclusion criteria of each group. The mRNA levels of IL-6, IL-1ß, TNF-α, MMP-1, MMP-2, MMP-8, MMP-9, TIMP-1, and TIMP-2 were evaluated by qPCR. The levels of IL-1ß were significantly higher in the PI group when compared to the other groups (p < 0.05), while the levels of IL-6 were significantly higher in the groups with periodontal and peri-implant disease when compared with the healthy groups (p < 0.05); however, the levels of IL-6 did not differ between the PI and P groups (p > 0.05). For all other studied biomarkers, no significant differences were observed between groups (p > 0.05). IL-6 and IL-1ß presented higher levels of mRNA in diseased periodontal and peri-implant tissues. However, the expression of metalloproteinases and their inhibitors did not differ between the different periodontal statuses.

Microbial Community-Driven Etiopathogenesis of Peri-Implantitis

Osseointegrated dental implants are a revolutionary tool in the armament of reconstructive dentistry, employed to replace missing teeth and restore masticatory, occlusal, and esthetic functions. Like natural teeth, the orally exposed part of dental implants offers a pristine nonshedding surface for salivary pellicle-mediated microbial adhesion and biofilm formation. In early colonization stages, these bacterial communities closely resemble those of healthy periodontal sites, with lower diversity. Because the peri-implant tissues are more susceptible to endogenous oral infections, understanding of the ecological triggers that underpin the microbial pathogenesis of peri-implantitis is central to developing improved prevention, diagnosis, and therapeutic strategies. The advent of next-generation sequencing (NGS) technologies, notably applied to 16S ribosomal RNA gene amplicons, has enabled the comprehensive taxonomic characterization of peri-implant bacterial communities in health and disease, revealing a differentially abundant microbiota between these 2 states, or with periodontitis. With that, the peri-implant niche is highlighted as a distinct ecosystem that shapes its individual resident microbial community. Shifts from health to disease include an increase in diversity and a gradual depletion of commensals, along with an enrichment of classical and emerging periodontal pathogens. Metatranscriptomic profiling revealed similarities in the virulence characteristics of microbial communities from peri-implantitis and periodontitis, nonetheless with some distinctive pathways and interbacterial networks. Deeper functional assessment of the physiology and virulence of the well-characterized microbial communities of the peri-implant niche will elucidate further the etiopathogenic mechanisms and drivers of the disease.

A novel circRNA-miRNA-mRNA network identifies circ-YOD1 as a biomarker for coronary artery disease

Circular RNAs (circRNAs) are involved in many physiological functions. Whether circulating circRNAs serve as markers for coronary artery disease (CAD) is unknown. Seven CAD-related microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database and were analyzed using clustering and functional enrichment to identify hub mRNAs and miRNAs. StarBase V3.0 and circinteractome databases were used to predict interactions between circRNAs and miRNAs whereas miRwalk and DIANA TOOLS were used to predict interactions between miRNAs and mRNAs. Altogether, this helped establish a circRNA-miRNA-mRNA triple network for diagnosis of CAD. Five non-coding RNAs (ncRNAs) were identified in our study population with the use of quantitative real-time PCR (RT-PCR). The prognostic values of circYOD1, hsa-miR-21-3p and hsa-miR-296-3p were evaluated using a receiver operating characteristic (ROC) curve. A CAD circRNA-miRNA-mRNA network was established from our analyses containing one circRNA, four miRNAs and thirteen mRNAs. After performing RT-PCR validation between CAD and non-CAD samples, only three ncRNAs of five ncRNAs showed significance for further analysis. The area under ROC curve (AUC) of circ-YOD1 was 0.824, the AUC of hsa-miR-21-3p was 0.731 and hsa-miR-296-3p was 0.776. The pairwise comparison results showed that circ-YOD1 had statistical significance (P_YOD1-21 < 0.01 and P_YOD1-296 < 0.05). The results of functional enrichment analysis of interacting genes and microRNAs showed that the shared circ-YOD1 may act as a new biomarker for CAD. Our investigation of the triple regulatory networks of circRNA-miRNA-mRNA in CAD revealed circ-YOD1 as a potential biomarker for CAD.

Molecular mechanisms linking peri-implantitis and type 2 diabetes mellitus revealed by transcriptomic analysis

Aims

To explore molecular mechanisms that link peri-implantitis and type 2 diabetes mellitus (T2DM) by bioinformatic analysis of publicly available experimental transcriptomic data.

Materials and methods

Gene expression data from peri-implantitis were downloaded from the Gene Expression Omnibus database, integrated and differentially expressed genes (DEGs) in peri-implantitis were identified. Next, experimentally validated and computationally predicted genes related to T2DM were downloaded from the DisGeNET database. Protein–protein interaction network (PPI) pairs of DEGs related to peri-implantitis and T2DM related genes were constructed, “hub” genes and overlapping DEG were determined. Functional enrichment analysis was used to identify significant shared biological processes and signaling pathways. The PPI networks were subjected to cluster and specific class analysis for identifying “leader” genes. Module network analysis of the merged PPI network identified common or cross-talk genes connecting the two networks.

Results

A total of 92 DEGs overlapped between peri-implantitis and T2DM datasets. Three hub genes (IL-6, NFKB1, and PIK3CG) had the highest degree in PPI networks of both peri-implantitis and T2DM. Three leader genes (PSMD10, SOS1, WASF3), eight cross-talk genes (PSMD10, PSMD6, EIF2S1, GSTP1, DNAJC3, SEC61A1, MAPT, and NME1), and one signaling pathway (IL-17 signaling) emerged as peri-implantitis and T2DM linkage mechanisms.

Conclusions

Exploration of available transcriptomic datasets revealed IL-6, NFKB1, and PIK3CG expression along with the IL-17 signaling pathway as top candidate molecular linkage mechanisms between peri-implantitis and T2DM.

A novel lncRNA-miRNA-mRNA triple network identifies lncRNA TWF1 as an important regulator of miRNA and gene expression in coronary artery disease

Background

Long non-coding RNAs (lncRNAs) are involved in numerous physiological functions. Yet, their mechanisms in coronary artery disease (CAD) are not well understood.

Methods

The expression profile of genes associated to CAD was reannotated into the lncRNA-mRNA biphasic profile. The target microRNA data were used to design a global CAD triple network. Thereafter, we conducted a functional enrichment analysis and clustering using the triple network from the level of topology analyses. The expression of four non-coding RNAs (ncRNAs) was measured by qRT-PCR and the risk of CAD was calculated by nomogram. The prognostic value of three ncRNAs was evaluated using receiver operating characteristic (ROC) curve.

Results

A CAD lncRNA-miRNA-mRNA network was constructed which included 15 mRNAs, 3 miRNAs, 19 edges and one lncRNA. Nomogram showed that four ncRNAs were the risk of CAD. After RT-PCR validation in four ncRNAs between CAD and non-CAD samples, only three ncRNAs had significant meaning for further analysis. ROC curve showed that TWF1 presented an area under curve (AUC) of 0.862, the AUC of hsa -miR-142-3p was 0.856 and hsa -miR126-5p was 0.822. After the pairwise comparison, we found that TWF1 had significant statistical significance (P _TWF1-142 < 0.05 and P _TWF1-126 < 0.01). The results of functional enrichment analysis of interacting gene and microRNA showed that the shared lncRNA TWF1 may be a new factor for CAD.

Conclusions

This investigation on the regulatory networks of lncRNA-miRNA-mRNA in CAD suggests that a novel lncRNA, lncRNA TWF1 is a risk factor for CAD, and expands our understanding into the mechanisms involved in the pathogenesis of CAD.

Differentially expressed gene profile and relevant pathways of the traditional Chinese medicine cinobufotalin on MCF‑7 breast cancer cells

Cinobufotalin is a chemical compound extracted from the skin of dried bufo toads that may have curative potential for certain malignancies through different mechanisms; however, these mechanisms remain unexplored in breast cancer. The aim of the present study was to investigate the antitumor mechanism of cinobufotalin in breast cancer by using microarray data and in silico analysis. The microarray data set GSE85871, in which cinobufotalin exerted influences on the MCF‑7 breast cancer cells, was acquired from the Gene Expression Omnibus database, and the differentially expressed genes (DEGs) were analyzed. Subsequently, protein interaction analysis was conducted, which clarified the clinical significance of core genes, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were used to analyze cinobufotalin‑related pathways. The Connectivity Map (CMAP) database was used to select existing compounds that exhibited curative properties similar to those of cinobufotalin. A total of 1,237 DEGs were identified from breast cancer cells that were treated with cinobufotalin. Two core genes, SRC proto‑oncogene non‑receptor tyrosine kinase and cyclin‑dependent kinase inhibitor 2A, were identified as serving a vital role in the onset and development of breast cancer, and their expression levels were markedly reduced following cinobufotalin treatment as detected by the microarray of GSE85871. It also was revealed that the 'neuroactive ligand‑receptor interaction' and 'calcium signaling' pathways may be crucial for cinobufotalin to perform its functions in breast cancer. Conducting a matching search in CMAP, miconazole and cinobufotalin were indicated to possessed similar molecular mechanisms. In conclusion, cinobufotalin may serve as an effective compound for the treatment of a subtype of breast cancer that is triple positive for the presence of estrogen, progesterone and human epidermal growth factor receptor‑2 receptors, and its mechanism may be related to different pathways. In addition, cinobufotalin is likely to exert its antitumor influences in a similar way as miconazole in MCF‑7 cells.