Gene Interaction Network Analysis Reveals IFI44L as a Drug Target in Rheumatoid Arthritis and Periodontitis

Extra Tree Classifier Predicts an Interactome Hub Gene as HSPB1 in Oral Cancer: A Bioinformatics Analysis

Introduction Oral cancer is a significant global health issue that is mainly caused by factors, such as smoking, alcohol consumption, poor oral hygiene, age, and the human papillomavirus. Unfortunately, delayed diagnosis contributes to high rates of illness and mortality. However, saliva shows promise as a potential source for early detection, prognosis, and treatment. By analyzing the proteins and their interactions in saliva, we can gain insights that can assist in early detection and prediction. In this study, we aim to identify and predict the key genes, known as hub genes, in the salivary transcriptomics data of oral cancer patients and healthy individuals. Methods The data used for the analysis were obtained from salivaryproteome.org (https://salivaryproteome.org/) . The retrieved data consisted of individuals with oral cancer who were assigned unique identification numbers (IDs) 1025, 1030, 1027, and 1029, while the healthy individuals were assigned IDs 4256, 4257, 4255, and 4258, respectively. Differential gene expression analysis was used to identify genes that showed significant differences between the two groups. Uniformity and clustering were assessed through heatmaps and principal component analysis. Protein-protein interactions were investigated using the STRING database and Cytoscape. In addition, machine learning algorithms were employed to identify key genes involved in the interatomic interactions by analyzing transcriptomics data generated from the differential gene expression analysis. Results The accuracy and class accuracy of the extra tree classifier showed 98% and 97% in predicting interactomic hub genes, and HSPB1 was identified as a hub gene using Cytohubba from Cytoscape. Conclusion The predictive extra tree classifier, with its high accuracy in analysing interactomic hub genes in oral cancer, can potentially improve diagnosis and treatment strategies.

Graph neural networks-based prediction of drug gene association of P2X receptors in periodontal pain

The P2X7 receptor, a member of the P2X receptor family, plays a crucial role in various physiological processes, particularly pain perception. Its expression across immune, neuronal, and glial cells facilitates the release of pro-inflammatory molecules, thereby influencing pain development and maintenance, as evidenced by its association with pulpitis in rats. Notably, P2X receptors such as P2X3 and P2X7 are pivotal in dental pain pathways, making them promising targets for novel analgesic interventions. Leveraging graph neural networks (GNNs) presents an innovative approach to model graph data, aiding in the identification of drug targets and prediction of their efficacy, complementing advancements in genomics and proteomics for therapeutic development. In this study, 921 drug-gene interactions involving P2X receptors were accessed through https://www.probes-drugs.org/. These interactions underwent meticulous annotation, preprocessing, and subsequent utilization to train and assess GNNs. Furthermore, leveraging Cytoscape, the CytoHubba plugin, and other bioinformatics tools, gene expression networks were constructed to pinpoint hub genes within these interactions. Through analysis, SLC6A3, SLC6A2, FGF1, GRK2, and PLA2G2A were identified as central hub genes within the context of P2X receptor-mediated drug-gene interactions. Despite achieving a 65 percent accuracy rate, the GNN model demonstrated suboptimal predictive power for gene-drug interactions associated with oral pain. Hence, further refinements and enhancements are imperative to unlock its full potential in elucidating and targeting pathways underlying oral pain mechanisms.

A Porphyromonas gingivalis hypothetical protein controlled by the type I-C CRISPR-Cas system is a novel adhesin important in virulence

The ability of many human pathogens to infect requires their ability to adhere to the host surfaces as a first step in the process. Porphyromonas gingivalis, a keystone oral pathogen, uses adhesins to adhere to the surface of the gingival epithelium and other members of the oral microbiome. In a previous study, we identified several proteins potentially linked to virulence whose mRNA levels are regulated by CRISPR-Cas type I-C. Among those, PGN_1547 was highly upregulated in the CRISPR-Cas 3 mutant. PGN_1547 is annotated as a hypothetical protein. Employing homology searching, our data support that PGN_1547 resembles an auto-transporter adhesin of P. gingivalis based on containing the DUF2807 domain. To begin to characterize the function of PGN_1547, we found that a deletion mutant displayed a significant decrease in virulence using a Galleria mellonela model. Furthermore, this mutant was significantly impaired in forming biofilms and attaching to the macrophage-like cell THP-1. Luminex revealed that the PGN_1547 mutant elicited a less robust cytokine and chemokine response from THP-1 cells, and TLR2 predominantly sensed that recombinant PGN_1547. Taken together, these findings broaden our understanding of the toolbox of virulence factors possessed by P. gingivalis. Importantly, PGN_1547, a hypothetical protein, has homologs in another member of the order Bacteroidales whose function is unknown, and our results could shed light on the role of this family of proteins as auto-transport adhesins in this phylogenetic group.IMPORTANCEPeriodontal diseases are among humans' most common infections, and besides their effect on the oral cavity, they have been associated with systemic inflammatory conditions. Among members of the oral microbiome implicated in the development of periodontitis, Porphyromonas gingivalis is considered a keystone pathogen. We have identified a new adhesin that acts as a virulence factor, PGN_1547, which contains the DUF2807 domain, which belongs to the putative auto-transporter adhesin, head GIN domain family. Deletion of this gene lowers the virulence of P. gingivalis and impacts the ability of P. gingivalis to form biofilm and attach to host cells. Furthermore, the broad distribution of these receptors in the order Bacteroidales suggests their importance in colonization by this important group of organisms.

The role of the CX3CL1/CX3CR1 axis as potential inflammatory biomarkers in subjects with periodontitis and rheumatoid arthritis: A systematic review

OBJECTIVE

This systematic review aimed to investigate the role of the C-X3-C motif ligand 1/chemokine receptor 1 C-X3-C motif (CX3CL1/CX3CR1) axis in the pathogenesis of periodontitis. Furthermore, as a secondary objective, we determine whether the CX3CL1/CX3CR1 axis could be considered complementary to clinical parameters to distinguish between periodontitis and rheumatoid arthritis (RA) and/or systemically healthy subjects.

METHODS

The protocol used for this review was registered in OSF (10.17605/OSF.IO/KU8FJ). This study was designed following Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines. Records were identified using different search engines (PubMed/MEDLINE, Scopus, Science Direct, and Web of Science) from August 10, 2006, to September 15, 2023. The observational studies on human subjects diagnosed with periodontitis and RA and/or systemically healthy were selected to analyze CX3CL1 and CX3CR1 biomarkers. The methodological validity of the selected articles was assessed using NIH.

RESULTS

Six articles were included. Biological samples (gingival crevicular fluid [GCF], saliva, gingival tissue biopsies, serum) from 379 subjects (n = 275 exposure group and n = 104 control group) were analyzed. Higher CX3CL1 and CX3CR1 chemokine levels were found in subjects with periodontitis and RA compared with periodontal and systemically healthy subjects.

CONCLUSION

Very few studies highlight the role of the CX3CL1/CX3CR1 axis in the pathogenesis of periodontitis; however, increased levels of these chemokines are observed in different biological samples (GCF, gingival tissue, saliva, and serum) from subjects with periodontitis and RA compared with their healthy controls. Future studies should focus on long-term follow-up of subjects and monitoring changes in cytokine levels before and after periodontal therapy to deduce an appropriate interval in health and disease conditions.

A systematic review of the impact of Porphyromonas gingivalis on foam cell formation: Implications for the role of periodontitis in atherosclerosis

BACKGROUND

The current literature suggests the significant role of foam cells in the initiation of atherosclerosis through the formation of a necrotic core in atherosclerotic plaques. Moreover, an important periodontal pathogen called Porphyromonas gingivalis (P. gingivalis) is indicated to play a significant role in this regard. Thus, the aim of this systematic review was to comprehensively study the pathways by which P. gingivalis as a prominent bacterial species in periodontal disease, can induce foam cells that would initiate the process of atherosclerosis formation.

METHODS

An electronic search was undertaken in three databases (Pubmed, Scopus, and Web of Science) to identify the studies published from January 2000 until March 2023. The risk of bias in each study was also assessed using the QUIN risk of bias assessment tool.

RESULTS

After the completion of the screening process, 11 in-vitro studies met the inclusion criteria and were included for further assessments. Nine of these studies represented a medium risk of bias, while the other two had a high risk of bias. All of the studies have reported that P. gingivalis can significantly induce foam cell formation by infecting the macrophages and induction of oxidized low-density lipoprotein (oxLDL) uptake. This process is activated through various mediators and pathways. The most important factors in this regard are the lipopolysaccharide of P. gingivalis and its outer membrane vesicles, as well as the changes in the expression rate of transmembrane lipid transportation channels, including transient receptor potential channel of the vanilloid subfamily 4 (TRPV4), lysosomal integral protein 2 (LIMP2), CD36, etc. The identified molecular pathways involved in this process include but are not limited to NF-κB, ERK1/2, p65.

CONCLUSION

Based on the results of this study, it can be concluded that P. gingivalis can effectively promote foam cell formation through various pathogenic elements and this bacterial species can affect the expression rate of various genes and the function of specific receptors in the cellular and lysosomal membranes. However, due to the moderate to high level of risk of bias among the studies, further studies are required in this regard.

Exploring animal models in oral cancer research and clinical intervention: A critical review

Cancer is a leading cause of death worldwide, but advances in treatment, early detection, and prevention have helped to reduce its impact. To translate cancer research findings into clinical interventions for patients, appropriate animal experimental models, particularly in oral cancer therapy, can be helpful. In vitro experiments using animal or human cells can provide insight into cancer's biochemical pathways. This review discusses the various animal models used in recent years for research and clinical intervention in oral cancer, along with their advantages and disadvantages. We highlight the advantages and limitations of the used animal models in oral cancer research and therapy by searching the terms of animal models, oral cancer, oral cancer therapy, oral cancer research, and animals to find all relevant publications during 2010-2023. Mouse models, widely used in cancer research, can help us understand protein and gene functions in vivo and molecular pathways more deeply. To induce cancer in rodents, xenografts are often used, but companion animals with spontaneous tumours are underutilized for rapid advancement in human and veterinary cancer treatments. Like humans with cancer, companion animals exhibit biological behaviour, treatment responses, and cytotoxic agent responses similar to humans. In companion animal models, disease progression is more rapid, and the animals have a shorter lifespan. Animal models allow researchers to study how immune cells interact with cancer cells and how they can be targeted specifically. Additionally, animal models have been extensively used in research on oral cancers, so researchers can use existing knowledge and tools to better understand oral cancers using animal models.

Biomolecular and Biochemical Aspects of the Oral Cavity

Recent advances in science, especially innovations in the field of biochemistry and materials science, greatly contribute to improvements in the prevention, diagnosis, and treatment of oral diseases [...].

Synthetic materials in craniofacial regenerative medicine: A comprehensive overview

The state-of-the-art approach to regenerating different tissues and organs is tissue engineering which includes the three parts of stem cells (SCs), scaffolds, and growth factors. Cellular behaviors such as propagation, differentiation, and assembling the extracellular matrix (ECM) are influenced by the cell's microenvironment. Imitating the cell's natural environment, such as scaffolds, is vital to create appropriate tissue. Craniofacial tissue engineering refers to regenerating tissues found in the brain and the face parts such as bone, muscle, and artery. More biocompatible and biodegradable scaffolds are more commensurate with tissue remodeling and more appropriate for cell culture, signaling, and adhesion. Synthetic materials play significant roles and have become more prevalent in medical applications. They have also been used in different forms for producing a microenvironment as ECM for cells. Synthetic scaffolds may be comprised of polymers, bioceramics, or hybrids of natural/synthetic materials. Synthetic scaffolds have produced ECM-like materials that can properly mimic and regulate the tissue microenvironment's physical, mechanical, chemical, and biological properties, manage adherence of biomolecules and adjust the material's degradability. The present review article is focused on synthetic materials used in craniofacial tissue engineering in recent decades.

The Cytotoxicity and Anticancer Effects of Propolis against the Oral Squamous Cell Carcinoma: In Vitro Study

Background and aim: A wide range of therapeutic properties, including anti-cancer properties, are attributed to propolis, a resinous product obtained from several plants that possess a variety of medicinal properties. A study on honeybee-produced propolis showed that in mice, it showed a significant reduction in the progression of squamous cell carcinoma in the head and neck, but in humans, its role in HNSCC remains unclear. Method and materials: Propolis was sampled from two types of Iranian. Extraction was done using ethanolic extracts of propolis. The cll viability was evaluated by MTT assay. Cancer cell lines were assessed for gene expression, such as  mmp-2, mmp-9, bax, and bcl-2. Results: Increased sample concentrations reduced cell viability but did not cause significant cytotoxicity. A RT-PCR indicated that the Khalkhal sample produced more effects among the two samples, and the level of bax mRNA gene expression in the Khalkhal sample was increased. With an increasing concentration of Khalkhal samples, the expression increased. Increasing Khalkhal sample concentration also reduced mRNA levels of bcl-2, mmp-2, and mmp-9. Conclusion: Khalkhal’s propolis can be considered a suitable sample for the study of antiapoptotic and proapoptotic gene expression. Additionally, it can be used as a potential candidate for inhibiting the proliferation and spread of oral cancer cells.