Bioinformatics, interaction network analysis, and neural networks to characterize gene expression of radicular cyst and periapical granuloma.

INTRODUCTION: Bioinformatics has emerged as an important tool to analyze the large amount of data generated by research in different diseases. In this study, gene expression for radicular cysts (RCs) and periapical granulomas (PGs) was characterized based on a leader gene approach. METHODS: A validated bioinformatics algorithm was applied to identify leader genes for RCs and PGs. Genes related to RCs and PGs were first identified in PubMed, GenBank, GeneAtlas, and GeneCards databases. The Web-available STRING software (The European Molecular Biology Laboratory [EMBL], Heidelberg, Baden-Württemberg, Germany) was used in order to build the interaction map among the identified genes by a significance score named weighted number of links. Based on the weighted number of links, genes were clustered using k-means. The genes in the highest cluster were considered leader genes. Multilayer perceptron neural network analysis was used as a complementary supplement for gene classification. RESULTS: For RCs, the suggested leader genes were TP53 and EP300, whereas PGs were associated with IL2RG, CCL2, CCL4, CCL5, CCR1, CCR3, and CCR5 genes. CONCLUSIONS: Our data revealed different gene expression for RCs and PGs, suggesting that not only the inflammatory nature but also other biological processes might differentiate RCs and PGs.

Assessment of Apical Expression of Alpha-2 Integrin, Heat Shock Protein, and Proinflammatory and Immunoregulatory Cytokines in Response to Endodontic Infection.

INTRODUCTION: The purpose of this study was to examine alpha-2 integrin, molecular mediators, cytokines, and chemokines from cells in periapical interstitial fluid from root canal infections before and after the reduction of the bacterial load using a cleaning procedure. METHODS: Subjects included 20 patients referred to the School of Dentistry at the Universidade Federal de Minas Gerais (Belo Horizonte, Minas Gerais, Brazil). Clinical samples were taken from teeth with pulp necrosis, and no patients had acute periapical symptoms at the time of the appointments. After cleaning and drying, 3 paper points were introduced into the root canal, passing passively through the root apex (2 mm) into the periapical tissues for 1 minute. The samples were collected immediately after root canal cleaning and 7 days later (restrained root canal bacterial load) to characterize those gene expressions using real-time polymerase chain reaction. RESULTS: Significantly lower levels of tumor necrosis factor alpha, chemokine ligand 5 (CCL5), chemokine ligand 2/monocyte chemotactic protein 1 (CCL2/MCP-1), and interleukin (IL)-8 in teeth with restrained bacterial loads (second collection) compared with the first collection were observed (P < .05). Similarly, the messenger RNA expression of the integrins secreted phosphoprotein 1 (SSP1)/ostepontin and focal adhesion kinase (FAK) decreased in samples from the second collection (P < .05). The messenger RNA for the regulatory cytokine IL-10 was significant higher in samples from the second collection (day 7) compared with the first collection (day 0) (P < .05). Messenger RNA expression of IL-1ß, IL-17A, interferon gamma, alpha-2 integrin, and Hsp47/SERPINH1 were similar at both time points (P > .05). CONCLUSIONS: These findings suggest that after reducing the root canal bacterial load a decrease in the inflammatory response took place in the periapical lesions.