Detection and quantification of mast cell, vascular endothelial growth factor, and microvessel density in human inflammatory periapical cysts and granulomas

The Expression of HIF-1α and VEGF in Radicular Cysts and Periapical Granulomas

OBJECTIVES

 This study aimed to evaluate the expression levels of hypoxia-inducible factor 1-α (HIF-1α) and vascular endothelial growth factor (VEGF) in radicular cysts and periapical granulomas, thereby contributing to the understanding of their potential significance in the differential diagnosis and treatment of these lesions.

MATERIALS AND METHODS

 In the present cross-sectional study, 51 samples of periapical lesions were included. Of them, 24 samples were radicular cysts, and 27 samples were periapical granulomas. Samples were immunohistochemically analyzed for HIF-1α and VEGF proteins expression. Chi-square tests and Spearman's rank correlation coefficient tests were used to detect differences and correlations among the parameters, respectively.

RESULTS

 In radicular cysts, HIF-1α expression was absent in 1 (4.2%), weak in 5 (20.8%), mild in 7 (29.2%), and strong in 11 (45.8%) cases, while VEGF expression was absent in 1 (4.2%), weak in 6 (25.0%), mild in 9 (37.5%), and strong in 8 (33.3%) of the cases; nevertheless, in periapical granulomas, HIF-1α expression was absent in 8 (29.6%), weak in 6 (22.2%), mild in 9 (33.3%), and strong in 4 (14.8%) of the cases, whereas VEGF expression was absent in 4 (14.8%), weak in 16 (59.3%), mild in 4 (14.8%), and strong in 3 (11.1%) of the cases. Chi-square test revealed a significant difference in the expression of HIF-1α and VEGF between radicular cysts and periapical granuloma (chi-square test = 8.906, p = 0.031; chi-square test = 10.401, p = 0.015, respectively). Spearman's correlation test showed a significant correlation between HIF-1α and VEGF in the total samples of both radicular cysts and periapical granulomas (rho = 0.385, p = 0.005).

CONCLUSION

 There is high expression of both HIF-1α and VEGF throughout the odontogenic epithelium and connective tissue of the radicular cyst and periapical granuloma. Both HIF-1α and VEGF are more highly expressed in radicular cysts than in periapical granulomas. These findings may aid in the diagnosis and management of suspected periapical lesions, suggesting that radicular cysts exhibit more advanced hypoxic conditions and associated pathways compared with periapical granulomas.

The Mystifying Role of Mast Cells in the Pathogenesis of Periapical Pathologies - a Systematic Review

INTRODUCTION

Oral periapical lesions present a significant global health burden, with their pathogenesis shrouded in complexity due to multifaceted mechanisms. Despite extensive research, the precise role of mast cells in their pathogenesis remains elusive. The present systematic review aimed to elucidate the mechanism of mast cells in the immunopathology of periapical lesions.

METHODS

An extensive literature search conducted across databases (MEDLINE via PubMed, Scopus, Cochrane Library, and EMBASE and gray literature) of original research articles that examined the role of mast cells in periapical lesions were investigated and selected for review. The risk of bias for each study was meticulously assessed using the QUADAS-2, and Review Manager 5.4 (RevMan v5.4, The Nordic Cochrane Centre, The Cochrane Collaboration, Copenhagen, Denmark) was utilized to generate the results.

RESULTS

A total of 41 published articles were included for data synthesis. The findings revealed significant variations in mast cell number within the fibrous capsule of periapical granuloma and periapical cyst, with notably elevated counts in the latter. Periapical granuloma manifested a predominance of granulated mast cells in the subepithelial region. In contrast, the periapical cyst exhibited a preponderance of degranulated mast cells in the deeper areas of the capsule.

CONCLUSIONS

The current evidence substantiates that mast cells play a crucial role in the pathogenesis, progression, fibrosis, and chronicity of periapical lesions.

Porous Hydrogels Prepared by Two-Step Gelation Method for Bone Regeneration

Hierarchical porous hydrogels possess advantageous characteristics that facilitate cell adhesion, promote tissue growth, and enhance angiogenesis and osteogenesis. In this study, porous composite hydrogels were successfully prepared by a two-step gelation method with sodium alginate (SA), gelatin (GEL), and calcium hydrogen phosphate (DCP) as the main components. The fabricated porous hydrogels initially featured small pores (approximately 60 μm), and gradually evolved to large pores (exceeding 250 μm) during the gradual degradation in the cellular microenvironment. In vitro cell culture experiments indicated that these hydrogels could enhance the proliferation and osteogenic differentiation of bone marrow mesenchymal stem cells due to the hierarchical porous structure and the incorporation of DCP. Subcutaneous implantation and cranial defect repair experiments in Sprague-Dawley rats further confirmed that the small initial pore size of hydrogel scaffolds can provide more sites for cell adhesion. Additionally, the gradual degradation to form large pores was conducive to cell/tissue growth and blood vessel formation, ultimately being beneficial for vascularized bone regeneration. In summary, this study proposes an innovative strategy for developing porous hydrogels with gradual degradation for functional bone regeneration.

CD34 and Ki-67 Immunoexpression in Periapical Granulomas: Implications for Angiogenesis and Cellular Proliferation

BACKGROUND/OBJECTIVES

The main mechanism of the formation of granulation tissue is the progression of an infection from the tooth to the periapical bone. At this level, the immune system tries to localize and annihilate the microorganism's injury. Ki-67 is a protein directly associated with the cell proliferation rate, while CD34 is a biomarker involved in angiogenesis, and studies suggest that they both have a positive correlation with the intensity of the local inflammatory infiltrate. This study will determine the immunoexpression of CD34 and Ki-67 in periapical granulomas and assess their impact on the growth and development of this tissue, as well as consider their roles in the proliferative process and aggressiveness of evolution.

METHODS

In the present study, 35 periapical granulomas obtained after a tooth extraction were included. The specimens were analyzed via histopathology and immunohistochemistry.

RESULTS

A positive reaction for the Ki-67 antibody was observed in 32 (86.5%) of the 35 periapical granuloma cases included in our study. We identified the overexpression of Ki-67 and CD34 and further calculated the Ki-67 index to evaluate and correlate the proliferation potential and angiogenesis with regard to the presence of an inflammatory infiltrate.

CONCLUSIONS

These findings suggest that the persistence of an inflammatory environment directly influences Ki-67 and CD34 expression, sustaining the proliferative capacity of cells and abnormal angiogenesis. This study is the first to evaluate the presence of the CD34+ and Ki-67+ proliferating vessels in periapical granulomas.

Integration of single-cell RNA sequencing of endothelial cells and proteomics to unravel the role of ICAM1-PTGS2 communication in apical periodontitis: A laboratory investigation

AIM

Endothelial cells (EDs) play a key role in angiogenesis and are associated with granulomatous lesions in patients with chronic apical periodontitis (CAP). This study aimed to investigate the diversity of EDs using single-cell ribonucleic acid sequencing (scRNA-seq) and to evaluate the regulation of intercellular adhesion molecule 1 (ICAM1) on the ferroptosis-related protein, prostaglandin-endoperoxide synthase 2 (PTGS2), in CAP.

METHODOLOGY

EDs from the uploaded scRNA-seq data of five CAP samples (GSE181688 and GSE197680) were categorized using distinct marker genes. The interactions between vein EDs (veinEndo) and other cell types were analysed using CellPhoneDB. Differentially expressed proteins in the proteomics of human umbilical vein EDs (HUVECs) and THP-1-derived macrophages infected with Porphyromonas gingivalis were compared with the differentially expressed genes (DEGs) of VeinEndo in scRNA-seq of CAP versus healthy control periodontal tissues. The protein-protein interaction of ICAM1-PTGS2 in macrophages and HUVECs was validated by adding recombinant ICAM1, ICAM1 inhibitor and PTGS2 inhibitor using real-time polymerase chain reaction (PCR), western blotting, and immunofluorescence staining.

RESULTS

EDs in patients with CAP were divided into eight subclusters: five vein ED, capillaries, arterials and EC (PLA). There were 29 mutually upregulated DEGs and two mutually downregulated DEGs in vein cells in the scRNA-seq data, as well as differentially expressed proteins in the proteomics of HUVECs. Real-time PCR and immunofluorescence staining showed that ICAM1 and PTGS2 were highly expressed in CAP, infected HUVECs, and macrophages. Recombinant protein ICAM1 may improve PTGS2 expression, reactive oxygen species (ROS), and Fe2+ levels and decrease glutathione peroxidase 4 (GPX4) and SLC7A11 protein levels. ICAM1 inhibitor may inverse the above changes.

CONCLUSIONS

scRNA-seq revealed the diversity of EDs in CAP and identified the possible regulation of ICAM1 by the ferroptosis-related protein, PTGS2, in infected HUVECs and macrophages, thus providing a basis for therapeutic approaches that target the inflammatory microenvironment of CAP.

Human Periapical Odontogenic Granulomas: Aspects of Microvessel Density (MVD), Heterogeneity of Blood Vessels and Mast Cells Density (MCD)

Periapical odontogenic granulomas are among the most encountered pathology that involve the alveolar bone, with severe consequences such as bone resorption, the presence of inflammatory infiltrate and the formation of abnormal vascularization. The present study aimed to quantify the existence of the microvessel density (MVD), mast cell density (MCD) and heterogeneity of the encountered blood vessels. A total of 37 patients diagnosed with odontogenic periapical granulomas were included, and the gender distribution, age and localization of the pathological lesions was assessed. After the surgical removal of the periapical odontogenic granuloma, the collected tissue was fixed in 10% buffered formalin. Primary processing, morphological analysis and immunohistochemical staining was performed in order to characterize the altered tissue. The results outlined the presence of a high number of mast cells, especially in the area of the inflamed tissue; the high heterogeneity of the blood vessels; and increased MVD with positive CD34. The conclusions of the study focus on the key role of the mast cells and their implication in the initiation and development of the angiogenesis process, triggering the inflammatory response of the host. Nevertheless, periapical odontogenic granulomas develop as an inflammatory response to the interaction between the host's immune system and microbial invasion.

Interplay of collagen and mast cells in periapical granulomas and periapical cysts: a comparative polarizing microscopic and immunohistochemical study

Objectives

This pilot study aimed to establish the interrelationship between collagen and mast cells in periapical granulomas and periapical cysts.

Materials and Methods

An observational cross-sectional study was conducted on the paraffin-embedded tissue sections of 68 specimens (34 periapical granulomas and 34 periapical cysts). The specimens were stained with picrosirius to observe collagen fiber birefringence and anti-tryptase antibody to evaluate the mast cell count immunohistochemically. The mean number and birefringence of collagen fibers, as well as the mean number of mast cells (total, granulated, and degranulated), and the mean inflammatory cell density were calculated. The data obtained were analyzed using the Kruskal Wallis test, Mann Whitney U test, and Spearman correlation test (p < 0.05).

Results

The mean number of thick collagen fibers was higher in periapical cysts, while that of thin fibers was higher in granulomas (p = 0.00). Cysts emitted orange-yellow to red birefringence, whereas periapical granulomas had predominantly green fibers (p = 0.00). The mean inflammatory cell density was comparable in all groups (p = 0.129). The number of total, degranulated, and granulated mast cells exhibited significant results (p = 0.00) in both groups. Thick cyst fibers showed significant inverse correlations with inflammation and degranulated mast cells (p = 0.041, 0.04 respectively).

Conclusions

Mast cells and inflammatory cells influenced the nature of collagen fiber formation and its birefringence. This finding may assist in the prediction of the nature, pathogenesis, and biological behavior of periapical lesions.

Vascular Endothelial Growth Factor: A Translational View in Oral Non-Communicable Diseases

Vascular endothelial growth factors (VEGFs) are vital regulators of angiogenesis that are expressed in response to soluble mediators, such as cytokines and growth factors. Their physiologic functions include blood vessel formation, regulation of vascular permeability, stem cell and monocyte/macrophage recruitment and maintenance of bone homeostasis and repair. In addition, angiogenesis plays a pivotal role in chronic pathologic conditions, such as tumorigenesis, inflammatory immune diseases and bone loss. According to their prevalence, morbidity and mortality, inflammatory diseases affecting periodontal tissues and oral cancer are relevant non-communicable diseases. Whereas oral squamous cell carcinoma (OSCC) is considered one of the most common cancers worldwide, destructive inflammatory periodontal diseases, on the other hand, are amongst the most prevalent chronic inflammatory conditions affecting humans and also represent the main cause of tooth loss in adults. In the recent years, while knowledge regarding the role of VEGF signaling in common oral diseases is expanding, new potential translational applications emerge. In the present narrative review we aim to explore the role of VEGF signaling in oral cancer and destructive periodontal inflammatory diseases, with emphasis in its translational applications as potential biomarkers and therapeutic targets.

Presence of langerhans cells, regulatory T cells (Treg) and mast cells in asymptomatic apical periodontitis

Asymptomatic Apical Periodontitis is essentially an inflammatory disease of microbial aetiology. Association and function of the cell components involved, or specific inductive factors and growth mediators associated with development, maintenance and resolution of the periapical lesions are still unknown. The objective of this study was to evaluate the concentration of Regulatory T cells (FoxP3+; Treg), Langerhans cells (CD1a+; LC) and mast cells in asymptomatic apical periodontitis. 73 cases were selected: 30 periapical granulomas, 29 radicular cysts and 14 residual cysts. All groups were submitted to morphological analysis for classification of inflammatory infiltrate and thickness of the epithelial lining as well as to immunohistochemical analysis for detection of LC and Treg cells. Toluidine blue staining was used for detecting mast cells. Analysis showed higher mean numbers of LC (8.2 cells/0.2mm2), and Treg cells in radicular cysts (5.910 cells/0.2mm2). As for mast cells, it was found that radicular cysts had a higher mean number of these cells compared to other periapical lesions (12.68 cells/0.2mm2). The association between thickness of the epithelial lining and inflammatory cells showed that the presence of hypertrophic epithelium in radicular cysts presented higher density of LC. The number of LC and Treg cells play an important role in the control of the inflammatory micro-environment in periapical granulomas and radicular cysts, respectively. The presence of mast cells in radicular cysts may be associated with progression of the lesion. Knowledge regarding the inflammatory cell profile is therefore essential for a better understanding of the pathogenesis of asymptomatic periapical periodontitis.

Adipose derived stem cells and platelet rich plasma improve the tissue integration and angiogenesis of biodegradable scaffolds for soft tissue regeneration

Current surgical reconstruction for soft tissue replacement involves lipotransfer to restore soft tissue replacements but is limited by survival and longevity of the fat tissue. Alternative approaches to overcome these limitations include using biodegradable scaffolds with stem cells with growth factors to generate soft tissue. Adipose derived stem cells (ADSCs) offer great potential to differentiate into adipose, and can be delivered using biodegradable scaffolds. However, the optimal scaffold to maximise this approach is unknown. This study investigates the biocompatibility of nanocomposite scaffolds (POSS-PCL) to deliver ADSCs with and without the addition of growth factors using platelet rich plasma (PRP) in vivo. Rat ADSCs were isolated and then seeded on biodegradable scaffolds (POSS-PCL). In addition, donor rats were used to isolate PRP to modify the scaffolds. The implants were then subcutaneously implanted for 3-months to assess the effect of PRP and ADSC on POSS-PCL scaffolds biocompatibility. Histology after explanation was examined to assess tissue integration (H&E) and collagen production (Massons Trichome). Immunohistochemistry was used to assess angiogenesis (CD3, α-SMA), immune response (CD45, CD68) and adipose formation (PPAR-γ). At 3-months PRP-ADSC-POSS-PCL scaffolds demonstrated significantly increased tissue integration and angiogenesis compared to PRP, ADSC and unmodified scaffolds (p < 0.05). In addition, PRP-ADSC-POSS-PCL scaffolds showed similar levels of CD45 and CD68 staining compared to unmodified scaffolds. Furthermore, there was increased PPAR-γ staining demonstrated at 3-months with PRP-ADSC-POSS-PCL scaffolds (p < 0.05). POSS-PCL nanocomposite scaffolds provide an effective delivery system for ADSCs. PRP and ADSC work synergistically to enhance the biocompatibility of POSS-PCL scaffolds and provide a platform technology for soft tissue regeneration.

Argon plasma surface modification promotes the therapeutic angiogenesis and tissue formation of tissue-engineered scaffolds in vivo by adipose-derived stem cells

Background

Synthetic implants are being used to restore injured or damaged tissues following cancer resection and congenital diseases. However, the survival of large tissue implant replacements depends on their ability to support angiogenesis that if limited, causes extrusion and infection of the implant. This study assessed the beneficial effect of platelet-rich plasma (PRP) and adipose-derived stem cells (ADSCs) on synthetic biomaterials in combination with argon plasma surface modification to enhance vascularisation of tissue-engineered constructs.

Methods

Non-biodegradable polyurethane scaffolds were manufactured and modified with plasma surface modification using argon gas (PM). Donor rats were then used to extract ADSCs and PRP to modify the scaffolds further. Scaffolds with and without PM were modified with and without ADSCs and PRP and subcutaneously implanted in the dorsum of rats for 3 months. After 12 weeks, the scaffolds were excised and the degree of tissue integration using H&E staining and Masson’s trichrome staining, angiogenesis by CD31 and immune response by CD45 and CD68 immunohistochemistry staining was examined.

Results

H&E and Masson’s trichrome staining showed PM+PRP+ADSC and PM+ADSC scaffolds had the greatest tissue integration, but there was no significant difference between the two scaffolds (p < 0.05). The greatest vessel formation after 3 months was shown with PM+PRP+ADSC and PM+ADSC scaffolds using CD31 staining compared to all other scaffolds (p < 0.05). The CD45 and CD68 staining was similar between all scaffolds after 3 months showing the ADSCs or PRP had no effect on the immune response of the scaffolds.

Conclusions

Argon plasma surface modification enhanced the effect of adipose-derived stem cells effect on angiogenesis and tissue integration of polyurethane scaffolds. The combination of ADSCs and argon plasma modification may improve the survival of large tissue implants for regenerative applications.

Electronic supplementary material

The online version of this article (10.1186/s13287-019-1195-z) contains supplementary material, which is available to authorized users.

Case-control study of mandibular canal branching and tooth-related inflammatory lesions

OBJECTIVES

Morphological variations of mandibular canals increase the risk of neurovascular damage and bleeding during surgical procedures by decreasing the predictability of the inferior alveolar neurovascular bundle location. To improve the predictability with such variations, the present study aimed to verify the possibility of a relationship between mandibular canal branches (MCBs) and tooth-related inflammatory lesions, using trough cone-beam computed tomography (CBCT) examinations.

METHODS

The sample comprised 150 age and sex-matched examinations (50 cases and 100 controls) from two databases. The CBCT examinations were grouped by the presence of MCBs starting in the mandibular body regions as the outcome variable. Tooth-related inflammatory lesions and measurements of gray levels in the posterior region of the alveolar ridge were assessed in both groups. A multiple logistic regression analysis was applied to verify the relationships between MCBs and independent variables (p < 0.05).

RESULTS

Occurrence of tooth-related inflammatory lesions increased the risk of MCBs in the mandibular body regions (p < 0.001; OR 11.640; 95% CI 4.327-31.311). High-contrast images had a weaker association with MCBs (p = 0.002; OR 1.002; 95% CI 1.002-1.003). The most frequent tooth-related inflammatory lesions in both groups were endodontic (34 lesions; 45.94% of the total lesions). Most of the tooth-related inflammatory lesions related to MCBs were endodontic (20 cases) and combined endodontic and periodontal inflammation (20 cases).

CONCLUSIONS

An association was observed between MCBs in the mandibular body regions and tooth-related inflammatory lesions. Inflammatory lesions of endodontic origin are most often associated with MCBs.

Immunohistochemical expression of TGF-β1 and MMP-9 in periapical lesions

The objective of this study was to evaluate the expression of matrix metalloproteinase 9 (MMP-9) and transforming growth factor beta (TGF-β1) in periapical lesion samples correlated with the intensity of the inflammatory infiltrate and thickness of the epithelial lining. Forty-five cases of periapical lesions (23 periapical granulomas and 22 radicular cysts) were subjected to morphological and immunohistochemical analyses using anti-MMP-9 and anti-TGF-β1 antibodies. The data were analyzed using the following tests: non-parametric Mann-Whitney, chi-square, Fisher's exact test and Spearman's correlation test (P<0.05). Analysis of inflammatory infiltrate revealed that 78% of periapical granulomas presented infiltrate grade III, in contrast with 32% of radicular cysts (P<0.001). Morphological evaluation of the epithelial thickness in radicular cysts revealed the presence of atrophic epithelium in 86% of the cysts. The immunostaining of MMP-9 was score 2 in 67% of the granulomas and 77% of the cysts. Both lesions were predominantly score 1 for TGF-β1. Significant differences were confirmed between the expression scores of TGF-β1 and MMP-9 in periapical granulomas (p = 0.004) and in radicular cysts (p < 0.001). Expression of TGF-β1 was different for periapical granulomas and radicular cysts. This immunoregulatory cytokine seems more representative in asymptomatic lesions. The extracellular matrix remodeling process dependent on MMP-9 seems to be similar for both periapical granulomas and radicular cysts. TGF-β1 and MMP-9 may play an important role in the maintenance of periapical lesions.

Enhancing tissue integration and angiogenesis of a novel nanocomposite polymer using plasma surface polymerisation, an in vitro and in vivo study

Current surgical reconstruction of facial defects including nose or ear involves harvesting patient's own autologous tissue, causing donor site morbidity and is limited by tissue availability. The use of alternative synthetic materials is also limited due to complications related to poor tissue integration and angiogenesis, which lead to extrusion of implants and infection. We intend to meet this clinical challenge by using a novel nanocomposite called polyhedral oligomeric silsesquioxane poly(carbonate-urea)urethane (POSS-PCU), which has already been successfully taken to the clinical bench-side as a replacement for trachea, tear duct and vascular by-pass graft. In this study, we aimed to enhance tissue integration and angiogenesis of POSS-PCU using an established surface treatment technique, plasma surface polymerisation (PSP), functionalising the surface using NH2 and COOH chemical groups. Physical characterisation of scaffolds was achieved by using a number of techniques, including water contact angle, SEM, AFM and XPS to study the effects of PSM modification on the POSS-PCU nanocomposite in detail, which has not been previously documented. Wettability evaluation confirmed that scaffolds become hydrophilic and AFM analysis confirmed that nano topographical alterations resulted as a consequence of PSP treatment. Chemical functionalisation was confirmed using XPS, which suggested the presence of NH2 and COOH functional groups on the scaffolds. The modified scaffolds were then tested both in vitro and in vivo to investigate the potential of PSP modified POSS-PCU scaffolds on tissue integration and angiogenesis. In vitro analysis confirmed that PSM modification resulted in higher cellular growth, proliferation and ECM production as assessed by biochemical assays and immunofluorescence. Subcutaneous implantation of modified POSS-PCU scaffolds was then carried out over 12-weeks, resulting in enhanced tissue integration and angiogenesis (p < 0.05). This study demonstrates a simple and cost effective surface modification method to overcome the current challenge of implant extrusion and infection caused by poor integration and angiogenesis.

VEGF and VEGFR2 in dentigerous cysts associated with impacted third molars

The aims of this study were to determine the presence and distribution of vascular endothelial growth factor (VEGF) and vascular endothelial growth factor receptor-2 (VEGFR2) in dentigerous cysts compared with normal dental follicles as a control tissue and to evaluate endothelial cells and proliferating cells as indicators of angiogenic activity in these tissues.Twenty specimens histologically diagnosed as dentigerous cysts and 20 dental follicle specimens were included. Immunohistochemistry (IHC) using anti-VEGF and anti-VEGFR2 antibodies stained for the growth factor and its receptor, while anti-CD34 and anti-CD146 antibodies were used to identify endothelial cells. Anti-proliferating cell nuclear antigen (PCNA) antibody detected proliferating cells within the specimens. Slides were examined microscopically and results evaluated using kappa statistics, negative binomial regression and ordinal logistic regression.The mean age for patients with dentigerous cysts was 23 years and they were more common in males. Proteins for VEGF, VEGFR2, PCNA, CD34, and CD146 were expressed in all dentigerous cysts and dental follicles. VEGF and VEGFR2 were expressed on several cell types within the tissues, however there was a significantly greater percentage of positive staining in dentigerous cysts compared with dental follicles (odds ratio = 31.24, p < 0.001). CD34(+), CD146(+), and PCNA(+) cells were observed in both dentigerous cysts and dental follicles but for all markers there were significantly more positive cells in dentigerous cysts (p < 0.001); this was especially evident in cases associated with inflammation. PCNA was seen in most endothelial cells lining small thin walled blood vessels suggesting endothelial proliferation. There was a high level of intra- and inter-examiner agreement (kappa 0.77 and 0.75, respectively).VEGF and VEGFR2 and angiogenic activity are present in dental follicles and dentigerous cysts and may contribute to local bone resorption for tooth eruption or the development and progression of dentigerous cysts.

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.