Bioinformatics and systems biology analysis of genes network involved in OLP (Oral Lichen Planus) pathogenesis

Exploring gene network and protein interaction analysis of neurotrophin signaling pathway in ameloblastoma

Ameloblastoma is a non-cancerous but aggressive oral tumor emerging from odontogenic epithelial tissue involved during odontogenesis. Since there is lack in unravelling the complete molecular pathogenesis of ameloblastoma, chemotherapy is less attempted and a lot of disagreement over the optimal treatment option. Hence, till date, wide surgical resection is considered to be the reliable treatment for ameloblastoma. The Neurotrophin Signaling pathway plays an important role in neuron signaling and it is closely related with the MAPK pathway, which on the other hand regulated cell differentiation, apoptosis, proliferation, plasticity and survival. Protein- Protein Interaction analysis was analysed with STRING tool using WNL value, identified that CTNNB1, HRAS, NGFR, NGFR, and SORT1 having high interacting with BDNF, NT4, p75NTR, NGF, and NT3. The results of ontology analysis revealed that Neurotrophin signaling pathway is associated with Cell surface receptor signaling pathway, regulation of cell differentiation, regulation of development process, EGFR tyrosine kinase inhibitor resistance, MAPK signaling pathway, PI3K-Akt signaling pathway and Ras signaling pathway leading to pathogenesis involving genes. Further, clustering coefficient values of proteins BDNF, NT4, p75NTR, NGF & NT3 were identified as 0.627, 0.708, 0.367, 0.644 & 0.415. The results of molecular docking studies revealed among the selected ligands Methyl-ɣ-oresellinate, N-(4-Hydroxy-phenyl)-2-phenyl-N-phenylacetyl-acetamide, Atranorin and Oresellinate exhibited high binding affinity with selected protein. The key genes involved in Neurotrophin signaling pathway leading to ameloblastoma pathogenesis is revealed, which are closely associated with cell differentiation, cell proliferation, pro-apoptosis, and pro-survival regulations. Further it can be concluded that Neurotrophin signaling pathway could be one of the promising pathway to tailor the targeted drug therapy for Ameloblastoma treatment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00223-2.

Potential Biomarkers and Signaling Pathways Associated with the Pathogenesis of Primary Ameloblastoma: A Systems Biology Approach

Objective

Ameloblastoma is a benign odontogenic tumor that may lead to ameloblastic carcinoma. This study aimed to determine potential signaling pathways and biological processes, critical genes and their regulating transcription factors (TFs), and miRNAs, as well as protein kinases involved in the etiology of primary ameloblastoma.

Methods

The dataset GSE132472 was obtained from the GEO database, and multivariate statistical analyses were applied to identify differentially expressed genes (DEGs) in primary ameloblastoma tissues compared to the corresponding normal gingiva samples. A protein-protein interaction (PPI) map was built using the STRING database. The Cytoscape software identified significant modules and the hub genes within the PPI network. Gene Ontology annotation and signaling pathway analyses were executed by employing the DAVID and Reactome databases, respectively. Significant TFs and miRNAs acting on the hub genes were identified using the iRegulon plugin and MiRWalk 2.0 database, respectively. A protein kinase enrichment analysis was conducted using the online Kinase Enrichment Analysis 2 (KEA2) web server. The approved drugs acting on the hub genes were also found.

Results

A total of 1,629 genes were differentially expressed in primary ameloblastoma (P value <0.01 and |Log2FC| > 1). HRAS, CDK1, MAPK3, ERBB2, COL1A1, CYCS, and BRCA1 demonstrated high degree and betweenness centralities in the PPI network. E2F4 was the most significant TF acting on the hub genes. BTK was the protein kinase significantly enriched by the TFs. Cholesterol biosynthesis was considerably involved in primary ameloblastoma.

Conclusions

This study provides an intuition into the potential mechanisms involved in the etiology of ameloblastoma.

Network Pharmacology and Molecular Docking Analysis Explores the Mechanisms of Cordyceps sinensis in the Treatment of Oral Lichen Planus

Objective

Oral lichen planus (OLP) is the most common potentially malignant disorder of the oral cavity. This study aimed to investigate the mechanism of action of Cordyceps sinensis in the treatment of OLP and provides a theoretical support for improving current treatment regimens for OLP.

Methods

The active components and therapeutic targets of Cordyceps sinensis were predicted and screened using the TCMSP, SymMap, PubMed, HIT 2.0, and PharmMapper databases, while the relevant OLP targets were predicted and screened using the DisGeNET and GeneCards databases. Protein-protein interactions (PPI) were examined using the String database, and Cytoscape was used to combine and illustrate the findings. GO and KEGG pathway enrichment analyses were carried out using RStudio, and AutoDock Vina and Pymol were used for molecular docking and visualization, respectively.

Results

A total of 404 potential target genes were discovered after evaluating 21 active compounds from Cordyceps sinensis. Potential therapeutic targets included 67 targets that matched and overlapped with OLP, including TNF, IL-6, CD4, EGFR, and IL1B. Key targets were predominantly engaged in the PI3K-Akt signaling pathway and the MAPK signaling pathway, according to the GO and KEGG analyses. These targets have a connection to biological processes including apoptosis signaling pathway regulation, T cell activation, and oxidative stress response. The molecular docking results showed that TNF, IL-6, CD4, EGFR, and IL1B could bind to their corresponding active components.

Conclusions

Cordyceps sinensis contains multiple components and acts on multiple targets and multiple pathways. Particularly, Cordyceps sinensis targets TNF, IL-6, CD4, EGFR, and IL1B, regulates PI3K-Akt and MAPK signaling pathways, as well as takes part in biological processes including apoptosis, T cell activation, and oxidative stress. Cordyceps sinensis could be a crucial choice in the therapy of OLP.

Immune mechanisms in oral lichen planus

Oral lichen planus (OLP) is a T-cell-mediated inflammatory disease of the oral mucosa that has been extensively researched over many years but as yet the mechanisms of pathogenesis are still not fully understood. Whilst the specific etiologic factors driving OLP remain ambiguous, evidence points to the development of a chronic, dysregulated immune response to OLP-mediating antigens presented by innate immune cells and oral keratinocytes leading to increased cytokine, chemokine and adhesion molecule expression. These molecules recruit T-cells and mast cells to the diseased site and orchestrate a complex interplay between cells that culminates in keratinocyte cell death, mucosal basement membrane destruction and long-term chronicity of the disease. The main lymphocytes involved are thought to be CD8+ cytotoxic and CD4+ Th1 polarised T-cells although recent evidence indicates the involvement of other Th subsets such as Th9, Th17 and Tregs, suggesting that a more complex immune cell relationship exists during the disease process. This review provides an overview of the immune mechanisms at play in OLP pathogenesis with particular emphasis on the role of the different Th subsets and how these recent discoveries may guide research toward identifying potential therapeutic targets.

Effects of cold physical plasma on oral lichen planus: An in vitro study (Effects of CAP on OLP)

OBJECTIVES

In the search for more effective and safe treatment avenues, we investigated cold physical plasma as a new treatment modality for therapy of oral lichen planus (OLP).

MATERIAL AND METHODS

Healthy and diseased human mucosal tissue samples with a size of 3 mm in diameter obtained from OLP patients were subjected to plasma treatment ex vivo or were left untreated. Tissue sections were quantified for immune-infiltration of CD4+ , CD8+ , CD45RA+ , and CD45R0+ T cells. Moreover, the tissues' inflammatory profile was assessed by analyzing 12 different cytokines in the surrounding media.

RESULTS

A significantly increased infiltrate of CD8+ and CD45-R0+ T cells was detected in OLP tissue samples when compared to healthy tissue. A higher concentration of interleukin (IL) 1β, IL6, IL8, and granulocyte macrophage-colony stimulating factor (GM-CMF) was detected in OLP samples compared to healthy mucosal tissue. For all cytokines and chemokines investigated, 23 out of 24 comparisons showed a decrease in tendency (significant for IL1β, IL2, IL10, and GM-CSF) in response to plasma treatment. In ex vivo-treated tissue, a decrease of T-cell infiltrate in OLP lesions compared with healthy tissue was observed.

CONCLUSION

Our findings suggest cold physical plasma can be a promising therapeutic option for OLP that requires further validation in vivo.

Acute oral treatment with resveratrol and Lactococcus Lactis Subsp. Lactis decrease body weight and improve liver proinflammatory markers in C57BL/6 mice

The present study aimed to evaluate the effects of resveratrol, a nutraceutical polyphenol, and Lactococcus lactis (bacteria probiotic), on metabolic parameters and hepatic proinflammatory markers expression. C57BL/6 mice were divided into 4 groups: Standard (ST), Lactococcus lactis (LL), Resveratrol (RSV), and Lactococcus lactis plus resveratrol (LL + RSV). Lactococcus lactis and resveratrol were administered by orogastric gavage. Blood parameters were assessed (total cholesterol, triglycerides, ALT and AST). IL-6 mRNA expression was evaluated by Real-time PCR and TNF-α protein expression was assessed by immunohistochemistry. The main findings showed that resveratrol and Lactococcus lactis association decreased body weight, aspartate aminotransferase and total cholesterol levels. LL and LL + RSV decreased triglycerides levels and IL-6 and TNF-α expression. These results open a perspective of using resveratrol and Lactococcus lactis to improve metabolic parameters and Lactococcus lactis in preventing inflammation and the hepatic diseases development.

Comparative proteomic analysis of human mesenchymal stromal cell behavior on calcium phosphate ceramics with different osteoinductive potential

In recent years, synthetic calcium phosphate (CaP) ceramics have emerged as an alternative to bone grafts in the treatment of large critical-sized bone defects. To successfully substitute for bone grafts, materials must be osteoinductive, that is, they must induce osteogenic differentiation and subsequent bone formation in vivo. Although a set of osteoinductive CaP ceramics has been developed, the precise biological mechanism by which a material directs cells toward osteogenesis and the role of individual chemical and physical properties in this mechanism remain incompletely understood. Here, we used proteomics to compare serum protein adsorption to two CaP ceramics with different osteoinductive potential, namely an osteoinductive β-tricalcium phosphate (TCP) and a non-osteoinductive hydroxyapatite (HA). Moreover, we analyzed the protein profiles of human mesenchymal stromal cells (hMSCs) cultured on these two ceramics. The serum protein adsorption experiments in the absence of cells highlighted the proteins that are highly abundant in the serum and/or have a high affinity to CaP. The extent of adsorption was suggested to be affected by the available surface area for binding and by the ion exchange dynamics on the surface. Several proteins were uniquely expressed by hMSCs on TCP and HA surfaces. Proteins identified as enriched on TCP were involved in processes related to wound healing, cell proliferation, and the production of extracellular matrix. On the other hand, proteins that were enriched on HA were involved in processes related to protein production, translation, localization, and secretion. In addition, we performed a separate proteomics analysis on TCP, HA, and two biphasic calcium phosphates with known osteoinductive potential and performed a clustering analysis on a combination of a set of proteins found to be enriched on osteoinductive materials with a set of proteins already known to be involved in osteogenesis. This yielded two protein networks potentially involved in the process of osteoinduction – one consisting of collagen fragments and collagen-related enzymes and a second consisting of endopeptidase inhibitors and regulatory proteins. The results of this study show that protein profiling can be a useful tool to help understand the effect of biomaterial properties on the interactions between a biomaterial and a biological system. Such understanding will contribute to the design and development of improved biomaterials for (bone) regenerative therapies.

Oral gallic acid improve liver steatosis and metabolism modulating hepatic lipogenic markers in obese mice

INTRODUCTION

Gallic acid (GA) is a natural endogenous polyphenol found in a variety of fruits, vegetables and wines, with beneficial effects on the energetic homeostasis.

AIM

The present study aimed to investigate oral gallic acid effects on liver steatosis and hepatic lipogenesis markers in obese mice evaluating new possible molecular related mechanisms.

METHODS

Twenty-four Swiss male mice were divided into four groups and fed for 60 days with standard diet (ST), standard diet plus gallic acid (ST + GA), high-fat diet (HFD), and high-fat diet plus gallic acid (HFD + GA). We evaluated the relationship between body weight, food intake and serum levels of total cholesterol, triglycerides, insulin, aspartate and alanine transaminases. Liver histology was analyzed by hematoxylin and eosin staining. These results were accompanied by bioinformatics analyses. The acetyl-CoA carboxylase (ACC), sterol regulatory element binding protein-1 (SREBP-1) and fatty acid synthase (FAS) expression was assessed by quantitative real-time reverse transcriptase PCR (qRT-PCR).

RESULTS

The main findings of the present study showed that GA reduced liver steatosis, body weight and plasma insulin levels. Analyzes of hepatic steatosis related genes expression showed that ACC and FAS mRNA were significantly suppressed in liver of HFD + GA mice. These data was corroborated by bioinformatics analysis.

CONCLUSION

These data suggest an important clinical application of GA in the prevention and treatment of liver diseases.

Oral gallic acid improves metabolic profile by modulating SIRT1 expression in obese mice brown adipose tissue: A molecular and bioinformatic approach

AIMS

The aim of the presente study was to examine the effects of oral gallic acid (GA) administration on the brown adipose tissue of obese mice fed with high-fat diet. New mechanisms and interactions pathways in thermogenesis were accessed through bioinformatics analyses.

MAIN METHODS

Swiss male mice were divided into four groups and fed during 60 days with: standard diet, standard diet combined with gallic acid, high-fat diet and high-fat diet combined with gallic acid. Body weight, food intake, and blood parameters (glucose tolerance test, total-cholesterol, high-density low-c, triglyceride and glucose levels) were evaluated. Brown and subcutaneous white adipose tissue histological analysis were performed. SIRT1 and PGC1-α mRNA expression in the brown adipose tissue were assessed.

KEY FINDINGS

Our main findings showed that the gallic acid improved glucose tolerance and metabolic parameters. These results were accompanied by bioinformatics analyses that evidenced SIRT1 as main target in the thermogenesis process, confirmed as increased SIRT1 mRNA expression was evidenced in the brown adipose tissue.

SIGNIFICANCE

Together, the data suggest that the gallic acid effect in brown adipose tissue may improve body metabolism, glucose homeostasis and increase thermogenesis.

Mechanism of Brassica oleracea performance in bovine infectious mastitis by bioinformatic analysis

Bovine mastitis affects dairy cattle worldwide and, despite the existing therapeutic measures, is not totally under control, leading to the need to develop alternative strategies. Brassica oleracea is a phytochemical commonly used in the control and prevention of human and animal diseases. The use of this plant in the treatment of infectious bovine mastitis has been little referenced in the literature and its molecular mechanism of action in this disease has not been clarified yet. This study aimed to reveal, through bioinformatic analysis, the molecular mechanism of action of Brassica oleracea in bovine mastitis. We investigated genes expressed in the signaling pathways of bovine mastitis and Brassica oleracea performance and elaborated the Venn diagram. A gene network was developed using the STRING 10 database. Leader genes were identified by calculating the weighted number of links (WNL). The NetworkAnalyzer plugin for Cytoscape software was used to characterize network topology. For the visualization of highly interconnected regions in the network, the MCODE was used. The BINGO and GFD-Net plugins were used to perform the ontological analysis. The TP53 and MTOR leader genes were identified in the sub-networks of the bovine mastitis signaling pathway and Brassica oleracea performance, respectively. Topological analysis confirmed the leader condition of the genes. Although the overlap of genes in the Venn diagram was not observed, the leader genes were found to be interconnected (confidence = 0.9). In the network that interconnected the leader genes two molecular complexes were detected and the ontological analysis revealed biological processes, cellular components and important molecular functions. It was concluded that Brassica oleracea may be a promising candidate to be included in a mammalian herbal cocktail against infectious bovine mastitis by interfering in the mechanisms of action of genes such as MTOR and TP53.

Leader gene of Corynebacterium pseudotuberculosis may be useful in vaccines against caseous lymphadenitis of goats: a bioinformatics approach

We conducted an in silico analysis to search for important genes in the pathogenesis of Caseous Lymphadenitis (CL), with prospects for use in formulating effective vaccines against this disease. For this, we performed a survey of proteins expressed by Corynebacterium pseudotuberculosis, using protein sequences collected from the NCBI GenPept database and the keywords “caseous lymphadenitis” and “Corynebacterium pseudotuberculosis” and “goats”. A network was developed using the STRING 10 database, with a confidence score of 0.900. For every gene interaction identified, we summed the interaction score of each gene, generating a combined association score to obtain a single score named weighted number of links (WNL). Genes with the highest WNL were named “leader genes”. Ontological analysis was extracted from the STRING database through Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A search in the GenPept database revealed 2,124 proteins. By using and plotting with STRING 10, we then developed an in silico network model comprised of 1,243 genes/proteins interconnecting through 3,330 interactions. The highest WNL values were identified in the rplB gene, which was named the leader gene. Our ontological analysis shows that this protein acts effectively mainly on Metabolic pathways and Biosynthesis of secondary metabolites. In conclusion, the in silico analyses showed that rplB has good potential for vaccine development. However, functional assays are needed to make sure that this protein can potentially induce both humoral and cellular immune responses against C. pseudotuberculosis in goats.

Metformin increases PDH and suppresses HIF-1α under hypoxic conditions and induces cell death in oral squamous cell carcinoma

Background

Metformin is a biguanide, belonging to the oral hypoglycemic agents and is a widely used in the treatment of type 2 diabetes. Evidence indicate that Metformin inhibits cell proliferation in several human cancers and inhibits the Warburg phenomenon in tumor cells.

Results

Low PDH levels were observed in OSCC, and Metformin promotes an increase in PDH levels in hypoxic conditions. Metformin also reduced HIF-1α mRNA and protein levels. Metformin demonstrated antiproliferative effects, inhibited migration, increased the number of apoptotic cells and increased the transcription of caspase 3.

Objective

The present study aims to explore the effects of Metformin in hypoxic conditions. Specifically, we focused on pyruvate dehydrogenase (PDH), (hypoxia-inducible factor 1α) HIF-1α levels and the oral squamous cell carcinoma (OSCC) cell phenotype. Additionally, we also investigated a theoretical consequence of Metformin treatment.

Methods

PDH levels in patients with OSCC and oral dysplasia were evaluated. Metformin was administered in vitro to test the effect of Metformin under hypoxic conditions. The results were complemented by Bioinformatics analyses.

Conclusions

In conclusion, our current findings show that Metformin reduces HIF-1α gene expression and increases PDH expression. Metformin inhibits cell proliferation and migration in the OSCC cell line model. Additionally, Metformin enhances the number of apoptotic cells and caspase 3 levels. Interestingly enough, Metformin did not increase the mutant p53 levels under hypoxic conditions.

Transcriptional and epigenetic analyses of the DMD locus reveal novel cis‑acting DNA elements that govern muscle dystrophin expression

The dystrophin gene (DMD) is the largest gene in the human genome, mapping on the Xp21 chromosome locus. It spans 2.2Mb and accounts for approximately 0,1% of the entire human genome. Mutations in this gene cause Duchenne and Becker Muscular Dystrophy, X-linked Dilated Cardiomyopathy, and other milder muscle phenotypes. Beside the remarkable number of reports describing dystrophin gene expression and the pathogenic consequences of the gene mutations in dystrophinopathies, the full scenario of the DMD transcription dynamics remains however, poorly understood. Considering that the full transcription of the DMD gene requires about 16h, we have investigated the activity of RNA Polymerase II along the entire DMD locus within the context of specific chromatin modifications using a variety of chromatin-based techniques. Our results unveil a surprisingly powerful processivity of the RNA polymerase II along the entire 2.2Mb of the DMD locus with just one site of pausing around intron 52. We also discovered epigenetic marks highlighting the existence of four novel cis‑DNA elements, two of which, located within intron 34 and exon 45, appear to govern the architecture of the DMD chromatin with implications on the expression levels of the muscle dystrophin mRNA. Overall, our findings provide a global view on how the entire DMD locus is dynamically transcribed by the RNA pol II and shed light on the mechanisms involved in dystrophin gene expression control, which can positively impact on the optimization of the novel ongoing therapeutic strategies for dystrophinopathies.

Identification of potential biomarkers and analysis of prognostic values in head and neck squamous cell carcinoma by bioinformatics analysis

The purpose of this study was to find disease-associated genes and potential mechanisms in head and neck squamous cell carcinoma (HNSCC) with deoxyribonucleic acid microarrays. The gene expression profiles of GSE6791 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were obtained with packages in R language and STRING constructed protein–protein interaction (PPI) network of the DEGs with combined score >0.8. Subsequently, module analysis of the PPI network was performed by Molecular Complex Detection plugin and functions and pathways of the hub gene in subnetwork were studied. Finally, overall survival analysis of hub genes was verified in TCGA HNSCC cohort. A total of 811 DEGs were obtained, which were mainly enriched in the terms related to extracellular matrix (ECM)–receptor interaction, ECM structural constituent, and ECM organization. A PPI network was constructed, consisting of 401 nodes and 1,254 edges and 15 hub genes with high degrees in the network. High expression of 4 genes of the 15 genes was associated with poor OS of patients in HNSCC, including PSMA7, ITGA6, ITGB4, and APP. Two significant modules were detected from the PPI network, and the enriched functions and pathways included proteasome, ECM organization, and ECM–receptor interaction. In conclusion, we propose that PSMA7, ITGA6, ITGB4, and APP may be further explored as potential biomarkers to aid HNSCC diagnosis and treatment.

Caveolin-1 expression in oral lichen planus, dysplastic lesions and squamous cell carcinoma

Caveolin-1(Cav-1), the main part of caveolae structure, is supposed to play a role in pathogenesis of many human tumors. Since oral lichen planus (OLP) is considered as a potential premalignant disease, this study evaluated Cav-1 expression in OLP in comparison with benign hyperkeratosis, dysplastic epithelium and oral squamous cell carcinoma (OSCC), to investigate its possible role in pathogenesis and malignant transformation of OLP. In this cross-sectional retrospective study, immunohistochemical expression of Cav-1 in the epithelial component and stroma was evaluated in 81 samples, including 12 cases of hyperkeratosis, 24 OLP, 22 epithelial dysplasia, and 23 OSCC samples. Correlations between Cav-1 expression and clinicopathological variables were evaluated statistically. Positive Cav-1 staining was found in 58% of OLP, 91% of hyperkeratosis, 100% of epithelial dysplasia, and 95% of OSCC samples. OSCC showed the highest Cav-1 expression and OLP had the lowest (P=0.001). The intensity of staining was significantly increased in stepwise manner from OLP to OSCC (P=0.001). Expression of Cav-1 was related to the grade of samples in OSCC and dysplastic samples (P=0.04). Based on the findings, it was concluded that Cav-1 may play a role in the pathogenesis of OLP and carcinogenesis of SCC, but its role in malignant transformation of OLP is not confirmed. Further studies are needed to evaluate its potential therapeutic function in OLP and SCC.

Effects of Dietary Macronutrient Composition on FNDC5 and Irisin in Mice Skeletal Muscle

BACKGROUND

Fibronectin type III domain containing 5 (FNDC5) and its protein product Irisin are therapeutic targets for obesity-associated disorders. Irisin plays an important role in energy regulation, inducing browning of white adipocytes, and improving obesity. We aimed to investigate the association between muscle Irisin expression and dietary quality.

METHODS

Twenty-eight female mice were divided into four groups and fed the following experimental diets for 60 days: standard diet (SD), high-carbohydrate diet (HCD), high-fat diet (HFD), and high-protein diet (HPD). We evaluated body weight, food intake, serum total cholesterol, triacylglycerol, and glucose. We also performed glucose tolerance and insulin sensitivity tests. Expression of FNDC5 was evaluated by quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) of soleus muscle. Western blot was used to assess Irisin protein expression.

RESULTS

The major finding of the present study was that HFD and HCD were associated with a downregulation of FNDC5. In addition to these results, we noted a significant reduction in skeletal muscle Irisin level. HPD prevented reductions of both FNDC5 and Irisin levels, as well as increased brown adipose tissue, compared to the control group.

CONCLUSIONS

In conclusion, we observed that the HPD type of diet can change both FNDC5 expression and Irisin levels. Thus, the HPD might be the most appropriate diet to achieve high amounts of Irisin, a target molecule for the treatment of obesity and its co-morbidities.

Identification of potential therapeutic target genes, key miRNAs and mechanisms in oral lichen planus by bioinformatics analysis

The study aimed to identify the potential target genes and key miRNAs as well as to explore the underlying mechanisms in the pathogenesis of oral lichen planus (OLP) by bioinformatics analysis. The microarray data of GSE38617 were downloaded from Gene Expression Omnibus (GEO) database. A total of 7 OLP and 7 normal samples were used to identify the differentially expressed genes (DEGs) and miRNAs. The DEGs were then performed functional enrichment analyses. Furthermore, DEG-miRNA network and miRNA-function network were constructed by Cytoscape software. Total 1758 DEGs (598 up- and 1160 down-regulated genes) and 40 miRNAs (17 up- and 23 down-regulated miRNAs) were selected. The up-regulated genes were related to nuclear factor-Kappa B (NF-κB) signaling pathway, while down-regulated genes were mainly enriched in the function of ribosome. Tumor necrosis factor (TNF), caspase recruitment domain family, member 11 (CARD11) and mitochondrial ribosomal protein (MRP) genes were identified in these functions. In addition, miR-302 was a hub node in DEG-miRNA network and regulated cyclin D1 (CCND1). MiR-548a-2 was the key miRNA in miRNA-function network by regulating multiple functions including ribosomal function. The NF-κB signaling pathway and ribosome function may be the pathogenic mechanisms of OLP. The genes such as TNF, CARD11, MRP genes and CCND1 may be potential therapeutic target genes in OLP. MiR-548a-2 and miR-302 may play important roles in OLP development.

Molecular finds of pressure ulcer: A bioinformatics approach in pressure ulcer

BACKGROUND

Understanding the biological processes underlying Pressure Ulcer (PU) is an important strategy to identify new molecular targets. Bioinformatics has emerged as an important screening tool for a broad range of diseases.

OBJECTIVE

This study aim of the current study is to investigate the protein-protein interaction in the PU context by bioinformatics.

METHODS

We performed a search in gene databases, and bioinformatics algorithms were used to generate molecular targets for PU based in silico investigation. Interactions networks between protein-coding genes were built and compared to skin.

RESULTS

TNFA, MMP9, and IL10 genes have higher disease-related connectivity than a connectivity general global. MAGOH, UBC, and PTCH1 as were leader genes related to skin. Ontological analysis demonstrated different mechanisms associated, such as response to oxidase stress.

CONCLUSION

TNFA, MMP9, and IL10 are possible therapeutic targets for pressure ulcer. Additional investigation of cell post-transcriptional machinery should be investigated in PU.

Evaluation of the antineoplastic activity of gallic acid in oral squamous cell carcinoma under hypoxic conditions

The purpose of the current study was to develop and test a theoretical model that could explain the mechanism of action of gallic acid (GA) in the oral squamous cell carcinoma context for the first time. The theoretical model was developed using bioinformatics and interaction network analysis to evaluate the effect of GA on oral squamous cell carcinoma. In a second step to confirm theoretical results, migration, invasion, proliferation, and gene expression (Col1A1, E-cadherin, HIF-1α, and caspase-3) were performed under normoxic and hypoxic conditions. Our study indicated that treatment with GA resulted in the inhibition of cell proliferation, migration, and invasion in neoplastic cells. Observation of the molecular mechanism showed that GA upregulates E-cadherin expression and downregulates Col1A1 and HIF-1α expression, suggesting that GA might be a potential anticancer compound. In conclusion, the present study demonstrated that GA significantly reduces cell proliferation, invasion, and migration by increasing E-cadherin and repressing Col1A1.

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.

A gene network bioinformatics analysis for pemphigoid autoimmune blistering diseases

OBJECTIVE

In this theoretical study, a text mining search and clustering analysis of data related to genes potentially involved in human pemphigoid autoimmune blistering diseases (PAIBD) was performed using web tools to create a gene/protein interaction network.

METHODS

The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database was employed to identify a final set of PAIBD-involved genes and to calculate the overall significant interactions among genes: for each gene, the weighted number of links, or WNL, was registered and a clustering procedure was performed using the WNL analysis. Genes were ranked in class (leader, B, C, D and so on, up to orphans). An ontological analysis was performed for the set of 'leader' genes.

RESULTS

Using the above-mentioned data network, 115 genes represented the final set; leader genes numbered 7 (intercellular adhesion molecule 1 (ICAM-1), interferon gamma (IFNG), interleukin (IL)-2, IL-4, IL-6, IL-8 and tumour necrosis factor (TNF)), class B genes were 13, whereas the orphans were 24. The ontological analysis attested that the molecular action was focused on extracellular space and cell surface, whereas the activation and regulation of the immunity system was widely involved.

CONCLUSIONS

Despite the limited knowledge of the present pathologic phenomenon, attested by the presence of 24 genes revealing no protein-protein direct or indirect interactions, the network showed significant pathways gathered in several subgroups: cellular components, molecular functions, biological processes and the pathologic phenomenon obtained from the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database.

CLINICAL RELEVANCE

The molecular basis for PAIBD was summarised and expanded, which will perhaps give researchers promising directions for the identification of new therapeutic targets.

Expression of COX-2 and bcl-2 in oral lichen planus lesions and lichenoid reactions

Oral lichen planus and lichenoid reactions are autoimmune type inflammatory conditions of the oral mucosa with similar clinical and histological characteristics. Recent data suggest that oral lichenoid reactions (OLR) present a greater percentage of malignant transformation than oral lichen planus (OLP).

Rethinking psychiatry with OMICS science in the age of personalized P5 medicine: ready for psychiatome?

The Diagnostic and Statistical Manual of Mental Disorders (DSM) is universally acknowledged as the prominent reference textbook for the diagnosis and assessment of psychiatric diseases. However, since the publication of its first version in 1952, controversies have been raised concerning its reliability and validity and the need for other novel clinical tools has emerged. Currently the DSM is in its fourth edition and a new fifth edition is expected for release in 2013, in an intense intellectual debate and in a call for new proposals. Since 1952, psychiatry has undergone many changes and is emerging as unique field in the medical area in which a novel approach is being demanded for properly treating patients: not the classical “one-size-fits-all” approach, but a more targeted and tailored diagnosis and therapeutics, taking into account the complex interactions among genes and their products, environment, culture and the psychological apparatus of the subject. OMICS sciences, being based on high-throughput technologies, are systems biology related fields (like genomics, proteomics, transcriptomics and so on). In the frame of the P5 medicine (personalized, participatory, predictive, preventive, psycho-cognitive), they could establish links between psychiatric diseases, which are disorders with a final common symptomatology with vastly heterogeneous biological, environmental and sociological underpinnings, and by understanding the psychiatric diseases beyond their classic symptomatic or syndromal definitions using OMICS research, one can have a broader picture and unprecedented links and reclassification of psychiatric nosology. Importantly, by understanding the basis of heterogeneity in diseases through OMICS research, one could also personalize treatment of psychiatric illnesses. In this manuscript, we discuss a gap in the current psychiatric research, namely the missing logical link among OMICS, personalized medicine and reclassification of diseases. Moreover, we explore the importance of incorporating OMICS-based quantitative dimensional criteria, besides the classical qualitative and categorical approach.

Situating Nutri-Ethics at the Junction of Nutrigenomics and Nutriproteomics in Postgenomics Medicine

Food has societal, economic, medical and ethical implications, being fundamental for life. It plays an important role also in sports medicine, since a healthy diet is an important part of an athlete's training. Nutrigenomics and nutriproteomics are emerging as a result of a convergence of nutritional, genomics and proteomics knowledge strands in the postgenomics era. These fields of inquiry present an opportunity for the design of customized diets potentially able to counterbalance the extant obesity epidemic and remedy metabolic diseases, among others. They are noteworthy for sport medicine as well since they could provide athletes with crucial information for personalized training and nutrition, in order to achieve the best results possible and express one's own potential. But they could also be used as a form of personalized doping, thus constituting an advancement of “classical nutrition-based doping” (i.e., the use of nutraceuticals, stimulants and supplements). However, nutrigenomics (or nutriproteomics)-based nutritional doping is different from the first-generation doping because it is specifically tailored to the genomics and proteomics makeup of the athlete, although their effectiveness remain to be discerned in future systematic studies. Against this scientific background, ethical issues of nutrigenomics and nutriproteomics are discussed in the present paper with emphasis on the current limitations and the dizzying potentials of the omics data-intensive research for science and society. Additionally, I discuss the need to communicate uncertainty as a fundamental construct and intrinsic part of postgenomics personalized medicine, not to forget the gaps regarding the lack of adequate governance, and issues over providing a proper nutritional education to athletes as onus of the international sports organizations.

“Let food be your medicine, and medicine be your food”

Hippocrates