Bioinformatics Analysis Of Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is the most common malignant oral cancer. It has properties of aggressive malignancy, high likelihood of lymphatic metastasis and poor prognosis. Research on the occurrence and development of OSCC plays an important role in the tumor prevention, control and treatment.Bioinformatics is an interdisciplinary subject that integrates the knowledge of biology, information and computer science to analyze the biological information contained massive biological data. By filtering massive data of biological chips and utilizing techniques such as sequence alignment, statistical analysis, clustering, visualization, and biological pathway analysis etc. to implement data mining, bioinformatics enriches the understandings about tumor occurrence and progression from molecular level. With the development of bioinformatics, a new biological research pattern is emerged. In this research pattern, researchers propose hypothesis based on the existing data and test the hypothesis.Based on GEO and TCGA database, this research screens microRNA,and lncRNA expression in OSCC by using BRB-ArrayTools software, analyzes the interaction between them by combining with bioinformatics software and text mining techniques, so that explores gene, microRNA and lncRNA associated with OSCC. It provides critical information for better understanding on the molecular mechanism of OSCC occurrence and development.Part Ⅰ:Bioinformatics analysis of differentially expressed genes in oral squamous cell carcinomaBackground:Oral squamous cell carcinoma (OSCC) is one of the common tumors national wide. The incidence of OSCC is about3.6to8.0per100thousands people. It has been confirmed that OSCC is a complex multi-gene diseases. The occurrence and development of this disease are influenced by both environmental and genetic factors. Gene chip is useful in detecting the abundance of genes in the genome level of gene analysis because of its high throughput, high speed and high specificity properties.Objective:To provide theoretical base for the mechanism of the development of OSCC by screening differential genes related to this tumor based on bioinformatics analysis of multiple chips of OSCC and implementing GO analysis> KEGG pathway analysis、protein-protein interaction network analysis.Methodology:In this research, we chose microarray datasets from GEO and analyzed OSCC microarray data thoroughly using the Affymetrix microarray gene expression data. After pre-processing the data, we used unpaired t-test to screen differential genes. Finally, we used analysis tools in DAVID software for GO analysis and KEGG pathway analysis, imported STRING online database for protein-protein interaction network analysis, and computed the network topology through Cytoscape software.Results:(1) We discovered92differentially expressed genes in OSCC in which61are up-regulated and31are down-regulated.(2) GO analysis indicated that up-regulated genes are mainly enriched in response to wounding, collagen metabolic process and multicellular organismal macromolecule metabolic process. MMP9, MMP1, MMP10, MMP11, MMP3, MMP7genes are involved in collagen metabolism. KEGG pathway analysis showed that these up-regulated genes are mainly enriched in the ECM-receptor interaction, focal adhesion,pathways in cancer, Toller-like receptor signaling pathway and other pathways.(3) Down-regulated genes mainly enriched in GO categories including epithelial cell differentiation, epithelium development, epidermis development, ectoderm development. KEGG pathway analysis revealed that these down-regulated genes are mainly enriched in retinol metabolism, metabolism of xenobiotics by cytochrome p450, drug metabolism.(4)35genes were screened to constructing interaction network though STRING software. Cytoscape software screened five key genes:MMP-9, MMP-1, COL1A2, MMP-7, PLAU.Conclusion:(1) We screened92differentially expressed genes in OSCC and conducted GO analysis and KEGG pathway analysis. We provided theoretical base for the lab research on OSCC.(2) We constructed protein-protein interaction network of differentially expressed genes and identified five key genes. We discovered that MMPs family may be involved in the development of OSCC so that provided direction for further research. Part II:Bioinformatics analysis of differentially expressed microRNAs in oral squamous cell carcinomaBackground:microRNA is endogenous non-coding RNA (18-25nt). It represses gene expression through post-transcription. It can bind the3’untranslated region (3’-untranslationalregion,3’UTR) to inhibit protein translation. MicroRNA are found to regulate60%of human genes, and may have regulating relationship among different target genes. More and more studies discovered that microRNA could play an important role in cell growth, differentiation, proliferation and apoptosis, and participate in occurrence and progression of OSCC.Objective:To implement bioinformatics analysis and explore differential microRNA in OSCC based on the organized microRNA data of OSCC from TCGA database. Furthermore, support the study on the role of target genes in the future.Methodology:To obtain the differential microRNA, we use BRB-Arraytools to analyze microRNA in OSCC from TCGA. MiRecords was used to predict microRNA target genes. Furthermore, we applied GO analysis and KEGG pathway analysis, imported STRING online database for protein-protein interaction network analysis, and computed the network topology through Cytoscape software.Results:(1) We obtained53differentially expressed miRNA, and miR-375may be a molecular marker of OSCC.Differential expression of miR-21、miR-101、let-7c and miR-200c provide bio-informational evidence for EMT process in OSCC.(2) GO analysis of target gene expression showed that target gene are involved in the regulation of cell proliferation, response to endogenousstimulus, response to organic substance and response to hormone stimulus.(3) KEGG pathway analysis disclosed that the target gene primarily participated in cell factor and its receptor interaction, MAPK signaling pathway, Wnt signaling pathway, and Jak-STAT signaling pathway.(4)73differentially expressed microRNA target genes have interactions and the protein-protein interaction network has been constructed by STRING software. Twelve key target genes were screened by Cytoscape software:STAT3,CCND1, PTGS2,IL8,PPARG,ERBB2,MMP2,PLAU,FGF1,CASP3,FASLG and IL10.Conclusions:(1) Differentially expressed microRNA of OSCC were identified. MiR-375may be the molecular markers in oral squamous cell carcinoma. The results that mir-200c is down-related suggest it may involves in EMT of OSCC.(2)Target genes of differentially expressed microRNA play a part in the regulation of cell proliferation, stimulation of the endogenous response, the response of organic substances, and hormones stimulate the response functions.(3)Target genes of differentially expressed microRNA primarily participate in the interaction of cytokines and their receptors, MAPK signaling pathway, Wnt signaling pathway, and Jak-STAT signaling pathway.(4) Protein-protein interaction network of target genes in OSCC was constructed and twelve key genes were identified. Part Ⅲ:Bioinformatic analysis of differentially expressed lncRNA in oral squamous cell carcinomaBackground:Long-chain non-coding RNA (long non-coding RNA) plays a potentially critical role in the biological aspects of gene regulation. Researches have publicized that lncRNA are related in the occurrence and progression of diseases. However, its functional mechanism is still unclear. Currently, the influence of lncRNA in OSCC is still poorly understood.Objective:To implement bioinformatics analysis and explore differentially expressed lncRNA in OSCC based on organized lncRNA data of oral squamous cell from GEO database. Moreover, to provide a new researching methodology in studying the mechanism of lncRNA in OSCC. Methodology:We use BRB Arraytools to analyze and screen the differentially expressed lncRNA of OSCC from the GEO database.Results:Comparing with normal tissue, we discovered17differentially expressed lncRNAs in oral squamous cell carcinoma, in which4up-regulated lncRNAs and13down-regulated lncRNAs. H19was significantly down-regulated in OSCC.Conclusions:(1)17differentially expressed lncRNA of OSCC were identified. This discovery provide new research direction in the function of lncRNA in OSCC.(2) H19was down-regulated in OSCC, which suggests that H19may interact with mir-200s and control the process of epithelial-mesenchymal transition (EMT) of OSCC.