Studies Of DNA Methylated Gene In Oral Verrucous Carcinoma

Oral verrucous carcinoma (oral verrucous carcinoma, OVC) is different from the squamous cell carcinoma, which has a unique pathological features and biological behavior. its pathogenesis is still unknown. The development of DNA methylated microarray and bioinformatics enable us to understand disease biology and molecular mechanisms of disease more efficient. In this study, we use the method of Methylated DNA immunoprecipitation and combine with NibleGen CpG promoter profiles to analyse genomic DNA methylated in oral verrucous carcinoma and normal tissue, meanwhile, we also use a variety of bioinformatics methods to initially screen disease genes, in order to further rexplore the molecular mechanism and potential markers/ targets for clinical utility in treatment of OVC.Objective:analysis of DNA methylated gene with oral verrucous carcinoma, then apply the bioinformatics tools for analyzing the DNA methylated genes in OVC to obtain the implied biological significance.Methods:Total methylated DNA immunoprecipitation (Met hylated DNA immunoprecipitation, MeDIP)was isolated from 5 OVC patients and corresponding normal mucosa and hybride with 10 NibleGen CpG promoter microarray,then scan the hybridization signals and get raw data and comparative analysis; Then several bioinformatic analysises were used in the second screening of genes in OVC, which included gene ontology(GO)analysis, pat-hway analysis, chromosomal assignment;Results:The results of microarray hybridization results accorded with quality control. Using a the Peak Count> 2 for the criteria.1023 DNA areas which contain 1248 genes occur methylation.Their methylated sites locate within or upstream and downstream their promoter.There are 952 (93.06%)methylated sites which were located on the promoter regions of genes and 489(47.8%) methylated sites occurred in the CpG islands.Correspondingly,the occurrence of de-methylated sites are 640, contains 780 genes.There are 474 (74.06%) methylated sites whi-ch were located on the promoter regions of genes, and 363 (56.71%) methylated sites occurred in the CpG islands.Chromosome 1 happen to methylate at most, a total of 125, followed by chromosomes 17, however, in the Y chromosome happen to methylat-ed sites for at least,a total of 7.Demethylated sites, in chromosome 19, up to a total of 90.In the Y chromosome methylated sites are at least,a total of 7.GO classification of differentially expressed DNA methylated genes identified cellular component subgroups consisted of genes mainly located in nucleus, integral to membrane; the biological process subgroups involved genes in signal transduction, regulation of transcription, DNA-dependent, G-protein coupled receptor protein signaling pathway, oxidation reduction; the function of most genes related to protein binding, calcium zinc ion binding et al. Pathway analysis showed that differentially expressed DNA methylated genes in oral verrucous carcinoma mainly involvedin pathways including Neuroactive ligand-receptor interaction, Natural killer cell mediated cytotoxicity, Apoptosis, Cytokine-cytokine receptor interaction,MARK signaling pathway.Conclusion The use of bioinformatics tools to quickly analyze a large number of parallel gene chip data that initially classified the functions of genes,which provide a new way of thinking for the pathogenesis of oral verrucous carcino-ma.Conclusion:1. DNA methylated and demethylated sites a-re different in Oral verrucous carcinoma and corresponding normal oral mucosa;2. The region of methylated and demethylated in oral verrucous carcinoma mostly locate in the gene promoter region and CpG islands;3. Bioinformatic tools Can provide the quick and parallel analysis of massive data derived from genechips and enable the function classification of the differentially expressed genes, which provides new clues on the research of pathogenesis and epidemiology of OVC.