| Objective: Epigenetic changes include DNA methylation,histone modification,RNA regulation and chromatin remodeling,which can regulate gene transcription and expression to affect gene mutation,expression regulation,cell proliferation,and so on.The methylation of the promoter region is one of the important mechanisms of epigenetic variation,which is closely related to tumorigenesis and development.Many studies have reported the methylation of suppressor genes such as P16,RASSF1 A,Runx3,PCDH10,hMLH1 were is closely related to gene expression silence participating in occurrence and development of gastric cancer.At present,there are many methods for differentially methylated and differentially expressed genes,of which bioinformatics analysis is to study biology by using the methods of applied mathematics,informatics,statistics and computer science.Compared with the basic biological research,bioinformatics research is based on genome wide data to obtain the research results,which is more macro.With the implementation of the Human Genome Project and the rapid development of related disciplines in molecular biology,gene sequence data are rapidly growing at an unprecedented rate and more and more genome sequences of animals,plants and microorganisms are determined.Gene chips are the main media tools for bioinformatics analysis.The sequencing principle is the hybridization sequencing method,that is,the method of nucleic acid sequence determination by hybridization with a set of known nucleic acid probes,The surface of the substrate is immobilized with a probe whose target nucleotide is known.Among them,methylated chips make genome-wide methylation analysis possible,and gene expression profiling chips can analyze tumor-related differentially expressed genes in the whole genome.In the past,gene chip-based research was usually only a single methylation profile or gene expression profiling,or only focusing on the methylation and expression association analysis of a certain gene,and the two were combined and analyzed by consensus And verify that it is expected to clear the genesis and development of gastric cancer real methylation regulation of genes,and as a basis for the study of epigenetic regulation of gastric cancer.In this study,methylated-differentially expressed genes(MDEGs)were obtained by detecting methylated microarray and microarray together.Through the enrichment analysis,we can get the main go terms and pathways of MDEGs.The Protein–protein interaction(PPI)analysis was obtained among MDEGs.Hub genes is obtained through their interaction.Then we verified the hub gene.Furthermore,we selected one of the hub genes,SST to detect the methylation and expression between gastric cancer and its normal tissues.Methods: Expression profiling(GSE13911,GSE29272)and methylation profiling(GSE25869,GSE30601)data were obtained from GEO DataSets.Differentially expressed genes and differentially methylated genes were identified using GEO2 R.Gene ontology and pathway enrichment analyses were performed for the MDEGs.Protein–protein interaction(PPI)networks were established by STRING and Cytoscape.Analysis of modules in the PPI networks was performed using MCODE.Furtherly,the hub genes derived from the PPI networks were verified by The Cancer Genome Atlas(TCGA)database and human tissues,with methylation-specific PCR(MSP)for genes methylation and real-time q-PCR for genes expression.This study included 139 gastric cancer(GC)patients underwent surgical treatment from the First Affiliated Hospital of China Medical University with tumor tissues and distal normal mucosa(NOR)The mRNA expressions of SST in gastric mucosa were detected by Real-time PCR.Direct bisulfite sequencing(BGS)was used to detect the methylation level of SST promoter region after sulfite modification.Results: A total of 445 genes were identified as hypermethylated,lowly expressed genes(Hyper-LGs),which were enriched in regulation of system process and channel activity.A total of 129 genes were identified as hypomethylated,highly expressed genes(HypoHGs),which were involved in cell adhesion,cell proliferation,and protein binding.Pathway analysis showed that Hyper-LGs were associated with neuroactive ligandreceptor interaction and calcium signaling pathway,while Hypo-HGs were enriched in pathways in cancer.In the PPI networks,after verification by TCGA analysis and human tissue detection,CASR,CXCL12 and SST were identified as significantly different hub genes.After tissue validation expression of SST between cancer and adjacent normal showed differences.The average methylation rate and hypermethylation sites of SST were not different.Methylation rates of methylation sites 12,15,16,23 and 24 of SST showed different Conclution: MDEG analysis help to understand the epigenetic regulation mechanisms involved in the development and progression of gastric cancer.The hub genes have predictive and prognostic value as methylation-based biomarkers for the precise diagnosis and treatment of gastric cancer. |
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