Screening Of DNA Methylation Sites Associated With Melanoma And Construction Of Aberrant Methylation Profile

Objective Gene chip technology was used to screen DNA abnormal methylation sites associated with melanoma,and a melanoma specific methylation profile was preliminarily constructed.Methods The whole genome DNA of 6 melanoma tissues and their adjacent tissues were detected by the Illumina Human Methylation 450 K chip and the differential DNA methylation sites were obtained.Gene Ontology(GO)analysis and KEGG_Pathway analysis were used to understand gene function.Results A total of 27779 differential methylation sites were found in melanoma tissues and adjacent tissues,including 16 673 hypermethylation sites and 11 106 hypomethylation sites.In order to further study the methylation sites associated with melanoma,more stringent screening conditions were established: P < 0.01,| beta.difference | > 0.2.All the SNP-related probes,probes on the XY chromosome and cross-reaction probes were filtered out.A total of4883 differential methylation sites were obtained,including those located in the promoter region.(including TSS1500,TSS200,5 'UTR,1stExon)had 1459(30%)differential methylation sites.GO analysis showed that the biological processes involved mainly include cell development,cell differentiation,cell adhesion,cell migration,signal transduction and transcriptional regulation.KEGG_Pathway analysis showed that the differentially expressed genes were involved in Focal adhesion,pathway in cancer,TGF-beta signaling pathway,phosphatidylinositol signaling pathway,melanogenesis,chemokine signaling pathway,adhesion junction,calcium signaling pathway,celladhesion molecule,MAPK signaling pathway,Wnt signaling pathway and Jak-STAT signaling pathway.By binding to the first 16 genes(KAAG1,DMC1,FLJ22536,CRYGD,SLC26A4,TFAP2 A,DGKE,HOXA10,PRR15,MIR375,KIAA1683,RALYL,HCG4P6DPYSL5,PAMR1,SOCS2)corresponding to the hypermethylation sites in the promoter region,the differentially methylated gene with the highest frequency(CpG site 7)among the methylation sites was selected :SOX2OT,GNMT,NFIX,FLJ22536,CITC2CD4 A,MIR196B,LOC100133991,KAAG1,SKI,CMYA5,GALNT3,ANK2,LOCI100132215RASA3,PAMR1,HOXA9.Eight candidate biomarkers(KAAG1,DGKE,SOCS2,TFAP2 A,GNMT,GALNT3,ANK2,HOXA9)were selected.Conclusion There are many differentially methylated genes between melanoma and adjacent tissues.Eight differential methylation genes may be used as biomarkers of melanoma,providing important evidence for melanoma research.