Differential Methylation Analysis Of Colorectal Cancer By Microarray

BackgroundColorectal cancer is a malignant tumor of lower digestive tract,including colon cancer and rectal cancer,which seriously endangers human life and health and reduces the quality of human life.Early identification,diagnosis and treatment of colorectal cancer is of great significance to improve the prognosis of the disease.However,the pathogenesis of colorectal cancer has not been fully elucidated,DNA methylation is a vital part of epigenetic modification,which is closely related to the development of multiple tumors including colorectal cancer.To screen specific methylation gene and construct the methylation expression profile of colorectal cancer has become one of current research hotspots.ObjectiveWe used microarray to investigate difference in methylation analysis between colorectal cancer and adjacent normal mucosa,preliminary screening the methylation variable positions and differentially methylated regions,and to construct specific methylation gene expression profile of colorectal cancer.Moreover,those methylation variable positions and differentially methylated regions which screened out need to be further analyzed by GO analysis and KEGG analysis,in order to further clarify the molecular mechanism of colorectal cancer,looking for potential specificity of molecular biomarkers,and providing the theoretical basis for potential loci of gene targeting treatment.MethodsAmerican Illumina DNA methylation 450 k bead chip was applied to conduct aberrant methylated analysis in colorectal cancer tissues and adjacent normal mucosa tissues from 6 pairs of colorectal cancer patients in Renji hospital affiliated to Shanghai Jiaotong University Medical School,including the analysis of methylation variable positions and differentially methylated regions and subgroup analysis.The total analysis sites were 431467,and methylation variable positions and differentially methylated regions were selected according to P value,and hypermethylation and hypomethylation were differentiated by delta beta value.The methylation variable positions and differentially methylated regions which selected out need to further analyzed by GO and KEGG analysis to understand the possible functions and pathways.ResultsThe total analysis sites of this study were 431467,with 22300 genes.The methylation variable positions were 3649 which selected by the P value <0.01 as the standard,with 1259 hypermethylated positions and 2390 hypomethylated positions.The differentially methylated regions were 3373 which selected by the P value <0.05 as the standard,with 1381 hypermethylated regions and 1992 hypomethylated regions.We screened out a panel of methylation biomarkers,including hypermethylated genes such as SLC15A3 and CBFA2T2 and hypomethylated genes such as ACOT2 and TTLL8.According to Gene Ontology analysis and KEGG analysis,the genes may be involved in some physiological processes,such as the activity of transcription factor? enzyme and ion channels and multiple signal transduction pathways.ConclusionThere are many methylation variable positions and differentially methylated regions in colorectal cancer and adjacent tissues,suggesting that aberrant DNA methylation is closely associated with the development of colorectal cancer.In the same way,there are many methylation variable positions in subgroups,which suggest that aberrant DNA methylation is closely involved with the proliferation ? infiltration and migration of colorectal cancer.DNA methylation microarray could be applied for initial screening of differential methylated genes.However,aberrant methylation panel of genes in colorectal cancer should be further validated before being applied as a promising clinical biomarker.