An Integrated Analysis Of Gene Expression And Epigenomic Modification In Colorectal Cancer Cells

Colorectal cancer is one of the most common malignant tumors of the digestive tract.It is the fourth leading cause of death arising from cancers,following lung cancer,gastric cancer and liver cancer.In recent years,incidence of colorectal cancer in our country is increasing.Cancers show an important epigenomic feature,which is the global absence of DNA methylation and local DNA hypermethylation.More and more researches have proved that specific long noncoding RNAs can change the methylation status of DNA by interacting with chromatin modifying complexes,and by doing so,regulate the expression of genes.Thus,long noncoding RNAs,as an important class of regulators of gene expression,are closely related to the occurrence and development of tumor.As new findings on the function of long noncoding RNA in cancers are just beginning to emerge,it is highly necessary to perform integrative analysis of transcriptomics and epigenomics in colorectal cancer.Since cancer cells show different degrees of differentiation,we believe to apply such analysis to cancer cells with different differentiation is important.In this study,12 colorectal cancer samples(4 high differentiation ones,4 moderate differentiation ones,and 4 low differentiation ones)and 3 normal colorectal tissue samples were analyzed.First,MeDIP-seq and RNA-seq were conducted.Then,the sequencing data were analyzed step by step,including:quality control,mapping,assembly,differential and functional enrichment analysis,weighted gene co-expression network,and co-methylation network analysis.This integrative analysis pipeline,combining transcriptomics and epigenomics,helps reveal the relationship between the differentially expressed long noncoding RNAs,the differentially changed DNA methylation status of some genomic regions,and the differentially expressed protein coding genes in these regions in colorectal cancer cells.In this study,compared with the normal colorectal tissues,we identified 1095 novel long noncoding RNA transcripts,in addition,screened out 116 differentially expressed long noncoding RNAs,1656 differentially expressed protein-coding genes,and 3994 differential DNA methylation sites in colorectal cancer tissues.According to GO(gene ontology)analysis,the differentially expressed long noncoding RNAs are mainly enriched in the GO "biological process" in digestive tract and lung morphogenesis,and the differentially expressed protein-coding genes are mainly enriched in the AGE-RAGE signaling pathway and the Wnt signaling pathway that are closely associated with cancer invasion and occurrence.Moreover,most of the genes near differential DNA methylation regions are related to colorectal cancer.We identified two weighted gene co-expresssion networks(the green-yellow module and the red module);the green-yellow module is positively,but the red module is negatively,correlated with colorectal cancer.In addition,we found three differentially expressed long noncoding RNAs(RP11-288121.1,RP11-35609.1,RP11-74M11.2),whose potential target genes(CLCNKA,TTC6,RNPS1P1)are differentially expressed,and the promoter region of these target genes undergoes differential DNA methylation.Our results indicate that gene expression shows significant differences between three cancer groups and the normal group,but the difference between the moderate differentiation cancer group and the normal group dose not lie between the differences generated by the other two cancer normal groups,as we expected.This may suggest that the differentiated status of cancer cells may not directly relevant to the change of gene expression.Consistent with many previous reports,compared with the normal samples,the genomes of colorectal cancer samples have a wide range of DNA methylation absence.The results of our integrative analysis of the gene expression profiles and DNA methylation profiles indicate that,while the potential target genes of many differentially expressed long noncoding RNAs are also differentially expressed,the promoter regions of few ones show differential DNA methylation.This may suggest that wrong DNA methylation in the promoter regions of protein coding genes is not a key feature of abbrent epigenomics modification in colorectal cancer cells.