| Objective: By using high-throughput sequencing technology,we looked for the difference of genomic methylation between prostate mesenchymal stem cells and early prostate cancer cells,analyzed the differential methylation genes involved in differential methylation regions,and analyzed the functional enrichment of differential genes.Furthermore,it fills the gap in the research of genome-wide methylation of prostate mesenchymal stem cells and early prostate cancer cells,and lays a foundation for exploring the role of prostate mesenchymal stem cells in prostate cancer and finding therapeutic targets of mesenchymal stem cells.Methods: In this study,3 cases of early prostate cancer cells were set as experimental group(Treat group)and 1 case of prostate mesenchymal stem cells as control group(Control group).After DNA was extracted,Illumina hiseq XTen sequencing platform was used for sequencing.The results of genomic DNA methylation sequencing of prostate cancer and human prostate mesenchymal stem cells were obtained,and the differentially methylated sites and regions were detected and annotated.Based on the results of the structural annotation of the differentially methylated regions on the genome,the genes with overlap between the promoter and genomic region and the differentially methylated regions were analyzed by GO,and the biological function of the differentially methylated genes was determined by GO analysis.The most important biochemical metabolic pathway of genes related to differentially methylated regions was determined by Pathway significant enrichment.Results: 1.In this study,genomic methylation high-throughput sequencing was performed on 3 cases of early prostate cancer and 1 case of human prostate mesenchymal stem cells.A total of 38951 differential methylation sites were found between early prostate cancer and human prostate mesenchymal stem cells,including10305 hypermethylation sites and 28646 hypomethylation sites.The average methylation level of genomic differentially methylated sites in early prostate cancer was significantly lower than that in human prostate mesenchymal stem cells(P≤ 0.05).The first five chromosomes with the most differentially methylated sites were 3353 on chromosome 1,2995 on chromosome 2,2646 on chromosome 3,2423 on chromosome 4 and 2410 on chromosome 6.There were 1412 differentially methylated regions,including 361 hypermethylation differential regions and 1051 hypomethylation differential regions.For the structural annotation of differentially methylated regions,the number of differentially methylated regions annotated to Intron was the most,followed by Promoter,and that to UTR3 was the least.2.GO analysis of differentially methylated genes between early prostate cancer and human prostate mesenchymal stem cells showed that there were 429 GO items significantly enriched and 410 GO items significantly enriched in hypomethylation differential genes,including 73 molecular functions,282 biological processes and 55 cellular components.A total of 19 GO items were significantly enriched in hypermethylation differential genes,including 7 molecular functions,5 biological processes and 5 cellular components.We screened and analyzed the significantly enriched GO items and the genes involved,and the results are as follows:(1)In terms of molecular function,hypomethylation differential genes are mainly concentrated in calcium channel and calcium transporter activity,prostate cancer-related differential methylation genes include CACNA1 A,CACNA2D2,CACNA2D3,TRPM8 and other genes;hypermethylation differential genes are mainly concentrated in protein phosphatase and GTPase binding,and prostate cancer-related differential methylation genes include PPP4R4,ELK and other genes.(2)In terms of biological process,hypomethylation differential genes are mainly concentrated in intercellular adhesion,c GMP metabolic process and blood vessel development,and prostate cancer-related differential methylation genes include RORA,RET,CEACAM1 and other genes;hypermethylation differential genes are mainly concentrated in ARF protein signal transduction and muscle cell apoptotic process,and prostate cancer-related differential methylation genes are GNB1.(3)In terms of cell composition,the gene products of hypomethylation differential genes are mainly concentrated in the plasma membrane and neuron part,while the gene products of hypermethylation differential genes are mainly concentrated in the cytoplasm,cytoskeleton and plasma membrane bounded cell projection part.3.KEGG analysis of differentially methylated genes between early prostate cancer and human prostate mesenchymal stem cells showed that five significantly enriched pathway;differentially methylated genes were mainly concentrated in the cancer pathway,and the differentially methylated genes related to prostate cancer included RB1,HSP90 A and BCL2.Conclusion:1.In this study,genomic methylation of three groups of early prostate cancer and one group of human prostate mesenchymal stem cells were analyzed by high-throughput sequencing technique.the average methylation level of genomic differential methylation sites in early prostate cancer was lower than that in human prostate mesenchymal stem cells.The differentially methylated sites were mainly concentrated on chromosome 1,chromosome 2,chromosome 3,chromosome 4 and chromosome 6.To annotate the structure of differentially methylated regions,the number of differentially methylated regions annotated to Intron was the most,followed by Promoter.2.GO enrichment analysis of differentially methylated genes showed that hypomethylation differential genes were mainly concentrated in calcium channel,calcium transporter activity,intercellular adhesion,c GMP metabolic process and blood vessel development,while hypermethylation differential genes were mainly concentrated in protein phosphatase,GTPase binding,ARF protein signal transduction and muscle cell apoptotic process.The KEGG enrichment analysis of differentially methylated genes showed that the differential genes were mainly concentrated in the cancer pathway. |
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