| As a highly heterogeneous tumor,colorectal cancer has serious challenges in cancer treatment and prolonging the survival time of patients.Epigenetic changes in colorectal tissue and accumulation of mutations in proto-oncogenes,tumor suppressor genes,and genes involved in DNA repair mechanisms may lead to the development of colorectal cancer.Partially methylated regions(PMRs)are extended regions of the genome that exhibit highly disordered and reduced average methylation levels,which are markers of cell differentiation.Current studies have shown that the formation of PMRs is closely related to tumors such as medulloblastoma,breast cancer,and lung cancer.Therefore,using single-cell sequencing technology to identify partial methylation regions in colorectal cancer,deeply analyze the tumor heterogeneity of partial methylation regions between cells,explore new diagnostic and prognostic markers of colorectal cancer,and decipher the relationship between genes in partial methylation regions and tumor microenvironment is of great significance for the accurate treatment of colorectal cancer.In this study,the genome-wide methylation profiles of colorectal cancer tissues detected by bisulfite sequencing technology were used to identify 15,019 and 14,519 PMRs in cancer and paracancerous tissues,respectively,and found that they were widely distributed in the genome.Compared with in the outer region,the methylation level of the inner Cp Gs sites is generally low.The identified PMRs were classified and analyzed in this study.By comparative analysis of PMRs in cancer and adjacent tissues,they were divided into Loss-PMRs,Conserved-PMRs and Gain-PMRs,and found that the length of Loss-PMRs and Gain-PMRs was relatively short.Functional analysis revealed that genes in Gain-PMRs were enriched in key biological processes that promote tumor growth,such as cell proliferation and mitosis.In order to mine the key functional genes in PMRs in colorectal cancer,this study used the EPIC algorithm to estimate the proportion of various cell types in colorectal cancer tissue,and mined the genes associated with endothelial cells,macrophages and cancer through the WGCNA co-expression network.Combined with the correlation between genes and genes in the module and the correlation between genes and traits,a total of 6 key functional genes were screened,namely BAALC,CNTN1,CPEB1,FAM43 B,SFRP1,TLL1.The potential of 6 functional genes in PMRs as new markers and prognostic molecules for colorectal cancer diagnosis was evaluated,and it was found that the genes CPEB1,FAM43 B and SFRP1 have potential as new markers for early diagnosis of colorectal cancer.The results indicated that high expression of CPEB1 was associated with poor prognosis in colorectal cancer patients.During the evolution of normal tissues to colorectal cancer,the DNA methylation level and expression value of CPEB1 promoter achieved synchronous changes.At the same time,this study found that the expression of CPEB1 was significantly positively correlated with the infiltration degree of endothelial cells,macrophages and cancer-associated fibroblasts.This indicated that the dysregulation of CPEB1 expression might interact with changes in the tumor microenvironment and has the potential to become a target for precise treatment of colorectal cancer.Since colorectal cancer PMRs were related to the tumor microenvironment,this study used colorectal cancer single-cell methylation profiles to explore the intercellular heterogeneity of Gain-PMRs.This study found differences in the methylation levels of PMRs in different regions of tumor cells and their microenvironment,which elucidated the molecular basis of gene expression heterogeneity in the tumor microenvironment.In this study,we analyzed the characteristics of colorectal cancer PMRs using single-cell methylation profiles,and found that Gain-PMRs in colorectal cancer cells contained a higher proportion of protein-coding genes.The methylation level in the Gain-PMRs showed a downward trend as a whole,but the methylation level of the Cp G island promoter was abnormally increased,which was obviously consistent with the expression changes of related genes.In conclusion,the detection of PMRs and their functional analysis were completed based on the methylation profiles of bulk sequencing and single-cell sequencing for colorectal cancer.CPEB1,a new prognostic marker associated with cancer-related fibroblast infiltration,was identified to provide a potential drug target for the precise treatment of colorectal cancer.The heterogeneity analysis and aberrant methylation study of PMRs in colorectal cancer cells provided a new perspective for in-depth understanding of gene expression heterogeneity in the tumor microenvironment. |
