Many reports have pointed out that liquid biopsy studies, including cfDNA tests, and their clinical application may be helpful for tumor diagnosis, drug screening, efficacy evaluation, prognosis prediction, and tumor surveillance[9, 21–23]. cfDNA also includes DNA fragments released into the blood after lysis by apoptotic or necrotic tumor cells, which is commonly referred to as circulating tumor DNA (ctDNA)[9, 20]. The ctDNA has methylation patterns similar to those found in tumor cells[24]. In recent years, there have been a few reports on the genome-wide detection of cfDNA methylation profiling by MeDIP-seq to screen potential tumor biomarkers. Xu et al.[25] identified hypermethylated DMRs in the promoter region, which could be used as the early diagnostic markers for lung cancer. Li et al. [26] identified hypermethylated DMRs which were located in promoter regions and completely overlapped with CGIs could be used for the non-invasive diagnosis of pancreatic cancer. So far, there have been few reports on the detection of cfDNA methylation profiling by MeDIP-seq in colorectal cancer in China.
Here in this study, we found 8398 DMRs in cfDNA collected from patients with colorectal cancer at the genome-wide level, and among these DMRs, 1875(22.3%) were hypermethylated and 6523(77.7%) were hypomethylated. And when we focused on DMRS located in the promoter region, 16(1.7%) were hypermethylated and 923(98.3%) were hypomethylated. This suggests that demethylation is widespread in cancer genomes at the genome-wide level[27], with a higher proportion of hypomethylation in promoter regions. Studies have shown that DNA demethylation plays an important role in activating specific gene expression and the initiation of reprogramming[28].
Subsequently, to evaluate the diagnostic value of hypermethylated genes in colorectal cancer, their methylation data were obtained from the publicly available DNA methylation datasets due to the lack of cfDNA methylation data in the public datasets. A predictive model was constructed to confirm its high validity. Methylation levels of the 12 probes in the public database were significantly different between colorectal cancer tissue and normal tissue. The corresponding genes of the 12 probes mentioned above are PRDM14, RALYL, ELMOD1 and TMEM132E. PRDM14 has been reported to be hypermethylated in lung cancer and has high accuracy in the diagnosis of lung cancer[29, 30]. Studies also have shown that the PRDM14 has several hypermethylated CpG sites in African-American colorectal cancer patients by using RRBS, which is consistent with our findings, although different from our experimental approach and the race we’ve studied[31]. RALYL has been reported to be down-regulated in clear cell renal cell carcinoma, and its reduced expression is associated with poor prognosis[32], which means it could serve as a tumor suppressor gene. These findings indicate that the methylated genes which were identified from cfDNA derived from colorectal cancer patients’ plasma may have potential clinical application value.