Deciphering the DNA methylation landscape of colorectal cancer in a Korean cohort

Abstract

Aberrant DNA methylation plays a pivotal role in the onset and progression of colorectal cancer (CRC), a disease with high incidence and mortality rates in Korea. Several CRC-associated diagnostic and prognostic methylation markers have been identified; however, due to a lack of comprehensive clinical and methylome data, these markers have not been validated in the Korean population. Therefore, in this study, we aimed to obtain the CRC methylation profile using 172 tumors and 128 adjacent normal colon tissues of Korean patients with CRC. Based on the comparative methylome analysis, we found that hypermethylated positions in the tumor were predominantly concentrated in CpG islands and promoter regions, whereas hypomethylated positions were largely found in the open-sea region, notably distant from the CpG islands. In addition, we stratified patients by applying the CpG island methylator phenotype (CIMP) to the tumor methylome data. This stratification validated previous clinicopathological implications, as tumors with high CIMP signatures were significantly correlated with the proximal colon, higher prevalence of microsatellite instability status, and MLH1 promoter methylation. In conclusion, our extensive methylome analysis and the accompanying dataset offers valuable insights into the utilization of CRC-associated methylation markers in Korean patients, potentially improving CRC diagnosis and prognosis. Furthermore, this study serves as a solid foundation for further investigations into personalized and ethnicity-specific CRC treatments. [BMB Reports 2023; 56(10): 569-574].

Fig. 1

Overview of sample preprocessing for CRC methylome profile construction. (A) Preparation of CRC samples for methylome profile. These consisted of 172 tumor samples and 128 adjacent normal samples from patients with CRC at Asan Medical Center. (B) Preprocessing of CRC methylome profile. The minfi pipeline was used for preprocessing, Subset-quantile Within Array Normalization (SWAN) method for normalization, and ComBat approach for batch correction. Poor-performing probes, SNPs, sex chromosomes, and low-variable sites were filtered out. Next, the methylation profiles were finalized. Methylation was quantified at 610,674 probes.

Fig. 2

Methylation differences between colorectal tumor and normal tissues. (A) Dimension reduction plot of methylation levels of the preprocessed 610,674 probes. (B) Comparisons of mean beta-values between normal and tumor tissue samples. (C) Heatmap of differentially methylated probe expression. Used probes were randomly selected by 5% of total DMPs. (D) Total number of DMPs between tumor and normal tissue samples. Purple and light-purple represents the genic and intragenic regions, respectively. (E) Log2 odds ratios of the number of defined hyper- and hypo-methylated probes according to each genic and CpG Island region.

Fig. 3

CpG Island Methylator Phenotype (CIMP) clustering of 172 colon tumor samples. (A) Heatmap of 172 colon tumor samples based on the methylation expression of CIMP marker probes. Samples were clustered in each CIMP-based group and sorted based on MLH1 methylation. For clinical abbreviations in the figure, MSI and MSS represent microsatellite instability and stability, respectively. LVI, PNI, and CEA represent lymphovascular invasion, perineural invasion, and preoperative carcinoembryonic antigen level, respectively. WD, MD, and PD represent well-differentiated, moderately-differentiated, and poorly-differentiated, respectively. (B) Boxplot represents mean CIMP marker gene methylations based on CIMP and MSI status. (C) Proportion of MSI and MSS status based on CIMP status. (D) Proportion of MLH1 promoter methylation status based on CIMP status. The categorization of samples into MLH1 promoter methylation-positive (MLH1me+) and methylation-negative (MLH1me-) is based on a predetermined methylation level threshold of 0.3. Samples with promoter methylation levels greater than 0.3 were classified as MLH1me+, while those with levels less than 0.3 were classified as MLH1me-. (E) Proportion of tissue location based on CIMP status. In the figure, left colons consist of splenic flexure, descending, sigmoid, and rectosigmoid tumors, and right colons consist of ascending, cecum, hepatic flexure, and transverse tumors. In panel (A), asterisks (*) denote significance (P < 0.05) as determined by the chi-square test, which was used to assess the association between CIMP and clinical characteristics.