Aging related methylation influences the gene expression of key control genes in colorectal cancer and adenoma.

AIM

To analyze colorectal carcinogenesis and age-related DNA methylation alterations of gene sequences associated with epigenetic clock CpG sites.

METHODS

DNA methylation analysis of 353 epigenetic clock CpG sites published by Steve Horvath was performed using methylation array data for a set of 123 colonic tissue samples [64 colorectal cancer (CRC), 42 adenoma, 17 normal; GEO accession number: GSE48684]. Among the differentially methylated age-related genes, secreted frizzled related protein 1 () promoter methylation was further investigated in colonic tissue from 8 healthy adults, 19 normal children, 20 adenoma and 8 CRC patients using bisulfite-specific PCR followed by methylation-specific high resolution melting (MS-HRM) analysis. mRNA expression of age-related "epigenetic clock" genes was studied using Affymetrix HGU133 Plus2.0 whole transcriptome data of 153 colonic biopsy samples (49 healthy adult, 49 adenoma, 49 CRC, 6 healthy children) (GEO accession numbers: GSE37364, GSE10714, GSE4183, GSE37267). Whole promoter methylation analysis of genes showing inverse DNA methylation-gene expression data was performed on 30 colonic samples using methyl capture sequencing.

RESULTS

Fifty-seven age-related CpG sites including hypermethylated , , and hypomethylated MGP, PIPOX were differentially methylated between CRC and normal tissues ( < 0.05, Δβ ≥ 10%). In the adenoma normal comparison, 70 CpG sites differed significantly, including hypermethylated , , , and hypomethylated , ( < 0.05, Δβ ≥ 10%). In MS-HRM analysis, the SFRP1 promoter region was significantly hypermethylated in CRC (55.0% ± 8.4 %) and adenoma tissue samples (49.9% ± 18.1%) compared to normal adult (5.2% ± 2.7%) and young (2.2% ± 0.7%) colonic tissue ( < 0.0001). DNA methylation of promoter was slightly, but significantly increased in healthy adults compared to normal young samples ( < 0.02). This correlated with significantly increased mRNA levels in children compared to normal adult samples ( < 0.05). In CRC tissue the mRNA expression of 117 age-related genes were changed, while in adenoma samples 102 genes showed differential expression compared with normal colonic tissue ( < 0.05, logFC > 0.5). The change of expression for several genes including , , and , followed the same pattern in aging and carcinogenesis, though not for all genes (., MGP).

CONCLUSION

Several age-related DNA methylation alterations can be observed during CRC development and progression affecting the mRNA expression of certain CRC- and adenoma-related key control genes.