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Aberrant methylation of CpG islands in the promoter region of genes is acommon epigenetic phenomenon found in early cancers. Therefore conducting genome-scalemethylation studies will enhance our understanding of the epigenetic etiologybehind carcinogenesis by providing reliable biomarkers for early detection ofcancer. To discover novel hypermethylated genes in colorectal cancer by genome-widesearch, we first defined a subset of genes epigenetically reactivated in coloncancer cells after treatment with a demethylating agent. Next, we identified anothersubset of genes with relatively down-regulated expression patterns in colorectalprimary tumors when compared with normal appearing-adjacent regions. Among 29 genesobtained by cross-comparison of the two gene-sets, we subsequently selected, throughstepwise subtraction processes, two novel genes, GABRA1 and LAMA2, as methylationtargets in colorectal cancer. For clinical validation pyrosequencing was usedto assess methylation in 134 matched tissue samples from CRC patients. Aberrantmethylation at target CpG sites in GABRA1 and LAMA2 was observed with high frequencyin tumor tissues (92.5% and 80.6%, respectively), while less frequently in matchedtumor-adjacent normal tissues (33.6% for GABRA1 and 13.4% for LAMA2). Methylationlevels in primary tumors were not significantly correlated with clinico-pathologicalfeatures including age, sex, survival and TNM stage. Additionally, we found thatectopic overexpression of GABRA1 in colon cancer cell lines resulted in stronginhibition of cell growth. These results suggest that two novel hypermethylatedgenes in colorectal cancer, GABRA1 and LAMA2, may have roles in colorectal tumorigenesisand could be potential biomarkers for the screening and the detection of colorectalcancer in clinical practice.

Identification of GABRA1 and LAMA2 as new DNA methylation markers in colorectal cancer