Enrichment of Hypermethylated DNA on Chip for Cervical Cancer Detection

Preselection of cancer-specific hypermethylated DNA (hmDNA) from a background of total DNA is important for developing urine-based cancer diagnostics. The challenge relates to the low concentration of hmDNA in absolute measures and compared to normal DNA derived from healthy cells. Here, a micropillar-structured microfluidic chip is developed for the selective enrichment of hmDNA from DNA isolated from cultured cervical cancer cells. During hmDNA enrichment, hmDNA binds at the surface-immobilized methyl binding domain 2 protein receptors, which is the capture coating for hmDNA, followed by the elution of surface-bound DNA. The ratio of hmDNA to non-methylated DNA in the enriched DNA mixtures is assessed using synthetic DNA by applying a digest with methyl-sensitive restriction enzymes to the enriched DNA mixtures, followed by quantitative polymerase chain reaction (qPCR). The hmDNA level in the enriched DNA mixture increased from 1% prior to enrichment to 30% afterward. The enrichment method enables selective enrichment of DNA isolated from the cervical cancer cell line, as confirmed by qPCR, which targets a hypermethylated gene associated with cervical cancer. Upon further development, this platform for selective hmDNA enrichment could be applied to urine samples to allow for simple and accurate methylation-based cancer detection.