Enrichment of Hypermethylated DNA on Chip for Cervical Cancer Detection

Abstract 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.