Determination of Global DNA Methylation in Biological Samples by Liquid Chromatography-Tandem Mass Spectrometry

Abstract

Abstract DNA methylation is one of the most common epigenetic modifications. Global genomic DNA hypomethylation is considered to induce chromosome instability and high incidence of genetic mutation, which is closely related to the emergence and development of cancer. In this study, a method based on liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) was developed to determine global DNA methylation ratios in various biological samples. DNA was extracted from the samples and hydrolyzed by three specific enzymes into single nucleosides. Liquid chromatography coupled to tandem mass spectrometry was used to measure the concentrations of 2'-deoxycytidine and 2'-deoxy-5-methylcytidine respectively, so as to calculate the global DNA methylation ratios. The developed method was further used to explore the global DNA methylation ratios in normal human liver cell L-02 exposed to perfluorooctane sulfonate (PFOS) and plasma samples of 10 hepatocellular carcinoma patients and 10 healthy participants as controls. This approach has high sensitivity and stability, and is easy to be operated, enabling us to analyze the global DNA methylation ratios in various biological samples, especially those valuable samples (such as serum, plasma et al.) with extremely low concentration of DNA.