Targeted Metabolomic Strategy for Epigenetic Modification-Related Metabolites Using Ultraperformance Liquid Chromatography-Tandem Mass Spectrometry

Epigenetics-related metabolites-substrates or cofactors that regulate epigenetic modifications, that play a critical role in regulating gene expression-are collectively referred to as the "epigenetic metabolome". Here, we developed a comprehensive targeted metabolomic method covering 33 metabolites involved in multiple types of epigenetic modifications. The detection panel included coenzyme A (CoA)/acetyl-CoAs-metabolites in the methionine cycle, those related to nicotinamide adenine dinucleotide (NAD⁺) metabolism─intermediates of carbohydrate metabolism, and acetylglucosamines. These metabolites were analyzed in two liquid chromatography-mass spectrometry runs based on their distinct chemical properties. For most metabolites (over 88%), the limits of quantification were below 16 ng, the dynamic ranges exceeded 3 orders of magnitude, and the precisions were above 80%. We profiled the epigenetic metabolome in a mouse model of diabetic cardiomyopathy and identified 8 significantly altered metabolites linked to various epigenetic modifications, including DNA/histone methylation, acetylation, and O-GlcNAcylation of histones. In conclusion, we established a reliable and sensitive method for detecting alterations in the epigenetic metabolome and demonstrated its applicability to disease-related studies.