Untargeted 2D NMR Metabolomics of [13C-methyl]Methionine-Labeled Tumor Models Reveals the Non-DNA Methylome and Provides Clues to Methyl Metabolism Shift during Tumor Progression

For more than a decade, DNA and histone methylationshave been the focus of extensive work, although their relationship withmethyl group metabolism was overlooked. Recently, it has emerged thatepigenetic methylations are influenced by methyl donor nutrientavailability, cellular levels ofS-adenosyl-methionine (SAM), andcytoplasmic methyltransferase activities. SAM-dependent methyl-transferases methylate a wide range of targets, from small molecules toproteins and nucleic acids. However, few investigations of the globalmethylome of tumors have been performed. Here, untargeted NMRmetabolomics of two mouse tumor models labeled with [13C-methyl]methionine were used to search for the NMR-visible set of cellular methyl acceptors denoted the global methylome.Tumor models were B16 melanoma cell cultures and B16 melanoma tumors, which may be considered as two stages of B16 tumordevelopment. Based on 2D1H-13C NMR spectra and orthogonal partial least squares discriminant analysis of spectra, our studyrevealed markedly different global methylomes for melanoma models. The methylome of B16 melanoma cell cultures was dominatedby histone methylations, whereas that of B16 melanoma tumors was dominated by cytoplasmic small-molecule methylations.Overall, the technique gave access to the non-DNA methylome. Comparison of tumor models also exhibiting differential expressionof aerobic glycolysis provided clues to a methyl metabolism shift during tumor progression.