S-adenosylmethionine supply controls DNA methylation turnover in synovial sarcoma

Background: Methionine is the nutrient source of the metabolite S-adenosylmethionine (SAM) used to methylate chromatin for regulation of gene expression. Disruptions to this metabolic supply, including nutritional deficiency of certain B vitamins, alter chromatin methylation and have been implicated in tumor growth. Objective: To define how cellular SAM supply controls DNA methylation dynamics and the disruption of oncogenic gene expression in synovial sarcoma. Methods: Cell line models of synovial sarcoma were treated with the DNA methyltransferase inhibitor azacitidine or the small-molecule MAT2A inhibitor AG-270, which blocks SAM synthesis from methionine. Intracellular SAM concentrations were quantified by liquid chromatography-mass spectrometry. Global DNA methylation rates were measured by stable isotope tracing with [2H3-methyl]-methionine. Genomic sites of altered DNA methylation were identified by EM-seq and the associated transcriptional changes measured by RNA-seq. Results: Inhibition of SAM synthesis reduced intracellular SAM concentration from 94 uM to 5.6 uM (p value < 0.0001) at 24 hours. This was associated with a 19% decrease (p value < 0.0001) in the global 5-methyldeoxycytosine turnover rate, while total DNA methylation levels were maintained. In contrast to the global DNA hypomethylation induced by azacitidine, SAM depletion resulted in a redistribution of DNA methylation with loss at 252 and gain at 206 genomic sites, and the transcriptional response to SAM depletion was not associated with changes in promoter methylation at the altered genes. Both azacitidine and SAM depletion activated mesenchymal genes, while suppressing cell cycle progression. Conclusions: Metabolic supply of SAM is a major regulator of DNA methylation turnover providing a mechanism by which nutritional or genetic disruptions to SAM metabolism can alter chromatin methylation and gene expression.