S-adenosylmethionine supply controls DNA methylation turnover in synovial sarcoma

Abstract

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 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.

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