Epigenetic biomarkers are emerging as determinants of breast cancer prognosis. Breast cancer cells display unique alterations in major cellular metabolic pathways and it is becoming widely recognized that enzymes that regulate epigenetic alterations are metabolically sensitive. In this study, we used microarray data from the GEO database to compare gene expression for regulators of metabolism and epigenetic alterations among non-invasive epithelial (MCF-7, MDA-MB-361, and T-47D) and invasive mesenchymal (MDA-MB-231, Hs-578T, and BT-549) breast cancer cell lines. The expression of genes, including GLS1, GFPT2, LDHA, HDAC9, MYST2, and SUV420H2, was assessed using RT-PCR. There was differential expression between epithelial and mesenchymal cell lines. MYST2 and SUV420H2 regulate the levels of the epigenetic biomarkers histone H4 lysine 16 acetylation (H4K16ac) and histone H4 lysine 20 trimethylation (H4K20me3), respectively. Reduced amounts of H4K16ac and H4K20me3 correlated with lower levels of MYST2 and SUV420H2 in mesenchymal cells and, along with reduced amounts of histone H3 lysine 9 acetylation (H3K9ac), were found to distinguish epithelial from mesenchymal cells. In addition, both GLS1 and GFPT2 play roles in glutamine metabolism and were observed to be more highly expressed in mesenchymal cell lines, and when glutamine and glutamate levels reported in the NCI-60 metabolomics dataset were compared, the ratio of glutamate/glutamine was found to be higher in mesenchymal cells. Blocking the conversion of glutamine to glutamate using an allosteric inhibitor, Compound 968, against GLS1, increased H4K16ac in T-47D and MDA-MB-231 cells, linking glutamine metabolism to a particular histone modification in breast cancer. These findings support the concept that metabolically sensitive histone modifications and corresponding histone modifying enzymes can be used as diagnostic and prognostic biomarkers for breast cancer. It also further emphasizes the importance of glutamine metabolism in tumor progression and that inhibitors of cellular metabolic pathways may join histone deacetylase inhibitors as a form of epigenetic therapy.