Post-Translational Modifications of Histone Variants in the Absence and Presence of a Methionine-Depleting Enzyme in Normal and Cancer Cells

SIMPLE SUMMARY: Cancer cells exhibit unique metabolic properties, including a high requirement for methionine. However, the mechanism that explains how cancer cells suffer from the absence of methionine more significantly than healthy cells remains elusive. Methionine is essential for epigenetic reprogramming of cells, both at the DNA level and for post-translation histone code modification. The post-translational modifications of histone variants (hPTMs) in normal and cancer cells were characterized by mass-spectrometry in the absence and presence of methionine gamma-lyase (MGL), a bacterial enzyme that degrades methionine and inhibits the growth of cancer cells. Results indicate a complex pattern of PTMs on histone variants and striking differences between normal and cancer cells that might help in the understanding of the molecular mechanisms triggered by methionine depletion and in the fine-tuning of MGL-based cancer therapy. ABSTRACT: Methionine is an essential amino acid involved in the formation of polyamines and a precursor metabolite for DNA and protein methylation. The dependence of cancer cells on methionine has triggered extensive investigations aimed at its targeting for cancer therapy, including the exploitation as a therapeutic tool of methionine γ-lyase (MGL), a bacterial enzyme that degrades methionine, capable of inhibiting cancer cells growth due to methionine starvation. We have exploited the high-resolution power of mass spectrometry to compare the effects of reduced availability of the methyl donor SAM, induced by MGL treatment, on the post-translational modifications of the histone tails in normal Hs27 and cancer HT-29 cells. In the absence of MGL, our analysis detected a three-fold higher relative abundance of trimethylated K25 of H1.4 in HT-29 than Hs27 cells, and a complex pattern of methylated, unmethylated and acetylated peptides in H2 and H3.3. In the presence of MGL, in HT-29, the peptide H2A1_4_11 is predominantly unmodified with mono-methylated K5 increasing upon treatment, whereas in Hs27 cells, H2A1_4_11 is monomethylated at K5 and K9 with these marks decreasing upon treatment. The time dependence of the effects of MGL-mediated methionine depletion on PTMs of histone variants in HT-29 cancer cells was also monitored. Overall, our present data on histone variants H1, H2A, H2B as well as H3.3 integrated with our previous studies on histones H3 and H4, shed light on the epigenetic modifications associated with methionine starvation and associated cancer cell death.