S-Adenosyl Methionine Synthesis Impacts Maintenance of Acute Myeloid Leukemia Cells with Regulation of Transcriptional Elongation

Epigenetic dysregulation is at the heart of Acute Myeloid Leukemia (AML), and its mechanistic understanding holds promise in improving AML dismal prognosis. Modification of chromatin accessibility through post-translational modification of histones alters gene expression activity and is directly dependent on cell metabolism for generation of the modifying groups. Methionine metabolism generates S-adenosyl methionine (SAM), the universal methyl donor in the cell, through the activity of multimeric methionine adenosyl transferase (MAT) enzymes. MAT2A is an obligatory subunit in hematopoietic cells, and we have recently tabled it in a CRISPR drop-out screen [1] as a candidate vulnerability in AML.

We have validated the anti-AML effects of MAT2A ablation using shRNA-mediated gene expression knockdown, and could further phenocopy cell line selectivity observed in our CRISPR screen through the use of the MAT2A selective inhibitor FIDAS-5 [2] (IC50 MOLM-13 1.0μM, OCI-AML3 0.7μM, MV4.11 11μM).

MAT2A inhibition significantly depleted SAM levels (fold change to DMSO, FC=0.20±0.07; p<0.05, MOLM-13 cells), and resulted in decreased growth and enhanced apoptosis (MOLM-13 FC=1.34±0.21;p<0.05, OCI-AML3 FC=3.0±0.34; p<0.05, MV4.11 FC=1.09±0.19;p=0.52) of cultured AML cells, without an obvious impact on differentiation. Similar results were observed in AML patient samples (n=11), which displayed reduced capacity to initiate colonies in semi-solid medium (FC=0.47±0.21; p<0.0005) and had hindered expansion in medium-term co-cultures on MS-5 stroma, with accumulation of cells with intermediate, but not high, levels of primitive marker CD34. MLL-AF9 transformed primary mouse bone marrow cells were equally affected (FC colony efficiency=0.05±0.03; p<0.005). Significantly, MAT2A inhibition did not affect colony-formation or multi-lineage differentiation of cord blood-derived CD34+ cells in colony-forming progenitor assays (FC=1.01±0.25p=0.97), indicating selective vulnerability of AML cells.

We analysed the consequences of MAT2A inhibition on chromatin methyl modifications, and observed a specific reduction in the active elongation mark H3K36me3. The associated transcriptional programme is currently being investigated. Interestingly, contrary to reports in colon cancer cells upon methionine restriction and reduced SAM levels [3], we did not observe loss of H3K4me3 at active promoters, suggesting a selective AML dependence on transcription elongation.

In conclusion, we identify SAM synthesis as a novel vulnerability in AML through regulation of transcriptional elongation. Our findings highlight the therapeutic potential of modulating metabolite availability for epigenetic and transcriptional re-programming in leukemia.

References

[1] Tzelepis, K., et al., A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia. Cell Rep, 2016. 17(4): p. 1193-1205.

[2] Zhang, W., et al., Fluorinated N,N‐Dialkylaminostilbenes Repress Colon Cancer by Targeting Methionine S‐Adenosyltransferase 2A.ACS Chem. Bio, 2013 (8): p. 796−803

[3] Mentch, S.J., et al., Histone Methylation Dynamics and Gene Regulation Occur through the Sensing of One-Carbon Metabolism.Cell Metab, 2015. 22(5): p. 861-73.