Targeting DNA methylation

Abstract

Two nucleoside inhibitors of DNA methylation, azacitidine and decitabine, are now standard of care for the treatment of the myelodysplastic syndrome, a deadly form of leukemia. These old drugs, developed as cytotoxic agents and nearly abandoned decades ago were resurrected by the renewed interest in DNA methylation. They have now provided proof of principle for epigenetic therapy, the final chapter in the long saga to provide legitimacy to the field of epigenetics in cancer. But challenges remain; we don't understand precisely how or why the drugs work or stop working after an initial response. Extending these promising findings to solid tumors faces substantial hurdles from drug uptake to clinical trial design. We do not know yet how to select patients for this therapy and how to move it from life extension to cure. The epigenetic potential of DNA methylation inhibitors may be limited by other epigenetic mechanisms that are also worth exploring as therapeutic targets. But the idea of stably changing gene expression in vivo has transformative potential in cancer therapy and beyond.

Figure 1

Chemical structure of nucleoside DNA Methylation Inhibitors. AZA and DAC are FDA approved for the treatment of MDS. Zebularine has not been pursued clinically because of toxicity in pre-clinical models. 5-FC is in early stage clinical trials, while S110 is still undergoing pre-clinical testing.

Figure 2

Mechanisms of action of hypomethylating nucleoside analogues. Azacitidine and decitabine are efficiently incorporated into cells by specialized transporters, following which their metabolism diverge. They are phosphorylated by different enzymes, eventually to 5-aza-CTP which incorporates into RNA and has poorly defined effects there and 5-aza-dCTP which incorporates into DNA. A fraction of 5-aza-CDP is also converted to 5-aza-dCDP. Once incorporated into DNA, 5-aza-dCTP forms irreversible covalent bonds with DNMTs, which result in bulky DNA-protein adducts and inhibition of DNA synthesis. At high doses, this results in cell death (and is therefore a cytotoxic intervention). At lower doses, the complexes are excised and degraded by the proteosome. DNA is repaired, following which DNA synthesis resumes in the absence of DNMTs, resulting in hypomethylation of newly synthesized DNA.

Figure 3

Pleiotropic Therapeutic Effects of DNA Methylation Inhibition and Gene Reactivation in Cancer. DNA methylation is maintained post replication by the action of DNA methyltransferases. DAC and AZA lead to degradation of the main DNA methyltransferases, and continued replication results in passive demethylation that eventually results in reactivated gene expression. Activated gene expression, in turn, has effects on multiple different pathways, each of which could contribute to a clinical response.