Despite the discovery of two major DNA demethylating agents (decitabine and azacitidine) decades ago, there has been a lot of debate over these agents’ actions that contribute to clinical responses, and how to best use them as drugs. As part of Stand-Up-To-Cancer research project, we successfully demonstrated that transient exposure of cultured and primary leukemic and breast cancer cells to the agents, decitabine or azacitidine, at doses in the nanomolar range, produces a memory for anti-tumour responses, without causing immediate cytotoxicity. The memory, or long lasting effects, indicates that the drugs work through epigenetic reprogramming to change cancer cells’ biological behavior, which is very different from traditional cancer chemotherapy. We also successfully characterized a human leukemia cell line model to study self-renewing cancer cells (cancer stem-like cells), and showed that decitabine and azacitidine at low doses were able to inhibit cancer stem-like cells. This is the first report that demonstrated epigenetic therapy could target cancer stem cells. The discovery also indicated that epigenetic mechanisms may play a significant role in regulating cancer stem cells.

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Epigenomic profiling revealed critical threshold levels of DNA methyltransferase (DNMT) 1 to maintain DNA methylation across the genome in human cancer cells.

There has been a controversy over whether DNMT1 is the sole DNMT in maintaining cancer-specific DNA methylation. Previous research efforts from world-renown epigenetic labs through knockout or knockdown studies yielded conflicting results. Besides, the studies were limited to certain genomic regions lacking the comprehensive insights of genome-wide epigenomic profiles. We used graded time-dependent shRNA approaches to create a DNMT1 gradient system, which contains clones derived from colorectal cancer cells, HCT116, with step-wise reduction of DNMT1 proteins. We discovered that lowering DNMT1 below a threshold level is required for maximal loss of DNA methylation at all genomic regions, including gene body and enhancer regions, and for maximally reversing abnormal promoter DNA hypermethylation and associated gene silencing to reexpress key genes. The study has significant clinical implications as it is difficult to reach this threshold with patient-tolerable doses of current DNMT inhibitors (DNMTIs). We showed that new approaches, like decreasing the DNMT targeting protein, UHRF1, can augment the DNA demethylation capacities of existing DNA methylation inhibitors for fully realizing their therapeutic potential.