Decitabine-induced DNA methylation-mediated transcriptomic reprogramming in human breast cancer cell lines; the impact of DCK overexpression

Abstract

Decitabine (DAC), a DNA methyltransferase (DNMT) inhibitor, is tested in combination with conventional anticancer drugs as a treatment option for various solid tumors. Although epigenome modulation provides a promising avenue in treating resistant cancer types, more studies are required to evaluate its safety and ability to normalize the aberrant transcriptional profiles. As deoxycytidine kinase (DCK)-mediated phosphorylation is a rate-limiting step in DAC metabolic activation, we hypothesized that its intracellular overexpression could potentiate DAC’s effect on cell methylome and thus increase its therapeutic efficacy. Therefore, two breast cancer cell lines, JIMT-1 and T-47D, differing in their molecular characteristics, were transfected with a DCK expression vector and exposed to low-dose DAC (approximately IC20). Although transfection resulted in a significant DCK expression increase, further enhanced by DAC exposure, no transfection-induced changes were found at the global DNA methylation level or in cell viability. In parallel, an integrative approach was applied to decipher DAC-induced, methylation-mediated, transcriptomic reprogramming. Besides large-scale hypomethylation, accompanied by up-regulation of gene expression across the entire genome, DAC also induced hypermethylation and down-regulation of numerous genes in both cell lines. Interestingly, TET1 and TET2 expression halved in JIMT-1 cells after DAC exposure, while DNMTs’ changes were not significant. The protein digestion and absorption pathway, containing numerous collagen and solute carrier genes, ranking second among membrane transport proteins, was the top enriched pathway in both cell lines when hypomethylated and up-regulated genes were considered. Moreover, the calcium signaling pathway, playing a significant role in drug resistance, was among the top enriched in JIMT-1 cells. Although low-dose DAC demonstrated its ability to normalize the expression of tumor suppressors, several oncogenes were also up-regulated, a finding, that supports previously raised concerns regarding its broad reprogramming potential. Importantly, our research provides evidence about the involvement of active demethylation in DAC-mediated transcriptional reprogramming.

Targeting the ADPKD methylome using nanoparticle-mediated combination therapy

“…Previous studies have observed Aza-induced hypermethylation in the cancer genome and attributed this phenomenon to a transient alteration in gene transcription reflecting the immediate response of cells to perturbation, 49 or downregulated activity of TET1, a demethylating enzyme. 50 We observed Aza-specific hypermethylation at gene promoters involved in cancer, which may seem potentially promising for repressing genes driving cystic growth; however, it is important to also consider the effects of Aza-mediated transcriptional repression of genes important for proper kidney development. For example, while we observed hypermethylation at the promoter of the oncogene Myc , we also observed slight hypermethylation at the promoter of Pkd2 , whose reactivation has been shown to reverse the ADPKD phenotype.…”

The Role of Epigenetic Modifier Mutations in Peripheral T-Cell Lymphomas

“…Both AZA and DAC have chemical structures like cytosine, with the main difference being that their aromatic ring has one additional nitrogen, which replaces the carbon atom in the 5 position where the methylation takes place (Figure 3). Thus, DNMT3A and DNMT3B are unable to add the methyl group at the 5 position, because the nitrogen atom has no more free electrons to share [82][83][84]. Both AZA and DAC have the potential to treat peripheral Tcell lymphomas because of their ability to target abnormal DNA methylation patterns.…”

“…has no more free electrons to share [82][83][84]. Both AZA and DAC have the potential to treat peripheral T-cell lymphomas because of their ability to target abnormal DNA methylation patterns.…”

Decitabine regulates the resistance of Hep3B to sorafenib through demethylation

“…Epigenetics encompasses genetic variation unrelated to changes in DNA base sequences, including DNA methylation [12], chromatin remodeling, and histone acetylation. Among these, DNA methylation is the most extensively studied aspect of epigenetics.…”