DNA Demethylation Activity Research Articles

Epigenome editing revealed the role of DNA methylation of T-DMR/CpG island shore on Runx2 transcription

RUNX2 is a transcription factor crucial for bone formation. Mutant mice with varying levels of Runx2 expression display dosage-dependent skeletal abnormalities, underscoring the importance of Runx2 dosage control in skeletal formation. RUNX2 activity is regulated by several molecular mechanisms, including epigenetic modification such as DNA methylation. In this study, we investigated whether targeted repressive epigenome editing including hypermethylation to the Runx2-DMR/CpG island shore could influence Runx2 expression using Cas9-based epigenome-editing tools. Through the transient introduction of CRISPRoff-v2.1 and gRNAs targeting Runx2-DMR into MC3T3-E1 cells, we successfully induced hypermethylation of the region and concurrently reduced Runx2 expression during osteoblast differentiation. Although the epigenome editing of Runx2-DMR did not impact the expression of RUNX2 downstream target genes, these results indicate a causal relationship between the epigenetic status of the Runx2-DMR and Runx2 transcription. Additionally, we observed that hypermethylation of the Runx2-DMR persisted for at least 24 days under growth conditions but decreased during osteogenic differentiation, highlighting an endogenous DNA demethylation activity targeting the Runx2-DMR during the differentiation process. In summary, our study underscore the usefulness of the epigenome editing technology to evaluate the function of endogenous genetic elements and revealed that the Runx2-DMR methylation is actively regulated during osteoblast differentiation, subsequently could influence Runx2 expression.

Synergistic Differential DNA Demethylation Activity of Danshensu (Salvia miltiorrhiza) Associated with Different Probiotics in Nonalcoholic Fatty Liver Disease.

Nonalcoholic fatty liver disease (NAFLD) is a major hepatic disorder occurring in non-alcohol-drinking individuals. Salvianic acid A or Danshensu (DSS, 3-(3, 4-dihydroxyphenyl)-(2R)-lactic acid), derived from the root of Danshen (Salvia miltiorrhiza), has demonstrated heart and liver protective properties. In this work, we investigated the antioxidant activity and hepatoprotective activity of Danshensu alone and in combination with different agents, such as probiotic bacteria (Lactobacillus casei and Lactobacillus acidophilus), against several assays. The inhibition mechanism of the methylation gene biomarkers, such as DNMT-1, MS, STAT-3, and TET-1, against DSS was evaluated by molecular docking and RT-PCR techniques. The physicochemical and pharmacokinetic ADMET properties of DSS were determined by SwissADME and pkCSM. The results indicated that all lipid blood test profiles, including cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C), were reduced after the oral administration of Danshensu combined with probiotics (L. casei and L. acidophilus) that demonstrated good, efficient free radical scavenging activity, measured using anti-oxidant assays. ADMET and drug-likeness properties certify that the DSS could be utilized as a feasible drug since DSS showed satisfactory physicochemical and pharmacokinetic ADMET properties.

Substrate DNA length regulates the activity of TET 5-methylcytosine dioxygenases.

The ten-eleven translocation (TET) isoforms (TET1-3) play critical roles in epigenetic transcription regulation. In addition, mutations in the TET2 gene are frequently detected in patients with glioma and myeloid malignancies. TET isoforms can oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, by iterative oxidation. The in vivo DNA demethylation activity of TET isoforms may depend on many factors including enzyme's structural features, its interaction with DNA-binding proteins, chromatin context, DNA sequence, DNA length, and configuration. The rationale for this study is to identify the preferred DNA length and configuration in the substrates of TET isoforms. We have used a highly sensitive LC-MS/MS-based method to compare the substrate preference of TET isoforms. To this end, four DNA substrate sets (S1, S2, S3, S4) of different sequences were chosen. In addition, in each set, four different lengths of DNA substrates comprising 7-, 13-, 19-, and 25-mer nucleotides were synthesized. Each DNA substrate was further used in three different configurations, that is, double stranded symmetrically-methylated, double stranded hemi-methylated, and single stranded single-methylated to evaluate their effect on TET-mediated 5mC oxidation. We demonstrate that mouse TET1 (mTET1) and human TET2 (hTET2) have highest preference for 13-mer dsDNA substrates. Increasing or decreasing the length of dsDNA substrate reduces product formation. In contrast to their dsDNA counterparts, the length of ssDNA substrates did not have a predictable effect on 5mC oxidation. Finally, we show that substrate specificity of TET isoforms correlates with their DNA binding efficiency. Our results demonstrate that mTET1 and hTET2 prefer 13-mer dsDNA as a substrate over ssDNA. These results may help elucidate novel properties of TET-mediated 5mC oxidation and help develop novel diagnostic tools to detect TET2 function in patients.

DNA damage, demethylation and anticancer activity of DNA methyltransferase (DNMT) inhibitors

Role of DNA damage and demethylation on anticancer activity of DNA methyltransferase inhibitors (DNMTi) remains undefined. We report the effects of DNMT1 gene deletion/disruption (DNMT1−/−) on anticancer activity of a class of DNMTi in vitro, in vivo and in human cancers. The gene deletion markedly attenuated cytotoxicity and growth inhibition mediated by decitabine, azacitidine and 5-aza-4′-thio-2′-deoxycytidine (aza-T-dCyd) in colon and breast cancer cells. The drugs induced DNA damage that concurred with DNMT1 inhibition, subsequent G2/M cell-cycle arrest and apoptosis, and upregulated p21 in DNMT1+/+ versus DNMT1−/− status, with aza-T-dCyd the most potent. Tumor growth and DNMT1 were significantly inhibited, and p21 was upmodulated in mice bearing HCT116 DNMT1+/+ xenograft and bladder PDX tumors. DNMT1 gene deletion occurred in ~ 9% human colon cancers and other cancer types at varying degrees. Decitabine and azacitidine demethylated CDKN2A/CDKN2B genes in DNMT1+/+ and DNMT1−/− conditions and increased histone-H3 acetylation with re-expression of p16INK4A/p15INK4B in DNMT1−/− state. Thus, DNMT1 deletion confers resistance to DNMTi, and their anti-cancer activity is determined by DNA damage effects. Patients with DNMT1 gene deletions may not respond to DNMTi treatment.

DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4+ T cells of neonatal mice with E. coli pneumonia

Bacterial pulmonary infections are a major cause of morbidity and mortality in neonates, with less severity in older children. Previous studies demonstrated that the DNA of CD4+ T cells in the mouse lung, whose primary responsibility is to coordinate the immune response to foreign pathogens, is differentially methylated in neonates compared with juveniles. Nevertheless, the effect of this differential DNA methylation on CD4+ T cell gene expression and response to infection remains unclear. Here we treated E. coli-infected neonatal (4-day-old) and juvenile (13-day-old) mice with decitabine (DAC), a DNA methyltransferase inhibitor with broad-spectrum DNA demethylating activity, and performed simultaneous genome-wide DNA methylation and transcriptional profiling on lung CD4+ T cells. We show that juvenile and neonatal mice experienced differential demethylation in response to DAC treatment, with larger methylation differences observed in neonates. By cross-filtering differentially expressed genes between juveniles and neonates with those sites that were demethylated in neonates, we find that interferon-responsive genes such as Ifit1 are the most down-regulated methylation-sensitive genes in neonatal mice. DAC treatment shifted neonatal lung CD4+ T cells toward a gene expression program similar to that of juveniles. Following lung infection with E. coli, lung CD4+ T cells in neonatal mice exhibit epigenetic repression of important host defense pathways, which are activated by inhibition of DNA methyltransferase activity to resemble a more mature profile.

Methylation and expression of glucocorticoid receptor exon-1 variants and FKBP5 in teenage suicide-completers

A dysregulated hypothalamic-pituitary-adrenal (HPA) axis has repeatedly been demonstrated to play a fundamental role in psychiatric disorders and suicide, yet the mechanisms underlying this dysregulation are not clear. Decreased expression of the glucocorticoid receptor (GR) gene, which is also susceptible to epigenetic modulation, is a strong indicator of impaired HPA axis control. In the context of teenage suicide-completers, we have systematically analyzed the 5’UTR of the GR gene to determine the expression levels of all GR exon-1 transcript variants and their epigenetic state. We also measured the expression and the epigenetic state of the FK506-binding protein 51 (FKBP5/FKBP51), an important modulator of GR activity. Furthermore, steady-state DNA methylation levels depend upon the interplay between enzymes that promote DNA methylation and demethylation activities, thus we analyzed DNA methyltransferases (DNMTs), ten-eleven translocation enzymes (TETs), and growth arrest- and DNA-damage-inducible proteins (GADD45). Focusing on both the prefrontal cortex (PFC) and hippocampus, our results show decreased expression in specific GR exon-1 variants and a strong correlation of DNA methylation changes with gene expression in the PFC. FKBP5 expression is also increased in both areas suggesting a decreased GR sensitivity to cortisol binding. We also identified aberrant expression of DNA methylating and demethylating enzymes in both brain regions. These findings enhance our understanding of the complex transcriptional regulation of GR, providing evidence of epigenetically mediated reprogramming of the GR gene, which could lead to possible epigenetic influences that result in lasting modifications underlying an individual’s overall HPA axis response and resilience to stress.

METABOLOMIC PROFILING OF THE POLYPHENOL QUERCETIN RESPONSE IN LEUKEMIA CELL LINES

Epigenetic changes play a crucial role in hematological malignancies and the protein network that regulates these mechanisms offers potential pharmacologic regulation. Flavonoids might exert antitumoral effects through induction of apoptosis and chromatin remodeling. Our previous study showed that Quercetin (Qu) induced apoptosis, partly due to its DNA demethylating activity, through HDAC inhibition and enrichment of H3ac and H4ac in the promoter regions of the genes involved in the apoptosis pathway, leading to their transcription activation (Alvarez, Clinical Epigenetics 2018). The 1 H NMR spectra of the aqueous extract of exponentially growing HL-60 and U937 cell lines untreated and treated with Qu (50 mM, 48h) were obtained and analyzed by Principal Component Analysis (PCA). PCA revealed discrimination between the intracellular metabolome of the cell lines regarding Qu treatment. The subtraction of the mean 1 H NMR spectra of each treated and untreated cell line, as well as the PCA loadings, identified as major discriminators in HL-60 cell line, lactate, alanine, acetate, phosphocholine, taurine, glycine, glutamate and myo -inositol. Lactate was elevated in Qu treated cells whereas the other metabolites were decreased compared to control cells. For the U937 cell line, the major discriminators were the same, with the addition of creatine and the exclusion of lactate. All of them were decreased in treated samples. It could be concluded that Qu induced intracellular lactate accumulation in the HL-60 cell line, contributing to apoptosis induction. Acetate and N -acetyl groups levels were decreased in treated cells, which is consistent with our previous results as Qu treatment induced H3 and H4 acetylation that may induce an increase in acetyl-CoA consumption. In summary, the data presented pointed to metabolic changes measurable by NMR induced by Qu in AMLs cell lines and reflect the direct connection between metabolism and chromatin dynamics.

The N-terminal domain of TET1 promotes the formation of dense chromatin regions refractory to transcription.

TET (ten-eleven translocation) enzymes initiate active cytosine demethylation via the oxidation of 5-methylcytosine. TET1 is composed of a C-terminal domain, which bears the catalytic activity of the enzyme, and a N-terminal region that is less well characterized except for the CXXC domain responsible for the targeting to CpG islands. While cytosine demethylation induced by TET1 promotes transcription, this protein also interacts with chromatin-regulating factors that rather silence this process, the coordination between these two opposite functions of TET1 being unclear. In the present work, we uncover a new function of the N-terminal part of the TET1 protein in the regulation of the chromatin architecture. This domain of the protein promotes the establishment of a compact chromatin architecture displaying reduced exchange rate of core histones and partial dissociation of the histone linker. This chromatin reorganization process, which does not rely on the CXXC domain, is associated with a global shutdown of transcription and an increase in heterochromatin-associated histone epigenetic marks. Based on these findings, we propose that the dense chromatin organization generated by the N-terminal domain of TET1 could contribute to restraining the transcription enhancement induced by the DNA demethylation activity of this enzyme.

Analysis at the single-cell level indicates an important role of heterogeneous global DNA methylation status on the progression of lung adenocarcinoma

Aberrant DNA modifications affect the tumorigenesis and progression of lung cancer. However, the global methylation status of tumor cells and the heterogeneous methylation status of cells within the same tumor need further study. We used publicly available single-cell RNAseq data to investigate the impact and diversity of global methylation status on lung adenocarcinoma. Clustering cells into subgroups and cell differentiation pseudotime analysis, based on expression profile, demonstrated that the global methylation status was crucial to lung adenocarcinoma function and progression. Hypermethylated tumor cells had increased activity related to the hypoxia response. Hyper- and hypomethylated cells indicated upregulation in pathways involving focal adhesion and cell junctions. Pseudotime analysis showed that cell clusters with unique methylation activities were located at the ends of the putative trajectories, suggesting that DNA methylation and demethylation activities were essential to tumor cell progression. Expression of SPP1 was associated with the global methylation status of tumor cells and with patient prognosis. Our study identified the importance and diversity of global DNA methylation status by analysis at the single-cell level. Our findings provide new information about the global DNA methylation status of tumor cells and suggest new approaches for precision medical treatments for lung adenocarcinoma.

Effect of potassium on DNA methylation of aldosterone synthase gene.

Aldosterone synthase gene, CYP11B2 is regulated by potassium and angiotensin II (Ang II). We have reported that Ang II could change the DNA methylation status around transcription factor-binding sites and a transcription start site (TSS) and activate expression of CYP11B2. Similar to Ang II, small increases in extracellular potassium levels also increase CYP11B2 mRNA levels. Adrenocortical H295R cells were treated with different doses of potassium. Methylation analysis of CYP11B2 promoter region was done by bisulfite sequencing. CYP11B2 mRNA and protein levels, chromatin accessibility, methylation and demethylation activity were estimated. The transcriptional ability of CYP11B2 promoter with or without methylation was assessed. Potassium stimulation caused DNA demethylation around cyclic AMP responsive element binding protein 1 (CREB1) and nuclear receptor subfamily 4 group A (NR4A) family-binding sites and a TSS; demethylation was accompanied by recruitment of CREB1 and NR4A1 and increased chromatin accessibility of the CYP11B2 promoter. DNA methylation activity decreased in the nucleus. DNA demethylation at CpG1 (Ad1), CpG2 (Ad5) and CpG3 were detected within 2 to 4 days after potassium (16 mmol/l) stimulation. The changes reached a maximum level by day 7. DNA at CpG2 (Ad5) and CpG3 was re-methylated to levels that were similar to those of nontreated cells at day 9. Potassium treatment significantly reduced DNA methylation activity at days 7 and 9. DNA demethylation activity was not changed by potassium. : Potassium induced reversibly DNA demethylation, which switches the phenotype of CYP11B2 expression from an inactive to an active state.

Development of a new in vitro assay system for evaluating the effects of chemicals on DNA methylation.

Epigenetic toxicity, a phenomenon in which chemicals exert epigenetic effects and produce toxicity, has been attracting attention in recent years due to advances in toxicology accompanying the development of life sciences. However, it has been difficult to identify epigenetic toxicants due to the lack of a simple experimental system to evaluate epigenetic toxicity. In this study, we developed a prototype of an in vitro reporter assay system for assessing the effects of chemicals on DNA methylation using two promoters showing different degrees of DNA methylation, Agouti IAP and Daz1 promoters, and a luciferase reporter. The system successfully detected DNA demethylating activity using 5-azacytidine, a chemical having DNA demethylation activity, as a positive control chemical, and demethylation of cytosine of CpG in the promoter was confirmed by pyrosequencing analysis. Next, in order to improve the detection sensitivity of the DNA demethylating activity of this system, we tried to increase the basal level of methylation of the Daz1 promoter by pre-methylase treatment of the reporter vectors. As a result, the detection sensitivity of the system was successfully improved in cells where the basal level of methylation was indeed increased by methylase treatment. Thus, the developed assay system here is effective for the simple evaluation of chemicals that affect DNA methylation.

Analysis of Global Methylome and Gene Expression during Carbon Reserve Mobilization in Stems under Soil Drying.

In rice (Oryza sativa), a specific temporary source organ, the stem, is important for grain filling, and moderate soil drying (MD) enhanced carbon reserve flow from stems to increase grain yield. The dynamics and biological relevance of DNA methylation in carbon reserve remobilization during grain filling are unknown. Here, we generated whole-genome single-base resolution maps of the DNA methylome in the stem. During grain filling under MD, we observed an increase in DNA methylation of total cytosines, with more hypomethylated than hypermethylated regions. Genes responsible for DNA methylation and demethylation were up-regulated, suggesting that DNA methylation changes in the stem were regulated by antagonism between DNA methylation and demethylation activity. In addition, methylation in the CG and CHG contexts was negatively associated with gene expression, while that in the CHH context was positively associated with gene expression. A hypermethylated/up-regulated transcription factor of MYBS2 inhibited MYB30 expression and possibly enhanced β-Amylase5 expression, promoting subsequent starch degradation in rice stems under MD treatment. In addition, a hypermethylated/down-regulated transcription factor of ERF24 was predicted to interact with, and thereby decrease the expression of, abscisic acid 8'-hydroxylase1, thus increasing abscisic acid concentration under MD treatment. Our findings provide insight into the DNA methylation dynamics in carbon reserve remobilization of rice stems, demonstrate that MD increased this remobilization, and suggest a link between DNA methylation and gene expression in rice stems during grain filling.

Anticancer efficacy of 6-thioguanine loaded chitosan nanoparticles with or without curcumin

6-Thioguanine encapsulated chitosan nanoparticles (6-TG-CNPs) has formulated by the ionic-gelation method. Morphologically, the 6-TG-CNPs were spherical and showed mean size, PDI, zeta potential, and entrapment efficiency of 261.63 ± 6.01 nm, 0.34 ± 0.10, +15.97 ± 0.46 mV and 44.27%, respectively. The IR spectra confirmed the 6-TG complex with chitosan. The in vitro drug release profile of 6-TG-CNPs revealed an increase in sustained-release (91.40 ± 1.08% at 48 h) at pH 4.8 compared to less sustained-release (73.96 ± 1.12% at 48 h) at pH 7.4. The MTT assay was conducted on MCF-7 and PA-1 cell lines at 48 h incubation to determine % cell viability. The IC50 values of 6-TG, 6-TG-CNPs, and curcumin for MCF-7 were 23.09, 17.82, and 15.73 μM, respectively. Likewise, IC50 values of 6-TG, 6-TG-CNPs, and curcumin for PA-1 were 5.81, 3.92, and 12.89 μM, respectively. A combination of 6-TG-CNPs (IC25) with curcumin (IC25) on PA-1 and MCF-7 showed % cell viability of 43.67 ± 0.02 and 49.77 ± 0.05, respectively. The in vitro cytotoxicity potential in terms of % cell viability, early apoptosis, G2/M phase arrest, and DNA demethylating activity of 6-TG-CNPs alone and combination with curcumin proved to be more effective than that of 6-TG on PA-1 cells.

Противоопухолевая активность индол-3-карбинола в клетках рака молочной железы: фенотип - генетический паттерн - обращение ДНК-метилирования

The effect of indole-3-carbinol on a number of functions and characteristics of MDA-MB-231 breast cancer cells and MCF-10A healthy breast tissue cells has been studied. It was shown that indole-3-carbinol significantly reduced the proliferation and migration of MDA-MB-231 cells and does not affect these functions in MCF-10A cells. Incubation of MDA-MB-231 tumor cells with indole-3-carbinol (100 uM) for 48 h resulted in a marked decrease in the expression of the Wnt cascade genes, CCND1 (by 28%), SP1 (by 44%), CDK6 (by 47%), as well as EGFR (by 64%) and FASN (by 22%) genes. Incubation of MCF-10A cell line under the same conditions induced a noticeable decrease in expression of only two genes, EGFR (by 16%) and CDK6 (by 9%). In addition, indole-3-carbinol was also shown to manifest a selective DNA demethylation activity in breast tumor cells and to reverse the process of abnormal methylation and functional blockage of the anti-tumor WIF1 gene. These data indicate that drags containing indole-3-carbinol as an active component can be potential regulators of epigenetic processes in the treatment of breast cancer and other tumors. indole-3-carbinol, breast cancer, epigenetics, Wnt

NRF2 Is Targeted By the Polyphenol Quercetin and Induces Apoptosis, in Part, through up Regulation of Pro Apoptotic Mirs

Nuclear factor-erythroid 2 related factor (NRF2) is involved in cell defense and survival against endogenous and exogenous stress. Constitutively active Nrf2 in malignant cells increases the expression of cytoprotective genes and consequently, enhances proliferation via metabolic reprograming and inhibition of apoptosis (Leinonem, Advances in cancer Research, 2014). NRF2 is persistently activated in many human tumors, including acute myelogenous leukemia thus, inhibition of NRF2 activity may be a promising strategy for leukemia therapy. Flavonoids, present in vegetables, fruit and propolis, might exert antitumoral effects through induction of apoptosis and chromatin remodeling (Link, Biochem Pharmacol., 2010). A previous study from our group showed that Quercetin (Qu), a natural polyphenolic flavonoid compound, induced apoptosis, partly due to its DNA demethylating activity, through HDAC inhibition and by the enrichment of H3ac and H4ac in the promoter regions of genes involved in the apoptosis pathway, leading to their transcription activation (Alvarez, Clinical epigenetics 2018). In the present study, we evaluated the effect of Qu as a modulator of NRF2. This study was performed in vivo in human xenograft acute myeloid leukemia (AML) models, and in vitro using leukemia cell lines. Qu treatment (50 µM Qu) for 48h downregulated HDAC4, NRF2 and p-NRF2 at protein levels (p<0.05; p<0.005; p<0.005 respectively). Imaging Flow Cytometry (AMNIS, ImageStream ISX mkIITM) and Confocal Microscopy evidenced a decrease in NRF2 nuclear localization. Furthermore, combined treatment with the proteasome inhibitor MG132 prevented degradation of NRF2, indicating that treatment increased proteasomal degradation. Loss of NRF2 decreases HDAC4, a redox sensitive histone deacetylase, resulting in an increased expression of miR-1 and miR-206 (Singh, J Clin Invest. 2013). Herein, expression profile of 84 miRNAs (Apoptosis miRNA PCR array) were performed in samples from human xenograft model. Treatment up-regulated the expression profile of 5% (n=4) of the 84 miRNAs evaluated, corresponding exclusively to miRNAs that target anti-apoptotic genes and to miRNAs that have been demonstrated to have pro-apoptotic functions. Furthermore, expression levels of miR-1, miR-133a/b, which target anti-apoptotic genes and miR-206, a pro apoptotic miR, were validated in xenograft model samples, resulting in a significant up-regulation of the expression levels in treated animals compared to controls (p<0.05). In addition, lentiviral sh down regulation of NRF2, led to an increased apoptosis, decreased cell survival and an up regulation of miRNA 206 expression in Qu treated cells. In summary, Qu might induce programmed cell death in part, by decreasing NRF2 nuclear localization, by inducing NRF2 proteasomal degradation and down regulation of HDAC4 which led to up-regulation of pro apoptotic miRNAs. Disclosures No relevant conflicts of interest to declare.

34.3 EFFECTS OF THIRD-TRIMESTER EQUIVALENT ETHANOL EXPOSURE ON NEURODEVELOPMENTAL GENE EXPRESSION

Third-trimester alcohol exposure has profound effects on neurodevelopmental gene expression, especially in brain regions that develop in late gestation such as the prefrontal cortex (PFC). Ethanol (EtOH) induces poly(ADP-ribose) polymerase (PARP) enzymatic activity in cell and animal models, which reportedly participates in 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) removal. We hypothesized that EtOH increases PARP activity, inducing its DNA demethylation activity, leading to increased expression of genes involved in neuronal development and cellular differentiation.

Novel prodrugs of decitabine with greater metabolic stability and less toxicity

BackgroundDNA demethylation therapy is now used in practice for hematological tumors and is being developed for solid tumors. Nevertheless, it is difficult to achieve stable pharmacokinetics with the current DNA-demethylating agents, azacitidine (AZA) and decitabine (DAC), because of their rapid deamination by cytidine deaminase in vivo and spontaneous hydrolytic cleavage. Here, we aimed to develop metabolically stable prodrugs of AZA and DAC as novel DNA-demethylating agents.ResultsThirty-five 5′-O-trialkylsilylated AZAs/DACs were synthesized with potential resistance to deamination. Out of these, 11 compounds exhibited demethylating activity similar to that of DAC and guadecitabine, and a suitable aqueous solubility. Pharmacokinetic analysis in mice showed that OR-2003 displayed the highest serum concentration and the area under the curve in an intraperitoneal experiment, whereas OR-2100 exhibited high stability to cytidine deaminase. Treatment of cells with OR-2003 and OR-2100 depleted DNA methyltransferase 1 completely and induced both gene-specific and genome-wide demethylation. The treatment suppressed the growth of multiple types of cancer cells and induced re-expression of tumor suppressor genes. The anti-tumor effect and DNA demethylation effect of OR-2003 and OR-2100 were comparable to that of DAC with fewer adverse effects in vivo.ConclusionsWe developed two novel prodrugs of DAC that exhibited greater stability, comparable DNA demethylation activity, and less toxicity. These compounds are expected to overcome the difficulty in achieving stable pharmacokinetics in patients, leading to maximum DNA demethylation activity with minimum adverse effects.

Molecular Mechanisms Underlying the Link between Diet and DNA Methylation

DNA methylation is a vital modification process in the control of genetic information, which contributes to the epigenetics by regulating gene expression without changing the DNA sequence. Abnormal DNA methylation—both hypomethylation and hypermethylation—has been associated with improper gene expression, leading to several disorders. Two types of risk factors can alter the epigenetic regulation of methylation pathways: genetic factors and modifiable factors. Nutrition is one of the strongest modifiable factors, which plays a direct role in DNA methylation pathways. Large numbers of studies have investigated the effects of nutrition on DNA methylation pathways, but relatively few have focused on the biochemical mechanisms. Understanding the biological mechanisms is essential for clarifying how nutrients function in epigenetics. It is believed that nutrition affects the epigenetic regulations of DNA methylation in several possible epigenetic pathways: mainly, by altering the substrates and cofactors that are necessary for proper DNA methylation; additionally, by changing the activity of enzymes regulating the one-carbon cycle; and, lastly, through there being an epigenetic role in several possible mechanisms related to DNA demethylation activity. The aim of this article is to review the potential underlying biochemical mechanisms that are related to diet modifications in DNA methylation and demethylation.

The polyphenol quercetin induces cell death in leukemia by targeting epigenetic regulators of pro-apoptotic genes

BackgroundIn the present study, we investigated the molecular mechanisms underlying the pro-apoptotic effects of quercetin (Qu) by evaluating the effect of Qu treatment on DNA methylation and posttranslational histone modifications of genes related to the apoptosis pathway. This study was performed in vivo in two human xenograft acute myeloid leukemia (AML) models and in vitro using HL60 and U937 cell lines.ResultsQu treatment almost eliminates DNMT1 and DNMT3a expression, and this regulation was in part STAT-3 dependent. The treatment also downregulated class I HDACs. Furthermore, treatment of the cell lines with the proteasome inhibitor, MG132, together with Qu prevented degradation of class I HDACs compared to cells treated with Qu alone, indicating increased proteasome degradation of class I HDACS by Qu. Qu induced demethylation of the pro-apoptotic BCL2L11, DAPK1 genes, in a dose- and time-dependent manner. Moreover, Qu (50 μmol/L) treatment of cell lines for 48 h caused accumulation of acetylated histone 3 and histone 4, resulting in three- to ten fold increases in the promoter region of DAPK1, BCL2L11, BAX, APAF1, BNIP3, and BNIP3L. In addition, Qu treatment significantly increased the mRNA levels of all these genes, when compared to cells treated with vehicle only (control cells) (*p < 0.05).ConclusionsIn summary, our results showed that enhanced apoptosis, induced by Qu, might be caused in part by its DNA demethylating activity, by HDAC inhibition, and by the enrichment of H3ac and H4ac in the promoter regions of genes involved in the apoptosis pathway, leading to their transcription activation.

DNA Demethylation by DNMT3A and DNMT3B in vitro and of Methylated Episomal DNA in Transiently Transfected Cells

The DNA methylation program in vertebrates is an essential part of the epigenetic regulatory cascade of development, cell differentiation, and progression of diseases including cancer. While the DNA methyltransferases (DNMTs) are responsible for the in vivo conversion of cytosine (C) to methylated cytosine (5mC), demethylation of 5mC on cellular DNA could be accomplished by the combined action of the ten-eleven translocation (TET) enzymes and DNA repair. Surprisingly, the mammalian DNMTs also possess active DNA demethylation activity in vitro in a Ca2+- and redox conditions-dependent manner, although little is known about its molecular mechanisms and occurrence in a cellular context. In this study, we have used LC-MS/MS to track down the fate of the methyl group removed from 5mC on DNA by mouse DNMT3B in vitro and found that it becomes covalently linked to the DNA methylation catalytic cysteine of the enzyme. We also show that Ca2+ homeostasis-dependent but TET1/TET2/TET3/TDG-independent demethylation of methylated episomal DNA by mouse DNMT3A or DNMT3B can occur in transfected human HEK 293 and mouse embryonic stem (ES) cells. Based on these results, we present a tentative working model of Ca2+ and redox conditions-dependent active DNA demethylation by DNMTs. Our study substantiates the potential roles of the vertebrate DNMTs as double-edged swords in DNA methylation-demethylation during Ca2+-dependent physiological processes.