Expression profiling of DNMT1 inhibitors in HCT116 cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Paul Mason
PROVIDER: E-GEOD-30985 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2016-06-30 | E-GEOD-72686 | biostudies-arrayexpress
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2022-07-12 | PXD034078 | Pride
Project description:Recently, various groups managed to isolate naïve human embryonic stem cell (hESC) state in vitro has come into acceptance. However, a thorough epigenetic characterization of this human ground state, defined as a state without any epigenetic restrictions, and how that compares to mouse is currently lacking. Also, the epigenomic remodeling required to obtain the ground state, and the important transient processes occurring during the remodeling, have remained elusive in human. Here, we address these issues by using an untargeted mass spectrometry-based (MS) approach to profile the histone epigenome in a time-resolved experimental design. Special care was given to defining the naïve hESC state that was reached over 12 passages (P12, 37 days) in feeder-free conditions in this study. We found that conversion is a multi-staged process with a prominent cellular disturbance after stimulation (P3), an increase in cell proliferation between P3 and P6 and a naïve cell state stabilizing between P9 and P12. In total, 20 different histone post-translational modifications (hPTMs) changed significantly over time from primed to naïve hESCs. Most notably, H3K27me3 is the most prominently increasing hPTM in naïve hESCs, in line with what we recently described in mouse. Essentially, we present a first roadmap of the changing human histone epigenome from primed to naïve state and emphasize that the overlap with mouse hints at a conserved Mammalian epigenetic signature of the ground state.
2019-11-27 | PXD013067 | Pride
Project description:Background Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization behavior of various degrees of mismatch (MM) structure has not been extensively studied. Here, we present the results of two large-scale microarray experiments on S.cerevisiae and H.sapiens genomic DNA, to explore MM oligonucleotide behavior with real sample mixtures under tiling-array conditions. Results We examined all possible nucleotide substitutions at the central position of 36-nucleotide probes, and found that nonspecific binding by MM oligos depends upon the individual nucleotide substitutions they incorporate: C->A, C->G and T->A (yielding purine-purine mispairs) are most disruptive, whereas A->X were least disruptive. We also quantify a marked GC skew effect: substitutions raising probe GC content exhibit higher intensity (and vice versa). This skew is small in highly-expressed regions (±0.5% of total intensity range) and large (±2% or more) elsewhere. Multiple mismatches per oligo are largely additive in effect: each MM added in a distributed fashion causes an additional 21% intensity drop relative to PM, three-fold more disruptive than adding adjacent mispairs (7% drop per MM). This SuperSeries is composed of the following subset Series: GSE13172: Mismatch oligonucleotides in human GSE13174: Mismatch oligonucleotides in yeast Refer to individual Series
2010-05-05 | E-GEOD-13175 | biostudies-arrayexpress
Project description:The DNA hypomethylating drug decitabine maintains normal hematopoietic stem and progenitor cell (HSPC) self-renewal but induces terminal differentiation in acute myeloid leukemia (AML) cells. To better understand the basis for this contrasting treatment effect, the baseline expression of key lineage-specifying transcription factor (TF) (eg., CEBPa) and key late differentiation TF (CEBPe), was examined in normal, myelodysplastic (MDS) and AML primary cells and cell lines. To appreciate the role of differentiation in hypomethylation of some CpG by decitabine treatment but not others, promoter CpGs, analyzed by microarray and mass spectrometry, were categorized by the direction of methylation change during normal myeloid differentiation. In MDS/AML cells, high expression of CEBPa, relatively low expression of CEBPe (a gene target of CEBPa), hypermethylation of CEBPe promoter CpG, and the methylation pattern at differentiation sensitive promoter CpGs analyzed by microarray, suggested lineage-commitment and aberrant epigenetic repression of late differentiation genes. DNA hypomethylation in response to decitabine was greatest at CpGs that are hypomethylated during normal myeloid differentiation. In contrast, normal HSPC treated with decitabine retained immature morphology, and methylation significantly decreased at CpG that are hypermethylated during myeloid differentiation. Partial differentiation at baseline, and repression of key late differentiation genes by epigenetic means, likely plays a role in methylation and phenotype responses of AML cells treated with decitabine. Bisulphite converted DNA from the 208 samples were hybridised to the Illumina Cancel Panel 1 GPL9183 methylation assay
2011-07-01 | E-GEOD-29047 | biostudies-arrayexpress
Project description:Background: Epigenetic modifications such as methylation silencing of genes with CpG-island-associated promoters is frequently observed in cancer. Studies regarding the implications of epigenetic modifications in osteosarcoma (OS) have been limited. The epigenetic drug decitabine is a potential re-activator of silenced genes through de-methylation, and is currently undergoing clinical trials for cancer treatment. No study to date has utilized decitabine to modify gene expression in OS-derived cells to identify gene-specific methylation targets that may have therapeutic importance. The objective of this study was to measure the response of the OS cell line, U-2OS, to decitabine treatment both in vitro and in vivo. Results: Genome-wide screening was used to distinguish decitabine-dependent changes in gene expression in U-2OS and to identify responsive loci with de-methylated CpG regions. U-2OS xenografts were established in the sub-renal capsule of immune-deficient mice to study the effect of decitabine in vivo on tumor growth and differentiation. Genome-wide screening of U-2OS cells in vitro revealed that decitabine treatment at low-dosage (1 µM) caused a significant induction (p<0.0025) in the expression of 88 genes, 13 had a â?¥2-fold change, 11 of which had CpG-island-associated promoters. Interestingly, 6 of these 11 were pro-apoptotic genes. 1 µM decitabine resulted in a significant induction of cell death in U-2OS cells in vitro (p<0.05). Decitabine treatment also reduced tumor volume size significantly (p<0.05) in U-2OS in vivo at a 2.5 mg/kg dose. Histological analysis of U-2OS xenograft sections revealed a lower mitotic activity (p<0.0001), a higher bone matrix production (p<0.0001), and higher apoptosis (p = 0.0329) after treatment. The 6 pro-apoptotic genes were also induced to â?¥2-fold in vivo. Quantitative Methylation Pyrosequencing (Pyro Q-CpG) showed that 4 pro-apoptotic genes had CpG-island DNA de-methylation as a result of treatment in vitro and in vivo. Conclusion: Our data provide new insights regarding the use of epigenetic modifiers in OS, and have important implications for therapeutic trials involving demethylation drugs. The findings of this study suggest an epigenetic mechanism, whereby OS tumor cells silence expression of pro-apoptotic genes through promoter-CpG methylation, to maintain high proliferation capacity and continuous growth. Experiment Overall Design: Total RNA was extracted using the RNeasy kit (Qiagen, Germany) from duplicate experiments of U-2OS cells at Day3 after treatment with 1 µM decitabine or medium alone (control). In each experiment RNA yields were pooled from two independent cultures per treatment arm to minimize experimental noise. For each case, 10 µg of RNA was labeled and hybridized to the Affymetrix HG-U133A GeneChips using the manufacturerâ??s protocol (Affymetrix, Santa Clara, CA) by the Center of Applied Genomics at the Hospital for Sick Children (Toronto, Canada). Data were extracted using the Microarray Suite (MAS) version 5.0 (Affymetrix) and linearly scaled to achieve an average intensity of 150 across each chip. The candidate gene list obtained from the MAS 5.0-extracted data was selected by eliminating genes that were not present in at least one experiment. The arrays were subjected to a pair wise comparison using MAS 5.0, with signal intensities from the no-treatment cells as the baseline. The statistical significance for the change of expression for each probe set between the decitabine treated and control was calculated by the MAS5.0 software. The criteria for gene selection for real-time expression validation analysis was based on the statistically significant up-regulation (p<0.0025) and fold change of â?¥ 2 for expression after decitabine treatment. The gene list was annotated based on the NetAffx data-base (http://www.affymetrix.com/analysis /index.affx) and further verified using the Human Genome Browser data base (http://genome.ucsc.edu/)
2008-06-15 | E-GEOD-7454 | biostudies-arrayexpress
Project description:Epigenetic drugs actively altering the epigenome of tumours have been developed for use in anti-cancer therapies. However, these drugs could potentially also affect the DNA methylome of spermatozoa that seems to be essential for male fertility. Here, we analysed possible direct and transgenerational effects of the epigenetic drug decitabine on the DNA methylome of spermatozoa. Our analysis revealed the absence of gross differences between the spermatozoal methylome of decitabine treated and untreated animals as well as between their F3 generations. Interestingly, the methylomes of spermatozoa from the selected mice of the F3-generations were also highly similar to the analysed parental samples. We studied genome-wide DNA methylation changes in decitabine treated mice and their F3-generation. For this, we treated male C57BL/6 mice (seven weeks old) for seven weeks (intraperitoneal, three times per week) with the DNMT inhibitor decitabine (5-aza-2'-deoxycytidine, 0.1 µg/g, n = 17) or with vehicle (7.5 % dimethyl sulfoxide in phosphate buffered saline, n = 16). The dose of decitabine per treatment was chosen according to the clinical application regimens in humans and refer to previous mice studies using this drug (Kelly et al, 2003; Oakes et al, 2007). For the investigation of transgenerational effects, 10 treated and untreated male mice were mated with four untreated female C57BL/6 mice each. The offspring was considered as F1-generation. The F2- and F3-generations were obtained by an identical mating scheme. Thus, only the P-generation males were treated with decitabine or control vehicle, the F1-, F2- and F3-generations were not subjected to any treatment. During this study, all mice were housed at 24 °C on a 12-h light, 12-h dark cycle and provided with food and tap-water ad libitum.
2015-03-03 | E-GEOD-59575 | biostudies-arrayexpress