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Examination of genome-wide methylation changes in lung cancer cell lines A549 (A) and HTB56 (H) [HumanMethylation27 BeadChip experiments]

ABSTRACT: Cancer cell phenotypes are partially determined by epigenetic specifications such as DNA methylation. Metastasis development is a late event in cancerogenesis and might be associated with epigenetic alterations. Here, we analyzed genome wide DNA methylation changes that were associated with pro-metastatic phenotypes in non-small cell lung cancer using the Illumina HumanMethylation27 BeadChip platform.

ORGANISM(S): Homo sapiens

PROVIDER: GSE52144 | GEO | 2013/12/18

SECONDARY ACCESSION(S): PRJNA227470

REPOSITORIES: GEO

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Examination of genome-wide methylation changes in lung cancer cell lines A549 (A) and HTB56 (H) [HumanMethylation27 BeadChip experiments]

2013-12-18 | E-GEOD-52144 | biostudies-arrayexpress

Examination of genome-wide methylation changes in lung cancer cell lines A549 (A) and HTB56 (H) [RRBS-Seq experiments]

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Examination of genome-wide methylation changes in lung cancer cell lines A549 (A) and HTB56 (H) [RRBS-Seq experiments]

Project description:Cancer cell phenotypes are partially determined by epigenetic specifications such as DNA methylation. Metastasis development is a late event in cancerogenesis and might be associated with epigenetic alterations. Here, we analyzed genome wide DNA methylation changes that were associated with pro-metastatic phenotypes in non-small cell lung cancer with Reduced Representation Bisulfite Sequencing. DNMT-inhibition by 5-Azacytidine at low concentrations reverted the pro-metastatic phenotype. 5-Azacytidine led to preferential loss of DNA methylation at sites that were DNA hypermethylated during the in vivo selection. Changes in DNA methylation persisted over time. Keywords: Methylation profiling by high throughput sequencing We studied genome-wide methylation changes in lung cancer cell lines A549 (A) and HTB56 (H). We generated NSCLC lines with highly increased propensity to form tumor nodules in murine lungs after intravenous injections. In addition to the normal cell lines (0R) we analyzed the methylome of the the cell lines after three rounds of in vivo selection towards a highly metastatic phenotype (3R). Next we studied changes in the methylome of highly metastatic cell lines after DNA Methyltransferase inhibition by 5-Azacytidine treatment at low concentrations (250 nM & 1000 nM) for 6 days. During treatment cells were supplemented with fresh medium every 48 hours. After 6 days of 5-Azacytidine exposure, cells were washed three times with PBS to wash out the drug. The cells were released for additional 7 days in regular medium. We followed up the DNA methylation changes at day 13 of the experiment.

2013-12-18 | E-GEOD-52140 | biostudies-arrayexpress

DNA Methyltransferase inhibition reverses epigenetically embedded phenotypes in lung cancer preferentially affecting Polycomb target genes

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DNA Methyltransferase inhibition reverses epigenetically embedded phenotypes in lung cancer preferentially affecting Polycomb target genes

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Global DNA methylation: Uncommon event in Oral Lichenoid Disease [Illumina HumanMethylation27 BeadChip]

Project description:Purpose Accumulating evidence indicates aberrant DNA methylation is closely related to oral carcinogenesis, and it has been shown that methylation changes might be used as prognostic biomarker in oral squamous cell carcinoma. Oral lichenoid disease (OLD) is the most common oral potentially malignant disorder in our region. In this study, we have performed a wide DNA methylation study of a series of oral lichenoid disease in order to assess the relevance of DNA methylation changes in this premalignant disorder. Experimental Design Discovery phase utilized HumanMethylation27 DNA Analysis BeadChip assay in 18 OLD and 5 control samples. The differently methylated loci and the global DNA methylation surrogate LINE-, were further validated in an independent sample set consisting in 158 OLD and 65 controls. Results DNA methylation profile of the OLD showed only minor significant differences when compared to controls. MGC40178, ADORA1 and LINE-1 were slightly hypomethylated in 23, 40 and 43 % of the OLD samples respectively, while only in 13, 18 and 15% of the controls. Conclusions In summary, our data indicates that the frequency of aberrant DNA alteration is very low in OLD, which support the low rate of malignization of this oral potentially malignant disorder.

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2012-04-29 | E-GEOD-33065 | biostudies-arrayexpress

DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time

Project description:We examined genome-wide DNA methylation with 22 human iPSC lines derived from different cell types and human ESC lines using Illumina’s Infinium HumanMethylation27 and focused on aberrant methylation sites in iPSCs for up to 42-week continuous cultivation. The iPSCs exhibited distinct epigenetic distances from ESCs at early passage. Continuous passaging of the iPSCs diminishes these differences between iPSCs and ESCs.

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