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Patterns of changes in DNA global methylation following the treatment with GC/RA and with GC/RA plus AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines

ABSTRACT: Comprehensive characterization of the DNA methylome regulated by the treatment with glucocorticoids (GC) and retinoic acid (RA) alone and combined with AZA/SAHA and the relationship of these features with the status of BRG1 and MYC in lung cancer cell lines. MYC amplified cell lines and BRG1 mutant cell lines were treated with glucocorticoids (GC) and retinoic acid (RA) alone and combined with AZA/SAHA and their methylation was then measured

ORGANISM(S): Homo sapiens

SUBMITTER: Manel Esteller

PROVIDER: E-GEOD-66087 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Treatment with GC/RA and combination with AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-09-08 | E-GEOD-66245 | biostudies-arrayexpress

Identification of expresion patterns after treatment with GC/RA and combination with AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines

Project description:To development our gene expression approach , we have employed whole genome microarray expression profiling as a discovery platform to identify genes potentialy regulated by the treatment with glucocorticoids (GC) and retinoic acid (RA) alone and combined with AZA/SAHA and the relationship of these features with the status of BRG1 and MYC in lung cancer cell lines. MYC amplified cell lines and BRG1 mutant cell lines were treated with glucocorticoids (GC) and retinoic acid (RA) alone and combined with AZA/SAHA and their expression was then measured

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An integrated systems biology approach reveals positive and negative effects of suberoylanilide hydroxamic acid (SAHA) on HIV reactivation from latency

Project description:Suberoylanilide hydroxamic acid (SAHA) has been assessed in clinical trials as part of a “shock and kill” strategy to cure HIV-infected patients. While it was effective at inducing expression of HIV RNA "shock" , treatment with SAHA did not result in the reduction of reservoir size "kill". We therefore utilized a systems biology approach to dissect the mechanisms of action of SAHA that may explain its limited success in “shock and kill” strategies. CD4+ T cells from HIV seronegative donors were treated with 1 uM SAHA or its solvent dimethyl sulfoxide for 24 hours. Differential protein expression and post-translational modification was measured with two-dimensional liquid chromatography - tandem mass spectrometry iTRAQ proteomics. Gene expression changes were assessed by Illumina microarrays. Using limma package in the R computing environment, we identified 185 proteins, 18 phosphorylated forms, 4 acetylated forms and 2,982 genes, whose expression was modulated by SAHA. A protein interaction network integrating these 4 data types identified the transcriptional regulator HMGA1 to be upregulated by SAHA at the transcript, protein and acetylated protein levels. HMGA1 has been shown to repress HIV transcription, which is not optimal with respect to a shock and kill strategy. Further functional category assessment of proteins and genes modulated by SAHA identified gene ontology terms related to NFB signaling, protein folding and autophagy, which are all relevant to HIV reactivation. In summary, this study identified a number of host factors that may be therapeutically targeted to achieve more potent HIV reactivation in the “shock and kill” treatment, when using SAHA, either through modification of SAHA itself or through combination with other latency reversing agents. Finally, proteome profiling highlighted a number of potential adverse effects of SAHA, which transcriptome profiling alone would not have identified.

2015-09-10 | PXD002150 | Pride

Patterns of changes in DNA global methylation following the treatment with GC/RA and with GC/RA plus AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines

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Global mRNA expression profiling of murine primary PDAC cells following JQ1 or SAHA monotherapy as well as JQ1-SAHA combination therapy

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2020-10-15 | PXD005911 | Pride

Phosphoproteome of RA-responsive and RA-resistant breast cancer cell lines

2016-07-05 | PXD004357 | Pride

miRNA expression data from human hepatic stellate cell line LX2 treated with suberoylanilide hydroxamic acid (SAHA) or valproic acid (VPA)

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