Unknown,Transcriptomics,Genomics,Proteomics

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Methylation analysis of locally advanced breast tumors treated with two drugs-doxorubicin and 5-fluorouracil

ABSTRACT: Genome wide DNA methylation profiling of locally advanced breast tumors before and after treatment with doxorubicin and 5-fluorouracil Mitomycin C Bisulphite converted DNA from the 33 paired tumor samples and 9 normal samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2. After preprocessing, seven paired samples treated with doxorubicin were excluded due to low methylation levels, resulting in 26 paired tumor samples that were further analyzed.

ORGANISM(S): Homo sapiens

SUBMITTER: Jovana Klajic

PROVIDER: E-GEOD-59724 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Despite extensive progress in Huntingtonâ??s Disease (HD) research, very little is known about the association of epigenetic variation and HD pathogenesis in human brain tissues. Moreover, its contribution to the tissue-specific transcriptional regulation of the huntingtin gene (HTT), in which HTT expression levels are highest in brain and testes, is currently unknown. To investigate the role of DNA methylation in HD pathogenesis and tissue-specific expression of HTT, we utilized the Illumina HumanMethylation450K BeadChip array to measure DNA methylation in a cohort of age-matched HD and control human cortex and liver tissues. In cortex samples, we found minimal evidence of HD-associated DNA methylation at probed sites after correction for cell heterogeneity but did observe an association to age of disease onset. By contrast, comparison of matched cortex and liver samples revealed tissue-specific DNA methylation of the HTT gene region at 38 sites (FDR < 0.05). Importantly, we identified a novel differentially methylated binding site in the HTT proximal promoter for the transcription factor CTCF. This CTCF site displayed increased occupancy in cortex, where HTT expression is higher, compared to liver. Additionally, CTCF silencing reduced the activity of a HTT promoter-reporter construct, suggesting that CTCF plays a role in regulating HTT promoter function. Overall, although we were unable to detect HD-associated DNA methylation alterations at queried sites, we found that DNA methylation may be correlated to age of disease onset in cortex tissues. Moreover, our data suggest that DNA methylation may, in part, contribute to tissue-specific HTT transcription through differential CTCF occupancy. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation measures in human cortex tissue (n = 13), with a subset of matched liver tissues (n = 5) , from a cohort of HD (n = 7) and control (n = 6) individuals in order to identify potential HD-related DNA methylation aberration in the brain as well as tissue-specific DNA methylation variation at the HTT gene locus.

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Methylation analysis of locally advanced breast tumors treated with two drugs-doxorubicin and 5-fluorouracil

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