Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Differential DNA methylation profiles in estrogen-pre-exposed breast epithelial cells

ABSTRACT: This study tried to determine whether exposure of breast stem/progenitor cells to estrogen disrupts the epigenome of progeny epithelial cells. DNA methylation profiles were compared between control and pre-exposed epithelial cells using a genome-wide detection method called MeDIP-chip. Keywords: MeDIP-chip Breast stem/progenitor cells were continuously exposed to 17beta-estradiol (E2, 70 nM) or DMSO (vehicle control) for two weeks and then placed on 2-dimensional collagen substratum for 2-3 weeks for epithelial cell differentiation. DNA from control and pre-exposed cells were extracted and MeDIP ssays were performed using antibodies against 5-methylcytosine. The immunoprecipitated and input DNA were used to probe the Agilent human CpG island microarray. Dye-swap experiments were also performed.

ORGANISM(S): Homo sapiens

SUBMITTER: Alfred Cheng

PROVIDER: E-GEOD-7844 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome.

Cheng Alfred S L AS Culhane Aedín C AC Chan Michael W Y MW Chan Michael W Y MW Venkataramu Chinnambally R CR Ehrich Mathias M Nasir Aejaz A Rodriguez Benjamin A T BA Liu Joseph J Yan Pearlly S PS Quackenbush John J Nephew Kenneth P KP Yeatman Timothy J TJ Huang Tim H-M TH

Cancer research 20080301 6

Estrogen imprinting is used to describe a phenomenon in which early developmental exposure to endocrine disruptors increases breast cancer risk later in adult life. We propose that long-lived, self-regenerating stem and progenitor cells are more susceptible to the exposure injury than terminally differentiated epithelial cells in the breast duct. Mammospheres, containing enriched breast progenitors, were used as an exposure system to simulate this imprinting phenomenon in vitro. Using MeDIP-chip ...[more]

PMID: 18339859

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Project description:In this study, we extend array CGH technology by making the accurate detection of segmental aneusomies possible from a single lymphoblast and fibroblast following Phi29 DNA polymerase amplification Array CGH experiments were performed on two segmental aneusomic cell lines derived from patients. As a proof of principle, an interstitial 4q-deletion (46, XX, del(4)(q13.1q22.3)) fibroblast cell line and an unbalanced reciprocal translocation involving chromosomes 14 and X (46, XX, der (X) t(X;14)(q21.3;q23.1)) EBV cell line were used. Array CGH experiments were performed using gDNA from the two cell lines to define the exact size of each rearrangement. For the 4q-deletion cell line, the size of the deleted region was 34 Mb corresponding to 39 clones spotted on the array (from RP11-340A13 to RP11-44P19). For the EBV cell line, the size of the 14q-duplication was 47 Mb corresponding to 63 clones (from RP11-62H20 to CTC-820M16) and the Xq-deletion was 58 Mb corresponding to 70 clones (from RP3-380C13 to RP11-218L14). For each cell line, three single cells were amplified. Following DNA amplification, all cells showed the expected DNA yields (n=6; ï?³ = 2.36 Âµg ï?± 0.12). Sex-mismatch array CGH experiments were conducted on amplified DNA samples obtained from the 4q-deletion cell line. Using the chromosome specific threshold obtained from our 18 experiments, sex chromosome and autosome ploidy levels were accurately identified with no false negative and no false positive results. Averaging the 39 clones within the chromosome 4q-deleted region enabled the accurate detection of the deletions. For each of the three amplified single-cell DNA of the unbalanced reciprocal translocation involving chromosomes 14 and X, male and female gDNA were used as references. Sex chromosome and autosome ploidy levels were accurately identified. Averaging intensity ratios of the 63 clones within the chromosome 14 duplicated region enabled the accurate detection of the duplications in the three replicate experiments. When, respectively, male or female gDNA were used as a reference, the average log2 mean ratio of the Xq-deleted region was â??0.04 or â??0.93, close to the theoretical expected value of 0 or minus 1. Interestingly, the log2 mean ratios of chromosomes 1 to 22 were highly similar when the same single cell amplified DNA was used for the two experiments using respectively female and male DNA as a reference. Hence, array CGH intensity ratio profiles were very reproducible.

Dataset Information

Differential DNA methylation profiles in estrogen-pre-exposed breast epithelial cells

Publications

Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome.

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