Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

Coordinated epigenetic remodelling occurs during early breast carcinogenesis [Expression profiling]


ABSTRACT: Dysregulation of the epigenome is a common event in malignancy. However, deciphering the earliest cancer associated epigenetic events remains a challenge. Cancer epigenome studies to date have primarily utilised cancer cell lines or clinical samples, where it is difficult to identify the initial epigenetic lesions from those that occur over time. Here, we analysed the epigenome of normal Human Mammary Epithelial Cells (HMEC) and a matched variant cell population (vHMEC) that has escaped senescence and undergone partial carcinogenic transformation. Using this model system we sought to identify the earliest epigenetic changes that potentially occur during carcinogenesis. First we show that the transcriptome of vHMEC resembles that of basal-like breast cancer. Moreover, in vHMEC there is significant deregulation of MYC, p53, EZH2/polycomb, the Aryl Hydrocarbon Receptor (AHR) and miRNAs-143, 145, 199a and 519a at the transcriptional level. Second, we find that vHMEC exhibit genome-wide changes in DNA methylation affecting key cancer-associated pathways. Hypermethylation predominately impacted gene promoters (particularly those targeted by AHR and TP53) and polycomb associated loci, whereas hypomethylation frequently affected enhancers. Next we show that long range epigenetic deregulation occurred in vHMEC involving concordant change in chromatin modification and gene expression across ~0.5-1Mb regions. Finally, we demonstrate that the DNA methylation changes we observe in vHMECs, occur in basal-like breast cancer (notably FOXA1 hypermethylation).. Overall our results suggest that the first steps of carcinogenesis are associated with a co-ordinated deregulation of DNA methylation and chromatin modification spanning a range of genomic loci potentially targeted by key transcription factors and a corresponding deregulation of transcriptional networks. We sought to compare the differences in gene expression in vHMEC when compared to isogenic HMEC cells. Two time points in the vHMEC growth phase were used to assess if continual passage of vHMEC contributed to expression differences. RNA was extracted from a total of 4 HMEC (and matched vHMEC) lines.

ORGANISM(S): Homo sapiens

SUBMITTER: Warwick Locke 

PROVIDER: E-GEOD-58879 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

Similar Datasets

2015-05-09 | E-GEOD-58880 | biostudies-arrayexpress
2015-05-09 | E-GEOD-58881 | biostudies-arrayexpress
2015-05-09 | GSE58880 | GEO
2015-05-09 | GSE58879 | GEO
2015-05-09 | GSE58881 | GEO
2024-11-02 | PXD047409 | Pride
2016-08-21 | E-GEOD-69996 | biostudies-arrayexpress
2014-11-14 | E-GEOD-63255 | biostudies-arrayexpress
2013-05-10 | E-GEOD-46074 | biostudies-arrayexpress
2007-11-01 | E-GEOD-2638 | biostudies-arrayexpress