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Transcription profiling by array of human MDA-MB-231 breast cancer cells with ATAD3A stable knockdown against no-knockdown controls

ABSTRACT: From our previous data, we found that loss of ATAD3A gene expression in breast cancer cells results in loss of cell motility in vitro and metastasis in vivo. To obtain a better understanding of oncogenic pathway of ATAD3A, we have established the stable ATAD3A knockdown MDA-MB-231 cells using lentiviral strategy. We used the whole genome microarrays to detail the global programme of gene expression after depleting of ATAD3A and identified distinct classes of up or down-regulated metastmir associated with breast cancer cells migration Total RNA was extracted from ATAD3A stable knockdown cells (shATAD3A) and the control cells (shGFP). The labeled RNA was hybridized on U133 plus 2.0 Array. To identify altered gene expression patterns with or without ATAD3A expression, we compared average mRNA expression levels between the ATAD3A knockdown and control MDA-MB-231 cells.

ORGANISM(S): Homo sapiens

SUBMITTER: teng yong

PROVIDER: S-ECPF-GEOD-56084 | biostudies-other |

REPOSITORIES: biostudies-other

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Project description:We used microarrays to detail the global programme of gene expression for MCF-7 and MDA-MB-231 and revealed the correlation between the methylation state of various genomic components and gene expression level. The expression analyses of the two breast cancer cell lines are a part of the whole study. The summary of our study is as follows: We establish a technique, called modified methylation-specific digital karyotyping (MMSDK) based on methylation-specific digital karyotyping (MSDK) with a novel sequencing approach. Briefly, after a tandem digestion of genomic DNA with a methylation-sensitive mapping enzyme and a fragmenting enzyme, short sequence tags are obtained. These tags are amplified, followed by direct, massively parallel sequencing (Solexa 1G Genome Analyzer). This method allows high-throughput and low-cost genome-wide DNA methylation mapping. We applied this method to investigate global DNA methylation profiles for widely used breast cancer cell lines, MCF-7 and MDA-MB-231, which are representatives for luminal-like and mesenchymal-like cancer types, respectively. By comparison, a highly similar overall DNA methylation pattern was revealed for the two cell lines. However a cohort of individual genomic loci with significantly different DNA methylation profile between two cell lines was identified. Furthermore, we revealed a genome-wide significant correlation between gene expression and the methylation status of gene promoters with CpG islands (CGIs) in the two cancer cell lines, and a correlation of gene expression and the methylation status of promoters without CGIs in MCF-7 cells. Experiment Overall Design: Breast cancer cell lines, MCF-7 and MDA-MB-231, were selected for the study of the impact of DNA methylation on gene expression regulation. Total RNA extraction was performed for both cell lines and hybridization was carried out using Affymetrix microarrays. We developed a modified methylation-specific digital karyotyping (MSDK) to obtain DNA methylation profiling genome wide. Then, we combined the analysis of DNA methylation data and gene expression data to reveal a correlation between epigenetic and transcriptional features genome wide.

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Transcription profiling by array of human MDA-MB-231 breast cancer cells with ATAD3A stable knockdown against no-knockdown controls

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