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DNA methylatioin analysis of breast cancer cell lines with TET1 knockout

ABSTRACT: DNA methylatioin analysis of breast cancer cell lines with TET1 knockout

PROVIDER: PRJNA475775 | ENA |

REPOSITORIES: ENA

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DNA methylation analysis of breast cancer Hs578T cells with TET1 knockout

Project description:Both gains and losses of DNA methylation are common in cancer but the factors controlling this methylation balance remain unclear. Triple negative breast cancer (TNBC), a subtype that does not overexpress hormone receptors or HER2/NEU is one of the most hypomethylated cancers observed. In search for an explanation for this, we discovered that the TET1 DNA demethylase is specifically overexpressed in about 40% of patients with TNBC, where it is associated with hypomethylation of up to 10% of queried CpG sites and a worse overall survival. Through bioinformatic analyses in both breast and ovarian cancer cell line panels, we uncovered an intricate network connecting TET1 to hypomethylation and activation of cancer specific oncogenic pathways including PI3K, EGFR and PDGF. TET1 expression correlated with sensitivity to drugs targeting the PI3K-mTOR pathway. CRISPR mediated deletion of TET1 in two independent TNBC cell lines resulted in reduced expression of PI3K pathway genes, upregulation of immune response genes and substantially reduced cellular proliferation, suggesting dependence of oncogenic pathways on TET1 overexpression. Our work establishes TET1 as a potential oncogene that contributes to aberrant hypomethylation in cancer and suggests that TET1 could serve as a novel druggable target for therapeutic intervention.

2018-06-28 | GSE115685 | GEO

DNA methylation analysis of breast cancer Hs578T cells with TET1 knockout

Project description:DNA methylation analysis of breast cancer Hs578T cells with TET1 knockout

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HMGA2/TET1/HOXA9 pathway regulates breast cancer growth and metastasis.

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Project description:Description A phase II metabolic enzyme, NAT1 is frequently upregulated in breast cancers. Previous studies have shown that inhibition or depletion of NAT1 in breast cancer cell lines leads to growth retardation both in vitro and in vivo, suggesting that NAT1 contributes to rapid growth of breast cancer cells. This project evaluated the effects of NAT1 knockdown on the proteome of a breast cancer cell line.hese groups include a parental MDA-MB-231 breast cancer cells and two separate NAT1 knockout (KO) cell lines differing by proliferation rates.

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Gene expression profiles of Tet1 knockout (T1KO), Tet2 knockout (T2KO) and Tet1/Tet2 double knockout (DKO) mouse embryonic stem cells.

Project description:Global gene expression profile of single and double mutant mouse ES cells were compared to wt ES cells. Two male Tet1 KO, one male Tet2 KO, two male double KO, two female double KO, two male WT and two female WT mouse ES cells were compared. Global gene expression profile of single and double knockout mouse embryonic stem cells were compared to that of wild type mouse ES cells. All used ES lines were derived from C57/BL/6 mixed background mice. RNA from feeder free mutant mouse ES cells was competetively hybridized against RNA from WT ES cells. Same sex lines were compared. Two independent ES line of each genotype were used, with the exception of Tet2 KO ES cells where only one male line was used.

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