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(CTA) expression after exposure to 5-aza-2'-deoxycytidine in HCT116 cells

ABSTRACT: The expression of CTAs is normally restricted to gametogenic tissue but is often reactivated in the tumorigenic setting. This tumorigenic reactivation is thought to be due to global demethylation events during tumorigenesis. To test this, we employed an affymetrix microarray in the hypermethylated colorectal carcinoma tumor-derived cell line, HCT116, following 5-aza-2'-deoxycytidine treatment. We used microarray analysis to uncover genes whose expression is modulated by DNA methylation in the colorectal carcinoma tumor derived cell line, HCT116.

ORGANISM(S): Homo sapiens

PROVIDER: GSE79041 | GEO | 2016/05/31

SECONDARY ACCESSION(S): PRJNA314780

REPOSITORIES: GEO

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(CTA) expression after exposure to 5-aza-2'-deoxycytidine in HCT116 cells

Project description:The expression of CTAs is normally restricted to gametogenic tissue but is often reactivated in the tumorigenic setting. This tumorigenic reactivation is thought to be due to global demethylation events during tumorigenesis. To test this, we employed an affymetrix microarray in the hypermethylated colorectal carcinoma tumor-derived cell line, HCT116, following 5-aza-2'-deoxycytidine treatment. We used microarray analysis to uncover genes whose expression is modulated by DNA methylation in the colorectal carcinoma tumor derived cell line, HCT116. HCT116 cells were exposed to 5-aza-2'-deoxycytidine for 72 hours. Total RNA was isolated and hybridized on to Affymetrix microarrays.

2016-05-31 | E-GEOD-79041 | biostudies-arrayexpress

MCF7 cells gene expression change by inducing CpG demethylation using 5-Aza-2'-deoxycytidine (Aza)

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5-aza-2-deoxycytidine treatment of Swarm rat chondrosarcoma cells

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Expression microarray with 5-aza-2'-deoxycytidine-treated Caco-2 cells

Project description:5-aza-2'-deoxycytidine (DAC) treated and untreated Caco-2 cells were compared using an expression microarray.

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5-aza-2-deoxycytidine treatment of Swarm rat chondrosarcoma cells

Project description:The puropose of this experiment was to identify gene expression changes that result from 5-aza-2-deoxycytidine induced DNA demethylation of Swarm rat chondrosarcoma cells. The gene expression profiles of untreated Swarm rat chondrosarcoma cells were compared to the gene expression profiles of Swarm rat chondrosarcoma cells that were treated for 5 passages with a low dose of 5-aza-2-deoxycytidine (0.1uM). Five chip study. For these experiments, microarray was carried out on untreated (control) Swarm rat chondrosarcoma cells (3 biological replicates), and microarray was also carried out on Swarm rat chondrosarcoma cells treated with 5-aza-2-deoxycytidine (2 biological replicates).

2010-08-06 | E-GEOD-17598 | biostudies-arrayexpress

MCF7 cells gene expression change by inducing CpG demethylation using 5-Aza-2'-deoxycytidine (Aza)

Project description:Promoter methylation is able to induce downregulation of gene expression. 5-Aza-2'-deoxycytidine(Aza), methytransferase inhibitor, induce CpG demethylation. Here, 5-Aza-2'-deoxycytidine(Aza) is treated in a human breast cancer cell, MCF7, for detection of gene expression change. To analyze gene expression change by aza, control RNA isolated from MCF-7 was compared with RNA isolated from MCF-7 treated with 5uM and 10uM aza.

2011-08-17 | E-GEOD-31441 | biostudies-arrayexpress

RNA-seq of the human colorectal adenocarcinoma cell line HCT-116 treated with 5-aza-2’-deoxycytidine

Project description:We performed poly(A)+ stranded RNA-seq of a panel of the human colorectal adenocarcinoma cell line HCT-116 treated with 5-aza-2’-deoxycytidine. In parallel, we determined the genomic location and DNA methylation levels of human full-length LINE-1 elements (L1) from the same samples using bs-ATLAS-seq (E-MTAB-12240). To link DNA methylation and L1 expression, we used cell pellets from the same cell culture to perform both RNA-seq and bs-ATLAS-seq.

2023-09-21 | E-MTAB-12245 | biostudies-arrayexpress

Genome-wide identification and DNA methylation of human full-length LINE-1 (L1) retrotransposons in HCT116 cells treated with 5-aza-2’-deoxycytidine.

Project description:We used bs-ATLAS-seq to comprehensively map the genomic location and assess the DNA methylation status of human full-length LINE-1 elements (L1). The approach is focused on the youngest family (L1HS), but it also catches a significant fraction of L1PA2 to L1PA8 elements. This was performed in HCT116 cells treated by the DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5-aza) or in mock-treated cells (DMSO).

2023-09-22 | E-MTAB-12240 | biostudies-arrayexpress

SUMO pulldown proteomics Namalwa 5-Aza-2' deoxycytidine treatment

Project description:Combination therapies targeting malignancies aim to increase treatment efficacy and reduce toxicity. Hypomethylating drug 5-Aza-2’-deoxycytidine (5-Aza-2’) enhances transcription of tumor suppressor genes and induces replication errors via entrapment of DNMT1. Post-translational modification by SUMO plays major roles in the DNA damage response and is required for degradation of entrapped DNMT1. Here, we combine SUMOylation inhibitor TAK981 and DNA-hypomethylating agent 5-Aza-2’ to improve treatment of MYC driven hematopoietic malignancies, since MYC overexpressing tumors are sensitive to SUMOylation inhibition. We studied the classical MYC driven malignancy Burkitt lymphoma, as well as diffuse large B-cell lymphoma (DLBCL) with and without MYC translocation. SUMO inhibition prolonged the entrapment of DNMT1 to DNA, resulting in DNA damage. An increase in DNA damage was observed in cells co-treated with TAK981 and 5-Aza-2’. Both drugs synergized to reduce cell proliferation in vitro in a B cell lymphoma cell panel, including Burkitt lymphoma and DLBCL. In vivo experiments combining TAK981 (25 mg/kg) and 5-Aza-2’ (2.5 mg/kg) showed a significant reduction in outgrowth of Burkitt lymphoma in an orthotopic xenograft model. In contrast, single dosing of TAK981 was ineffective and single dosing of 5-Aza-2’ only led to a modest outgrowth reduction. TAK981 and 5-Aza-2’ synergize to reduce B cell Lymphoma outgrowth in vitro and in vivo. SUMOylation is a key-player in the repair of DNA damage, hence upon TAK981 treatment the repair of DNA damage induced by 5-Aza-2’ treatment is impaired. Our results demonstrate the potential of tailored combination of drugs, based on insight in molecular mechanisms, to improve the efficacy of cancer therapies.

2023-03-17 | PXD038620 | Pride

Genome-wide DNA demethylation of TGW (neuroblastoma cell line) after treatment of mock and 5-aza-2'-deoxycytidine (5-aza-dC)

Project description:A neuroblasoma cell line, TGW, was treated with a DNA demethylating agents (5-aza-2'-deoxycytidine: 5-aza-dC). Genome-wide DNA methylation was analyzed using the Infinium Human MethylationEPIC BeadChip.

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