Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq of SUPT1, LOUCY, JURKAT and DND41 after treatment with 5-azacytidine and Vitamin C

ABSTRACT: TET2 is a know tumorsuppressor gene involved in the demethylation of DNA. TET2 catalyses the conversion of 5-methyl cytosine (5-mC) to 5-hydroximethyl cytosine (5-hmC), an important step in the removal of methylation from the DNA. In T-All mutations in TET2 are rare, however we have found that it is often silenced by DNA Methylation. 5-Azacytidine (5-AZA) is a an effective demethylating agent used as a cancer treatment and has been showed to be able to reactivate methylated genes. Similarly, Vitamin C is an important co-factor for TET2 and has been shown to have synergistic effects with 5-Azacytidine. By treating the TET2 methylated T-ALL cell lines Loucy and DND41 and comparing to TET2 expressing T-ALL cells lines such as SUP-T1 and Jurkat we aimed to explore if 5-AZA could reactivate TET2 in T-ALL, what effects this would have on tumorgenicity and whether Vitamin C had any synergy with these effects in T-ALL. As part of this effort we treated the cell lines SUP-T1, Jurkat, Loucy and DND41 with 5-AZA and Vitamin C and performed Total RNA-seq to explore the effects of 5-AZA and Vitamin C on the expression of genes and non-coding elements such as retrotransponsons.

INSTRUMENT(S): DNBSEQ-G400

ORGANISM(S): Homo sapiens

SUBMITTER: Colm Nestor

PROVIDER: E-MTAB-10512 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia.

Bensberg Maike M Rundquist Olof O Selimović Aida A Lagerwall Cathrine C Benson Mikael M Gustafsson Mika M Vogt Hartmut H Lentini Antonio A Nestor Colm E CE

Proceedings of the National Academy of Sciences of the United States of America 20210801 34

Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy resulting from overproduction of immature T-cells in the thymus and is typified by widespread alterations in DNA methylation. As survival rates for relapsed T-ALL remain dismal (10 to 25%), development of targeted therapies to prevent relapse is key to improving prognosis. Whereas mutations in the DNA demethylating enzyme TET2 are frequent in adult T-cell malignancies, <i>TET2</i> mutations in T-ALL are rare. Here, ...[more]

PMID: 34413196

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Project description:The epigenetic regulation of transcription factor genes is critical for T cell lineage specification. A specific methylation pattern within a conserved region of the lineage specifying transcription factor gene FOXP3, the Treg-specific demethylated region (TSDR), is restricted to regulatory T (Treg) cells and required for stable expression of FOXP3 and suppressive function. We analyzed the impact of hypomethylating agents 5-Aza-2`-deoxycytidine and Epigallocatechin-3-gallate (EGCG) on human CD4+CD25- T for generating Treg cell specific DNA methylation pattern within FOXP3-TSDR and inducing functional Treg cells. Gene expression, including lineage specifying transcription factors of the major T cell lineages and their leading cytokines, functional properties and global transcriptome changes were analyzed. 5-Aza-2`-deoxycytidine induced FOXP3-TSDR methylation and expression of Treg cell specific genes FOXP3 and LRRC32. Proliferation of 5-Aza-2Â´deoxycytidine treated cells was reduced, but they did not show suppressive function. Hypomethylation was not restricted to FOXP3-TSDR and expression of master transcription factors and leading cytokines of Th1 and Th17 cells were induced. EGCG induced global DNA hypomethylation to a lower degree than 5-Aza-2Â´deoxycitidine, but no relevant hypomethylation within FOXP3-TSDR or expression of Treg cell specific genes. Both DNMT inhibitors did not induce full functional human Treg cells. Although 5-Aza-2`-deoxycytidine treated cells phenotypically appeared to be Treg cells, they did not suppress proliferation of responder cells, which is an essential capability to be used in Treg cell transfer therapy. In this study we analyze the potency of the two hypomethylating agents 5-Aza-2`-deoxycytidine (5-Aza-dC) and Epigallocatechin-3-gallate (EGCG) for in vitro induction of functional Treg cell cells through generation of a specific methylation pattern within FOXP3-TSDR. We analyzed the expression of Treg cell specific genes and for their functional properties from CD4+CD25- T cells. 5-Aza-dC is a derivative of 5-Azacytidine. Both substances are inhibitors of DNA methyltransferases (DNMTs) and used for therapy of patients with myelodysplastic syndrome and acute myeloid leukaemia. In these patients, 5-Azacytidine has been reported to augment regulatory T cell expansion in blood. EGCG is the most abundant catechin of green tea and has been reported to have cardio protective, anti-cancer, anti-infective properties and protective effects on autoimmune diseases. EGCG has also been described as a potent inhibitor of DNMTs and to induce Foxp3 in Jurkat T cell line.

Dataset Information

RNA-seq of SUPT1, LOUCY, JURKAT and DND41 after treatment with 5-azacytidine and Vitamin C

Publications

TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia.

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