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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Remodelling of the DNA methylation landscape of leukemic cells upon FOSL2 KO or CD34 + cells upon CRISPR mediated t(4:11) rearrangement

ABSTRACT: In this dataset we used the most recent Illumina MethylationEPIC Beadchip platform to describe the genome-wide DNA methylation changes observed upon FOSL2 KO in SEM leukemia cells. In addition, we explored the DNA methylation effect of t(4:11) translocation in the context of CD34+ cells. These samples correspond to additional experimental work from the manuscript and are related to the ArrayExpress entry E-MTAB-8505.

ORGANISM(S): Homo sapiens

SUBMITTER: Pablo Menéndez

PROVIDER: E-MTAB-10090 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Remodeling of the DNA methylation landscape of CD34+ cells from fetal liver / cord blood upon upon CRISPR mediated t(4:11) rearrangements.

Project description:The prognosis of infant B-cell acute lymphoblastic leukemia (iB-ALL) remains dismal, especially in patients harboring the MLL-AF4 (KTM2A-AFF1) rearrangement, which arises prenatally in early hematopoietic stem/progenitor cells (HSPCs). MLL-AF4+ B-ALL shows a bimodal localization of the MLL gene breakpoint within the MLL break cluster region, and two subgroups of patients based on the gene expression pattern of the HOXA/MEIS cluster have been identified. The pathogenic mechanisms in MLL-AF4+ B-ALL are challenging to study functionally due to the absence of faithful human cellular models recapitulating the disease phenotype and latency. Here, we assess the molecular contribution and leukemogenic capacity of MLL breakpoints occurring in either intron 10 (MLLi10, centromeric) or intron 12 (MLLi12, telomeric) in ontogenically-different human HSPCs sourced prenatally (fetal liver) and neonatally (cord blood). CRISPR-Cas9-induced MLL-AF4 (MA) targeting either MLLi10 (Mi10A) or MLLi12 (Mi12A) causes MA-driven in vitro myeloid immortalization in both fetal liver- and cord blood-CD34+ HSPCs. The cellular ontogeny and the location of the MLL breakpoint influenced the capacity of MLL-edited CD34+ HSPCs to initiate pro-B-ALL in vivo, which faithfully recapitulated the molecular, transcriptomic and methylome profiles of patients with primary MA+ iB-ALL. This dataset contains the DNA methylation information (Illumina MethylationEPIC Beadchip platform) of MLL-edited CD34+ cells (i10 or i12). BCPs, used as controls, were obtained from E-MTAB-8505

2023-10-29 | E-MTAB-12806 | biostudies-arrayexpress

The Methylome Landscape of Infant B-cell precursor Acute Lymphoblastic Leukemia (iB-ALL)

Project description:B-cell acute lymphoblastic leukemia (B-ALL) is the most prevailing childhood cancer. As predicated by its prenatal origin, infant B-ALL (iB-ALL) show a silent mutational landscape irrespective of the MLL rearrangement/status, suggesting that other regulatory mechanisms might be impaired in the context of the disease. Here we used the most recent Illumina MethylationEPIC Beadchip platform to describe the genome-wide DNA methylation changes observed in a total of 69 de novo MLL-AF4+, MLL-AF9+ and non-rearranged MLL iB-ALL leukemias uniformly treated according to Interfant 99/06 protocol. Please note that samples X8 and X9 (pool of B cells and BCP) correspond to samples 200340580160_R08C01 and 200340580161_R07C01 from study E-MTAB-6315, respectively.

2021-03-12 | E-MTAB-8505 | biostudies-arrayexpress

DPPA3-HIF1a axis controls colorectal cancer chemoresistance by imposing a slow cell-cycle phenotype (DNA methylation arrays)

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Global DNA methylation profiling of CD4+ T cells from patients with systemic lupus erythematosus

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2011-06-10 | E-GEOD-27895 | biostudies-arrayexpress

Whole DNA methylome of an extramedullary multiple myeloma patient derived orthotopic xenograft

Project description:A patient derived orthotopic xenograft (PDOX) was generated from a patient with an 53 aggressive extramedullary multiple myeloma (EMM) to study in-depth genetic and epigenetic events and drug responses related to extramedullary disease. Whole DNA methylome of the EMM PDOX was also evaluated and compared with a published dataset of 101 newly-diagnosed and chemotherapy-naïve MM patients and normal plasma cells (NPC) (Agirre et al., 2015) A rather balanced proportion of hyper/hypomethylated sites different to previously reported widespread hypomethylation in MM was observed.

2021-06-25 | E-MTAB-10654 | biostudies-arrayexpress

Methylation profiling by array of 108 clear cell renal cell carcinoma

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Methylation arrays elucidate 5mC and 5hmC levels of human glioblastoma cell line LN229 upon restoration of TET3 expression.

Project description:DNA hydroxymethylation is frequently lost in glioblastoma. We hypothesized that reduced 5hmC levels might be related to the impaired expression of TET proteins in brain tumors. In this study we performed a genome-wide methylation analysis of LN229 cells stably transfected with scramble or TET3 overexpressing vectors. TET3 overexpression partially restored the genome-wide patterns of 5hmC characteristic of control brain samples in glioblastoma cell lines.

2018-03-03 | E-MTAB-6001 | biostudies-arrayexpress

DNA methylation profiles of freshly isolated CD34+ cells and upon expansion on either tissue culture plastic (TCP) or mesenchymal stromal cells (MSCs)

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2013-12-03 | E-GEOD-40799 | biostudies-arrayexpress

Recurrent TCF12 mutations in anaplastic oligodendroglioma

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