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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Addiction of t(8;21) and inv(16) AML to native RUNX1 [ChIP-Seq data]

ABSTRACT: Cancer cells maintain a sensitive balance between growth-promoting oncogenes and apoptosis inhibitors. We show that WT RUNX1 is required for survival of t(8;21)-Kasumi-1 and inv(16)-ME-1 AML cell lines. The malignant AML phenotype is sustained by a delicate AML1-ETO/RUNX1 balance that involves competition for common DNA binding sites regulating a subset of AML1-ETO/RUNX1 targets. Genomewide sequencing data is included herein: Transcription factors RUNX1 c-terminus and n-terminus which is shared with AML1-ETO were profiled independently), AML1-ETO and AP4 were profiled using ChIP-Seq in Kasumi-1 cells, as well as control ChIP-Seq experiments of non immune serum. Two replicates were performed for each transcription factor profiling and control experiment.

ORGANISM(S): Homo sapiens

SUBMITTER: Dan Friedman

PROVIDER: E-GEOD-45738 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Addiction of t(8;21) and inv(16) AML to native RUNX1 [Gene Expression data]

Project description:Cancer cells maintain a sensitive balance between growth-promoting oncogenes and apoptosis inhibitors. We show that WT RUNX1 is required for survival of t(8;21)-Kasumi-1 and inv(16)-ME-1 AML cell lines. The malignant AML phenotype is sustained by a delicate AML1-ETO/RUNX1 balance that involves competition for common DNA binding sites regulating a subset of AML1-ETO/RUNX1 targets. Genome expression was profiled after performing knockdown of RUNX1 and AML1-ETO in Kasumi-1 cells using specific siRNA-oligo nucleotides, and analyzed using Affymetrix Gene 1.0 ST arrays.

2013-08-18 | E-GEOD-45743 | biostudies-arrayexpress

Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells

Project description:This study characterizes the genome-side occupancy of AML1, AML1-ETO and the cofactors N-CoR and p300 in leukemics cells (Kasumi-1) to discover novel regulatory mechanisms involving genes bound by the t(8:21) fusion protein AML1-ETO. A significant discovery of our study is the co-localization of AML1-ETO with the N-CoR co-repressor on genomic regions that are primarily distal to the transcriptional start sites (TSSs). These regions exhibit over-representation of the PU.1 motif: PU.1 is a key hematopoietic regulator and member of the ETS family of transcription factors. Functionally, genes co-occupied by AML1-ETO and N-CoR (e.g., TYROBP and LAPTM5) are associated with the leukemic phenotype, as determined by analyses of gene ontology and by the observation that these genes are predominantly up-regulated upon AML1-ETO depletion. To further probe the regulatory context of these leukemic cells, genome-wide enrichment of the transcriptional initiation-associated histone modification H3K4me3 was also measured. Genome-wide study of transcription factor-DNA binding for AML1 (RUNX1) and the t(8;21) fusion protien AML1-ETO (RUNX1T1) in the Kasumi-1 leukemia cell line. The genome-wide binding of the disease-related cofactors N-CoR and p300 was assayed, along with enrichments of the H3K4me3 and H3K27me3 histone modifications.

2015-05-26 | E-GEOD-62847 | biostudies-arrayexpress

Addiction of t(8;21) and inv(16) AML to native RUNX1 [ChIP-Seq data]

2013-08-18 | GSE45738 | GEO

Addiction of t(8;21) and inv(16) AML to native RUNX1 [Gene Expression data]

2013-08-18 | GSE45743 | GEO

HDAC3 preferentially binds to RUNX1 in t(8;21) AML cells and collaborates with RUNX1 to repress AML1-ETO-mediated transcriptional activation

Project description:Human histone deacetylase 3 (HDAC3) plays an important role in gene transcription in diseased human cells, such as leukemia. The t(8;21) chromosomal translocation is one of the most commonly observed genetic abnormalities associated with acute myeloid leukemia. This translocation generates the AML1-ETO fusion protein between the wild-type RUNX1 transcription factor and wild-type ETO transcriptional corepressor. To better understand the role of HDAC3 in t(8;21) leukemogenesis, the human HDAC3-containing complexes were isolated from stably-transfected HeLa cells by using anti-FLAG immunoprecipitation. The resulting complexes were resolved in SDS-PAGE. The components of the complexes were identified using LC-MS/MS. We report here that the human RUNX1 transcription is a component of the HDAC3 complexes. We demonstrate that HDAC3 and RUNX1 collaboratively repress AML1-ETO-mediated transcription. These results reveal new insight into how AML1-ETO, RUNX1, and HDAC3 crosstalk to deregulate gene transcription in t(8;21) leukemia cells.

2020-02-17 | PXD017230 | Pride

Kasumi-1 AML1-ETO knockdown samples

2009-05-01 | GSE15646 | GEO

RNAi profiling of human Kasumi-1 AML1-ETO knockdown samples

Project description:Kasumi-1 AML cells that were transfected in triplicate with AML1-ETO or luciferase siRNA constructs by either Amaxa nucleofection or Biorad siLentFect and incubated for 96 hours. Microarrays used to discover an AML1-ETO signature for a GE-HTS screen to identify AML1-ETO modulators. Experiment Overall Design: Kasumi-1 AML cells incubated for 96 hours after they were transfected in triplicate with AML1-ETO or luciferase siRNA constructs by either Amaxa nucleofection or Biorad siLentFect along with three control samples not transfected with a construct.

2009-05-11 | E-GEOD-15646 | biostudies-arrayexpress

Nascent RNA-seq in Kasumi-1 cells

Project description:Amino Enhancer of Split (AES) is essential for AML1-ETO induced self-renewal and leukemogenesis. To study the effect of AES on transcription regulation in AML1-ETO expressing Kasumi-1 cells, nascent transcripts in control (shctr) and AES knockdown (shAES) Kasumi-1 cells were labelled with uridine analogue 4-thioduridine with subsequent nascent RNA purification and next generation sequencing (Nascent RNA-seq).

2017-06-20 | GSE80582 | GEO

Transcription profiling and RNAi of human Kasumi-1 AML cell line and U937 cell lines - AML1-ETO induction and knockdown

Project description:This SuperSeries is composed of the following subset Series:; GSE15646: Kasumi-1 AML1-ETO knockdown samples; GSE15647: U937 AML1-ETO inducible samples Experiment Overall Design: Refer to individual Series

2009-05-08 | E-GEOD-15648 | biostudies-arrayexpress

Paired ChIP-Seq studies of Kasumi-1 t(8;21) AML cells

Project description:Nearly 10-15% of all acute myeloid leukemia (AML) cases are caused by a recurring chromosomal translocation between 8 and 21, t(8;21). The t(8;21) translocation generates the AML1-ETO leukemia fusion protein. AML1-ETO promotes leukemogenesis by transcriptionally dysregulating important cell-fate genes. Here, to better understand how AML1-ETO deregulates transcription, we performed paired ChIP-Seq analyses of sequence-specific transcription factors, coactivators, corepressors, HDACs, RNA Pol II and acetyl-histone marks in both control and AML1-ETO-depleted Kasumi-1 t(8;21) AML cells.

2020-02-14 | GSE131939 | GEO

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