Leukemogenic MLL-ENL fusions induce alternative chromatin states to drive a functionally dichotomous group of target genes
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REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR899346.fastq.gz | Fastqsanger.gz | |||
| ERR899347.fastq.gz | Fastqsanger.gz | |||
| ERR899348.fastq.gz | Fastqsanger.gz | |||
| ERR899349.fastq.gz | Fastqsanger.gz | |||
| ERR899350.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Leukemogenic MLL-ENL fusions induce alternative chromatin states to drive a functionally dichotomous group of target genes
| PRJEB9518 | ENA
Project description:MLL fusions are leukemogenic transcription factors that enhance transcriptional elongation through modification of chromatin and RNAPolII. Global transcription rates and chromatin changes accompanying the transformation process were monitored by nascent-RNA-seq and ChIP-seq identifying 165 targets separated into two distinct clades. ChIP-seq data complementing this RNA-seq data set can be found in ArrayExpress under accession number E-MTAB-3593 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3593)
2016-03-31 | E-MTAB-3591 | biostudies-arrayexpress
Project description:MLL fusions are leukemogenic transcription factors that enhance transcriptional elongation through modification of chromatin and RNAPolII. Global transcription rates and chromatin changes accompanying the transformation process were monitored by nascent-RNA-seq and ChIP-seq identifying 165 targets separated into two distinct clades. This accession contains ChIP Seq experiments for MLLENL and a negative control. The RNA-seq data set could also be found in ArrayExpress under accession number E-MTAB-3591 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3591/ ).
2016-03-31 | E-MTAB-3593 | biostudies-arrayexpress
Project description:Leukemogenic MLL-ENL fusions induce alternative chromatin states to drive a functionally dichotomous group of target genes
| PRJEB9384 | ENA
Project description:RNA-Seq of 1) human AML samples; 2) sorted, uncultured distinct population from human cord blood (CB); 3) short-term (ST) cultured sorted CB cells transduced with MLL-ENL, MLL-AF6 or untransduced; and 4) cultured (LT) sorted CB cells transformed with MLL-ENL or MLL-AF6. Cells from MLL-fusion AML patients are bulk. Several cords were used for the sorting (CB1, CB2, CB3, 135, 141...) and these represent biological replicates. Several samples were sequenced several times in different lanes and results were merged together for the analysis (rep1,rep2...). Samples were used to determine the different effect of MLL-fusions in different celltypes just after the transduction, and after a longer time period when cells were transformed. Sorted CB samples, uncultured as well as transformed by MLL-fusions, were used in machine learning approach to predict which of the patients originated from which cell-type of origin.
2021-01-31 | E-MTAB-5501 | biostudies-arrayexpress
Project description:Acute myeloid leukemia (AML) is characterized by dysregulated transcriptional programs and these programs require support from chromatin regulators to maintain their hyperactive state. Recent studies have identified the histone acylation ‘reader’ ENL as being a critical dependency in AML, but the potential of therapeutic applications targeting this chromatin reader remains poorly understood. Here, we present a potent and orally bioavailable small-molecule inhibitor of ENL, TDI-055, which displaces ENL from chromatin by competitively blocking the interaction of its YEATS domain with acylated histones. We show that TDI-055 treatment preferentially inhibited the proliferation of human leukemia cells harboring MLL translocations or NPM1 mutations. Through a CRISPR/Cas9 saturated mutagenesis screen, we uncovered an ENL mutant that could confer cells resistance to TDI-055, thus providing compelling proof for the on-target activity of the compound. Rapid displacement of ENL from chromatin resulted in decreased recruitment of select ENL-associated complexes and impaired RNA polymerase II elongation which, in turn, led to the suppression of critical leukemogenic gene expression programs. Finally, pharmacological inhibition of ENL in vivo led to reduced AML growth and prolonged survival in cell line and patient-derived xenograft (PDX) models. Collectively, these results provide critical evidence and mechanistic insights to establish inhibition of ENL as a potential therapeutic strategy against molecularly defined AML, laying the foundation for rapid clinical translation of this approach.
2022-10-05 | GSE185093 | GEO
Project description:Acute myeloid leukemia (AML) is characterized by dysregulated transcriptional programs and these programs require support from chromatin regulators to maintain their hyperactive state. Recent studies have identified the histone acylation ‘reader’ ENL as being a critical dependency in AML, but the potential of therapeutic applications targeting this chromatin reader remains poorly understood. Here, we present a potent and orally bioavailable small-molecule inhibitor of ENL, TDI-055, which displaces ENL from chromatin by competitively blocking the interaction of its YEATS domain with acylated histones. We show that TDI-055 treatment preferentially inhibited the proliferation of human leukemia cells harboring MLL translocations or NPM1 mutations. Through a CRISPR/Cas9 saturated mutagenesis screen, we uncovered an ENL mutant that could confer cells resistance to TDI-055, thus providing compelling proof for the on-target activity of the compound. Rapid displacement of ENL from chromatin resulted in decreased recruitment of select ENL-associated complexes and impaired RNA polymerase II elongation which, in turn, led to the suppression of critical leukemogenic gene expression programs. Finally, pharmacological inhibition of ENL in vivo led to reduced AML growth and prolonged survival in cell line and patient-derived xenograft (PDX) models. Collectively, these results provide critical evidence and mechanistic insights to establish inhibition of ENL as a potential therapeutic strategy against molecularly defined AML, laying the foundation for rapid clinical translation of this approach.
2022-10-05 | GSE185091 | GEO
Project description:To investigate the contribution of ENL YEATS domain and downstream sequences in MLL-ENL leukemogenesis program, we generated MLL-ENL and MLL-ENL ∆YEATS (ENL aa372-559) cell lines by retrovirally introducing these constructs into lineage negative hematopoietic stem and progenitor cells (HSPCs).
2023-02-27 | GSE211523 | GEO
Project description:PAX5 encodes a master regulator of B-cell development. It fuses to other genes associated with acute lymphoblastoid leukemia (ALL). These fusion products are potent dominant-negative (DN) inhibitors of wild-type PAX5, resulting in a blockade of B-cell differentiation. Here, we show that multimerization of PAX5 DNA-binding domain (DBD) is necessary and sufficient to cause extremely stable chromatin binding and DN activity. ALL-associated PAX5-C20S results from fusion of the N-terminal region of PAX5, including its paired DBD, to the C-terminus of C20orf112, a protein of unknown function. We report that PAX5-C20S is a tetramer, which interacts extraordinarily stably with chromatin as determined by Fluorescence Recovery After Photobleaching in living cells. Tetramerization, stable chromatin binding and DN activity all require a putative five-turn amphipathic ?-helix at the C-terminus of C20orf112, and does not require potential corepressor binding peptides elsewhere in the sequence. In vitro, the monomeric PAX5 DBD and PAX5-C20S binds a PAX5-binding site with equal affinity when it is at the center of an oligonucleotide too short to bind to more than one PAX5 DBD. But, PAX5-C20S binds the same sequence with 10-fold higher affinity than the monomeric PAX5 DBD when it is in a long DNA molecule. We suggest that the increased affinity results from interactions of one or more of the additional DBDs with neighboring non-specific sites in a long DNA molecule, and that this can account for the increased stability of PAX5-C20S chromatin binding compared with wild-type PAX5, resulting in DN activity by competition for binding to PAX5-target sites. Consistent with this model, the ALL-associated PAX5 fused to ETV6 or the multimerization domain of ETV6 SAM results in stable chromatin binding and DN activity. In addition, PAX5 DBD fused to artificial dimerization, trimerization and tetramerization domains results in parallel increases in the stability of chromatin binding and DN activity. Our studies suggest that oncogenic fusion proteins that retain the DBD of the transcription factor (TF) and the multimerization sequence of the partner protein can act in a DN manner by multimerizing and binding avidly to gene targets, preventing the normal TF from binding and inducing expression of its target genes. Inhibition of this multimeriztion may provide a novel therapeutic approach for cancers with this or similar fusion proteins.
| S-EPMC3197879 | biostudies-literature
Project description:This ChIP-seq experiment was done to investigate the global distribution of H2A ubiquitination (a hallmark of polycomb mediated repression), H2B ubiquitination (introduced by PAF-complex associated ubiquitin ligases and connected to active transcription), and PAF1 occupation in Meer cells. Meer cells are primary cells transformed by a knock-in of an inducible Mll-ENL oncogene. ENL and ENLins ChIP-seqs were done in CD117-positive primary hematopoietic cells without any pretransformation by other oncogenes.
2018-01-23 | E-MTAB-5569 | biostudies-arrayexpress