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The next-generation RNA and ATAC sequencing of MLL-ENL transformed cell lines reveals that C/EBP transcription factors coordinate the expression of the MLL-ENL/Hoxa target genes [RNA-seq]

ABSTRACT: We report the application of next-generation RNA and ATAC sequencing technology for high-throughput profiling of MLL-ENL transformed cell lines. According to our results, the C/EBP transcription factors coordinate the expression of the MLL-ENL/Hoxa target genes. Genetic removal of both Cebpa and Cebpb revealed a surrogate function of C/EBPε for myeloid MLL-ENL transformation.

ORGANISM(S): Mus musculus

PROVIDER: GSE153622 | GEO | 2020/10/30

REPOSITORIES: GEO

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Project description:Activation of the MLL-ENL-ERtm oncogene initiates aberrant proliferation of myeloid progenitors. Here, we show induction of a fail-safe mechanism mediated by the DNA damage response (DDR) machinery that results in activation of the ATR/ATM-Chk1/Chk2-p53/p21 checkpoint and cellular senescence at early stages of cellular transformation caused by a regulatable MLL-ENL-ERtm in mice. Furthermore, we identified the transcription program underlying this intrinsic anti-cancer barrier, and DDR-induced inflammatory regulators that fine-tune the signaling towards senescence, thereby modulating the fate of MLL-ENL-immortalized cells in a tissue-environment-dependent manner. Our results indicate that DDR is a rate-limiting event for acquisition of stem cell-like properties in MLL-ENL-ERtm-mediated transformation, as experimental inhibition of the barrier accelerated the transition to immature cell states and acute leukemia development. We created a mouse model wherein the protein function of the MLL-ENL oncogene depends on tamoxifen due to fusion with the mutated estrogen-binding domain of the estrogen receptor (ERtm). After 7 months of tamoxifen administration, the MLL-ENL-ERtm mice developed a myeloproliferative disease, which progressed into the terminal stage after a long period (mean survival: 592 ± 112 days) of continuous tamoxifen provision. We have profiled gene expression at three time-points of tamoxifen treatment corresponding to three distinct cellular states of the MLL-ENL-ERtm-induced myeloproliferation in the bone marrow: 1. 7 months - high proliferation state with low DDR signaling (4 biological replicates), 2. 7-8 months - the transition period of lower proliferation and high DDR activity (4 biogical replicates) and 3. 8 months - the senescence (3 biological replicates). Time-matched tamoxifen-treated wild-type bone marrow analysed in 4 biological replicates. We have profiled gene expression in three disease stages in the spleen: 1. 7 months - early stage - induced proliferation and DDR (3 biological replicates), 2. 9-10 months - progression - partial senescence and DDR is maintained (3 biological replicates) and 3. 16-23 months - terminal stage - proliferation, low or absent DDR and no senescence (3 biological replicates). Time-matched tamoxifen-treated and age-matched wild-type spleens analysed in 5 biological replicates.

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The next-generation RNA and ATAC sequencing of MLL-ENL transformed cell lines reveals that C/EBP transcription factors coordinate the expression of the MLL-ENL/Hoxa target genes [RNA-seq]

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