BCR::ABL1-induced enhancer reprogramming uncovers hypersensitivity of Ph+B-ALL cells to enhancer-targeting drugs [RNA-Seq]

To better understand how BCR::ABL1 establishes the Ph+B-ALL-defining transcriptional program, we adopted an integrative multi-omics approach to study the transcriptome, enhancer activities, and 3-dimensional interactions of enhancers with target genes in Ph+B-ALL cells. We performed an in-depth analysis of cells from human Ph+B-ALL patients and a murine Ph+B-ALL model using ChIP-Seq, RNA-Seq, and Hi-C-based methods to link enhancers to the promoters they regulate. Overall design: This dataset contains several different experimental designs: (1) Monitoring of transcriptional deregulation during BCR::ABL1-induced malignant transformation using murine primary B-cell precursors from Trp53bp1-/- mice: RNA-Seq was done on primary B-cell precursors from Trp53bp1-/- mice cultured for 7 or ~60 days and either transduced with BCR::ABL1(p210)-encoding retrovirus or empty vector (EV) as controls. Culture was done in presence of mIL3 throughout. (2) Monitoring of transcriptional deregulation during BCR::ABL1-induced malignant transformation using murine primary B-cell precursors from C57BL/6 mice: RNA-Seq was done on primary B-cell precursors from C57BL/6 mice cultured for 3 or ~60 days and either transduced with BCR::ABL1(p190)-encoding retrovirus or empty vector (EV) as controls. Culture was done in presence of mIL3 throughout. For successfully transformed BCR::ABL1(p190) expressing cells (at ~D60), cells were additionally treated with 10nM Ponatinib or DMSO as control for analysis of BCR::ABL1 kinase-dependent enhancer activation. (3) Monitoring of transcriptional differences between human Ph+B-ALL cells and normal bone marrow B-cell precursors: RNA-Seq was done on Ph+B-ALL cell lines (SUP-B15, TOM-1, BV-173) or primary leukaemia cells (BAL08), and bone marrow B-cells purified from healthy mononuclear bone marrow cells (obtained from The John Goldman Centre for Cellular Therapy of Hammersmith Hospital/Imperial College London). (4) Analysis of the effect of BCR::ABL1 kinase inhibition by Ponatinib on transcription in human Ph+B-ALL cells for comparison to PCHI-C and H3K27ac ChIP-Seq data: RNA-Seq was done on Ph+B-ALL cell lines (SUP-B15, TOM-1, BV-173) or primary leukaemia cells (BAL08) treated for 24h with DMSO or 100nM Ponatinib. Primary BAL08 cells were co-cultured on mitotically-inactivated OP9 feeder cells for 3 weeks before experiment. (5) Analysis of the effect of global enhancer inhibition on transcription in human Ph+B-ALL cells for comparison to PCHI-C, H3K27ac ChIP-Seq and RNA-Seq data: RNA-Seq was done on the Ph+B-ALL cell lines SUP-B15 and TOM-1 treated for 24h with DMSO or 250nM dCBP-1, or for 48h with DMSO or 0.5uM A-485.