EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. [DND41_ATACseq]

Purpose: To investigate the mechanisms of 3D genome organization in drug-resistant T-ALL Methods: We used multiple epigenomics, chromatin conformation, and transcriptomic assays to study the mechanisms of chromatin adaptation in GSI-sensitive and GSI-resistant T-ALL Results: We report here that T/B cell lineage determining transcription factors are differentially expressed in GSI-resistant T-ALL cells, driving enhancer switching and genome folding reorganization events to promote GSI-resistance. Conclusions: These observations suggest a general mechanism that diffenrential activity of pioneering factors can be exploited to evade addiction to oncogenic signals. For comparison of chromatin accessibility in parental and GSI-resistant DND41 cells, parental DND41 was treated with DMSO or 125 nM GSI for 24 hours and GSI-resistant cells were refreshed with media containing 125 nM GSI for 24 hours. For assessing the impact of LEF1 or TCF1 loss on parental DND41 genome, DND41-Cas9 cells carrying LRG2.1-LEF1-g3 or LRmCherry2.1-TCF7-g5 were sorted 6 days post transduction. To assess the impact of LEF1 and TCF1 loss on parental DND41 genome, DND41-Cas9 carrying LRG2.1-LEF1-g3 and LRmCherry2.1-TCF7-g5 were sorted 3, 6 and 9 days post transduction. DND41-Cas9 carrying LRG2.1 and LRmCherry2.1 were sorted 3 days post transduction as control.To assess the impact of EBF1 loss on GSI-resistant DND41 genome, DND41-Res-Cas9 with LRmCherry2.1-EBF1-g7 were sorted 3, 6 and 9 days post transduction and control cells were sorted 3 days post transduction. ATAC-seq experiment was performed in triplicates.