Multi-omics and machine learning reveal context-specific gene regulatory activities of PML-RARA in Acute Promyelocytic Leukemia [Cut&Run]

The PML-RARA fusion protein is the hallmark driver of Acute Promyelocytic Leukemia (APL) and disrupts retinoic acid signaling, leading to wide-scale gene expression changes and uncontrolled proliferation of myeloid precursor cells. While known to be recruited to binding sites across the genome, its impact on gene regulation and expression is under-explored. Using integrated multi-omics datasets, we characterize the influence of PML-RARA binding on gene expression and regulation in an inducible cell line model and APL patient ex vivo samples. We find that genes whose regulatory elements recruit PML-RARA are not uniformly transcriptionally repressed, as commonly suggested, but also may be upregulated or remain unchanged. We develop a novel, computational machine learning application to deconvolute the complex, local transcription factor binding site environment at PML-RARA bound positions to reveal distinct signatures that modulate how PML-RARA directs the transcriptional response. Application of Cut&Run to the U937-PR9 cell line system, before and after PML-RARA induction. Application of Cut&Run to two ex vivo APL patient samples

PML-RARA融合蛋白是急性早幼粒细胞白血病（Acute Promyelocytic Leukemia, APL）标志性的驱动因子，可干扰视黄酸信号通路，引发大规模基因表达改变与髓系前体细胞的失控增殖。尽管已知该蛋白会被招募至全基因组的结合位点，但其对基因调控与表达的影响仍未得到充分探索。本研究通过整合多组学数据集，在诱导型细胞系模型以及APL患者的离体样本中，解析了PML-RARA结合对基因表达与调控的影响。研究发现，调控元件招募PML-RARA的基因，其转录抑制并非如学界普遍认为的那样均一发生，反而可能出现表达上调或维持不变的情况。本研究开发了一种全新的计算机器学习工具，以解析PML-RARA结合位点处复杂的局部转录因子结合位点环境，进而揭示能够调控PML-RARA介导转录反应的不同特征信号。本研究分别在PML-RARA诱导前后的U937-PR9细胞系系统中开展了Cut&Run实验，并对两例离体APL患者样本实施了Cut&Run检测。