The response of the human acute myeloid leukemia cell line THP-1 to phorbol esters has been widely studied to test candidate leukemia therapies and as a model of cell cycle arrest and monocyte-macrophage differentiation. Here we have employed Cap Analysis of Gene Expression (CAGE) to analyze a dense time course of transcriptional regulation in THP-1 cells treated with phorbol myristate acetate (PMA) over 96 h. PMA treatment greatly reduced the numbers of cells entering S phase and also blocked cells exiting G2/M. The PMA-treated cells became adherent and expression of mature macrophage-specific genes increased progressively over the duration of the time course. Within 1–2 h PMA induced known targets of tumor protein p53 (TP53), notably CDKN1A, followed by gradual down-regulation of cell-cycle associated genes. Also within the first 2 h, PMA induced immediate early genes including transcription factor genes encoding proteins implicated in macrophage differentiation (EGR2, JUN, MAFB) and down-regulated genes for transcription factors involved in immature myeloid cell proliferation (MYB, IRF8, GFI1). The dense time course revealed that the response to PMA was not linear and progressive. Rather, network-based clustering of the time course data highlighted a sequential cascade of transient up- and down-regulated expression of genes encoding feedback regulators, as well as transcription factors associated with macrophage differentiation and their inferred target genes. CAGE also identified known and candidate novel enhancers expressed in THP-1 cells and many novel inducible genes that currently lack functional annotation and/or had no previously known function in macrophages. The time course is available on the ZENBU platform allowing comparison to FANTOM4 and FANTOM5 data.

已经广泛研究了人类急性髓样白血病细胞系THP-1对佛波酯的反应，以测试候选白血病疗法，并将其作为细胞周期停滞和单核细胞-巨噬细胞分化的模型。在这里，我们采用了基因表达的上限分析（CAGE）来分析经佛波醇肉豆蔻酸酯乙酸（PMA）处理的THP-1细胞在96小时内转录调控的密集时间过程。PMA处理大大减少了进入S期的细胞数量，也阻止了离开G2 / M的细胞。经PMA处理的细胞在一段时间内持续粘附，成熟的巨噬细胞特异性基因的表达逐渐增加。在1至2小时内，PMA诱导了已知的肿瘤蛋白p53（TP53）靶标CDKN1A，然后逐渐下调细胞周期相关基因。同样在最初的2小时内，PMA诱导了立即早期基因，包括编码参与巨噬细胞分化的蛋白质的转录因子基因（EGR2，JUN，MAFB）和参与未成熟骨髓细胞增殖的转录因子的下调基因（MYB，IRF8，GFI1）。密集的时间过程表明，对PMA的反应不是线性的和渐进的。而是，基于时程数据的网络聚类突出显示了编码反馈调节剂的基因以及与巨噬细胞分化有关的转录因子及其推断的目标基因的瞬时上调和下调表达的连续级联。CAGE还鉴定了在THP-1细胞中表达的已知和候选新型增强子以及目前在巨噬细胞中缺乏功能注释和/或不具有先前已知功能的许多新型诱导型基因。时间过程在ZENBU平台上可用，可以与FANTOM4和FANTOM5数据进行比较。