The Transcriptional Network That Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1

The response of the human acute myeloid leukemia cell line THP-1 to phorbol esters has been widely-studied to test candidateleukemia therapies and as a model of cell cycle arrest and monocyte-macrophage differentiation. Here we have employed CapAnalysis of Gene Expression (CAGE) to analyse a dense time course of transcriptional regulation in THP-1 cells treated with phorbolmyristate acetate (PMA) over 96 hours. PMA treatment greatly reduced the numbers of cells entering S phase and also blockedcells exiting G2/M. The PMA-treated cells became adherent and expression of mature macrophage-specific genes increasedprogressively over the duration of the time course. Within 1-2 hours PMA induced known targets of tumour protein p53 (TP53),notably CDKN1A, followed by gradual down-regulation of cell-cycle associated genes. Also within the first 2 hours, PMA inducedimmediate 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). Thedense time course revealed that the response to PMA was not linear and progressive. Rather, network-based clustering of thetime course data highlighted a sequential cascade of transient up- and down-regulated expression of genes encoding feedbackregulators, as well as transcription factors associated with macrophage differentiation and their inferred target genes. CAGEalso identified known and candidate novel enhancers expressed in THP-1 cells and many novel inducible genes that currently lackfunctional annotation and/or had no previously known function in macrophages. The time course is available on the ZENBUplatform allowing comparison to FANTOM4 and FANTOM5 data.