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 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 analyse a dense time course of transcriptional regulation in THP-1 cells treated with phorbol
myristate acetate (PMA) over 96 hours. 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 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 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.