Edinburgh Explorer 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 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.

[1]  Parul Sharma,et al.  CRISPR/Cas9 , 2021, Plant-Microbial Interactions and Smart Agricultural Biotechnology.

[2]  E. Chan,et al.  Kruppel‐like factor 6 promotes macrophage inflammatory and hypoxia response , 2020, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[3]  Robin Andersson,et al.  CAGEfightR: analysis of 5′-end data using R/Bioconductor , 2019, BMC Bioinformatics.

[4]  F. Ginhoux,et al.  Fate Mapping via Ms4a3-Expression History Traces Monocyte-Derived Cells , 2019, Cell.

[5]  J. Schütte,et al.  LSD1 inhibition by tranylcypromine derivatives interferes with GFI1-mediated repression of PU.1 target genes and induces differentiation in AML , 2019, Leukemia.

[6]  B. Scheijen,et al.  Tumor suppressors BTG1 and BTG2: Beyond growth control , 2018, Journal of cellular physiology.

[7]  Y. Saeys,et al.  The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages , 2018, Immunity.

[8]  Piero Carninci,et al.  Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli , 2018, Open Biology.

[9]  R. König,et al.  USP18 (UBP43) Abrogates p21-Mediated Inhibition of HIV-1 , 2018, Journal of Virology.

[10]  Stefan Wiemann,et al.  Assembly of a parts list of the human mitotic cell cycle machinery , 2018, bioRxiv.

[11]  T. Hughes,et al.  The Human Transcription Factors , 2018, Cell.

[12]  Q. Mo,et al.  The stem cell factor SALL4 is an essential transcriptional regulator in mixed lineage leukemia-rearranged leukemogenesis , 2017, Journal of Hematology & Oncology.

[13]  D. Hume,et al.  Transcriptional mechanisms that control expression of the macrophage colony-stimulating factor receptor locus. , 2017, Clinical science.

[14]  R. Baron,et al.  ZFP521 regulates murine hematopoietic stem cell function and facilitates MLL-AF9 leukemogenesis in mouse and human cells. , 2017, Blood.

[15]  R. Schinazi,et al.  A CRISPR/Cas9 approach reveals that the polymerase activity of DNA polymerase β is dispensable for HIV-1 infection in dividing and nondividing cells , 2017, The Journal of Biological Chemistry.

[16]  Michael P Snyder,et al.  Static and dynamic DNA loops form AP-1 bound activation hubs during macrophage development , 2017, bioRxiv.

[17]  M. Fischer,et al.  Census and evaluation of p53 target genes , 2017, Oncogene.

[18]  Geoffrey J Faulkner,et al.  Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease , 2017, PLoS genetics.

[19]  G. Basso,et al.  ZNF521 sustains the differentiation block in MLL-rearranged acute myeloid leukemia , 2017, Oncotarget.

[20]  A. Mandoli,et al.  MLL-AF9 and MLL-AF4 oncofusion proteins bind a distinct enhancer repertoire and target the RUNX1 program in 11q23 acute myeloid leukemia , 2017, Oncogene.

[21]  Ashley R. Woodfin,et al.  Therapeutic Targeting of MLL Degradation Pathways in MLL-Rearranged Leukemia , 2017, Cell.

[22]  K. Shah,et al.  ABL2 suppresses FLT3-ITD-induced cell proliferation through negative regulation of AKT signaling , 2017, Oncotarget.

[23]  C. Glass,et al.  Deleting an Nr4a1 Super-Enhancer Subdomain Ablates Ly6Clow Monocytes while Preserving Macrophage Gene Function. , 2016, Immunity.

[24]  J. Hess,et al.  A new target for differentiation therapy in AML , 2016, Cell Research.

[25]  M. Heinzelmann,et al.  THP-1 cells as a model for human monocytes. , 2016, Annals of translational medicine.

[26]  F. Wang,et al.  The PU.1-Modulated MicroRNA-22 Is a Regulator of Monocyte/Macrophage Differentiation and Acute Myeloid Leukemia , 2016, PLoS genetics.

[27]  N. Dyson.  RB1: a prototype tumor suppressor and an enigma , 2016, Genes & development.

[28]  Lei Dong,et al.  ZFP36L1 promotes monocyte/macrophage differentiation by repressing CDK6 , 2015, Scientific Reports.

[29]  M. L. Le Beau,et al.  Reduced DOCK4 expression leads to erythroid dysplasia in myelodysplastic syndromes , 2015, Proceedings of the National Academy of Sciences.

[30]  Thomas J. Ha,et al.  Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells , 2015, Science.

[31]  Piero Carninci,et al.  Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells , 2015, Journal of leukocyte biology.

[32]  Boris Lenhard,et al.  CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses , 2015, Nucleic acids research.

[33]  M. Malumbres.  Cyclin-dependent kinases , 2014, Genome Biology.

[34]  K. Helin,et al.  The Histone Lysine Demethylase JMJD3/KDM6B Is Recruited to p53 Bound Promoters and Enhancer Elements in a p53 Dependent Manner , 2014, PloS one.

[35]  Piero Carninci,et al.  Transcription and enhancer profiling in human monocyte subsets. , 2014, Blood.

[36]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[37]  Cesare Furlanello,et al.  A promoter-level mammalian expression atlas , 2015 .

[38]  C. Carlson,et al.  Genetic variation associated with circulating monocyte count in the eMERGE Network. , 2013, Human molecular genetics.

[39]  A. Ross,et al.  Retinoic acid and tumor necrosis factor-α induced monocytic cell gene expression is regulated in part by induction of transcription factor MafB. , 2012, Experimental cell research.

[40]  S. Armstrong,et al.  EVI1 is critical for the pathogenesis of a subset of MLL-AF9-rearranged AMLs. , 2012, Blood.

[41]  Piero Carninci,et al.  5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing , 2012, Nature Protocols.

[42]  Johann Meyer,et al.  CCAAT/Enhancer-binding Protein β Inhibits Proliferation in Monocytic Cells by Affecting the Retinoblastoma Protein/E2F/Cyclin E Pathway but Is Not Directly Required for Macrophage Morphology , 2011, The Journal of Biological Chemistry.

[43]  S. Lorkowski,et al.  Selection of reliable reference genes during THP-1 monocyte differentiation into macrophages , 2010, BMC Molecular Biology.

[44]  K. Nakai,et al.  The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection , 2010, Nature Immunology.

[45]  Jun Kawai,et al.  The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells. , 2010, Molecular immunology.

[46]  M Suzuki,et al.  Explorer Induction of microRNAs , mir-155 , mir-222 , mir-424 and mir-503 , promotes monocytic differentiation through combinatorial regulation , 2010 .

[47]  N. Wilson,et al.  Gfi1 Expression Is Controlled by Five Distinct Regulatory Regions Spread over 100 Kilobases, with Scl/Tal1, Gata2, PU.1, Erg, Meis1, and Runx1 Acting as Upstream Regulators in Early Hematopoietic Cells , 2010, Molecular and Cellular Biology.

[48]  Sobia Raza,et al.  Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations. , 2010, Genomics.

[49]  Valerio Embrione,et al.  A Gene Network Regulating Lysosomal Biogenesis and Function , 2009, Science.

[50]  Martin S. Taylor,et al.  The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line , 2009, Nature Genetics.

[51]  D. Cooper,et al.  Distinct Mechanisms of Regulation by Ca2+/Calmodulin of Type 1 and 8 Adenylyl Cyclases Support Their Different Physiological Roles* , 2009, Journal of Biological Chemistry.

[52]  E. Stupka,et al.  Tprg, a gene predominantly expressed in skin, is a direct target of the transcription factor p63. , 2008, The Journal of investigative dermatology.

[53]  B. Ducommun,et al.  G2/M checkpoint stringency is a key parameter in the sensitivity of AML cells to genotoxic stress , 2008, Oncogene.

[54]  Brad T. Sherman,et al.  The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists , 2007, Genome Biology.

[55]  R. Verhaak,et al.  A distal single nucleotide polymorphism alters long-range regulation of the PU.1 gene in acute myeloid leukemia. , 2007, The Journal of clinical investigation.

[56]  J. Savickienė,et al.  PI 3-K signaling pathway suppresses PMA-induced expression of p21WAF1/Cip1 in human leukemia cells , 2007, Molecular and Cellular Biochemistry.

[57]  Nicola K. Wilson,et al.  A Two-Step, PU.1-Dependent Mechanism for Developmentally Regulated Chromatin Remodeling and Transcription of the c-fms Gene , 2006, Molecular and Cellular Biology.

[58]  P. Biswas,et al.  Monocyte‐derived macrophages and myeloid cell lines as targets of HIV‐1 replication and persistence , 2006, Journal of leukocyte biology.

[59]  F. Ferrari,et al.  Identification of a molecular signature predictive of sensitivity to differentiation induction in acute myeloid leukemia , 2006, Leukemia.

[60]  P. Lásló,et al.  Multilineage Transcriptional Priming and Determination of Alternate Hematopoietic Cell Fates , 2006, Cell.

[61]  R. Zini,et al.  Virally mediated MafB transduction induces the monocyte commitment of human CD34+ hematopoietic stem/progenitor cells , 2006, Cell Death and Differentiation.

[62]  N. Pavletich,et al.  Structure of the Rb C-Terminal Domain Bound to E2F1-DP1: A Mechanism for Phosphorylation-Induced E2F Release , 2005, Cell.

[63]  K. Traore,et al.  Signal transduction of phorbol 12-myristate 13-acetate (PMA)-induced growth inhibition of human monocytic leukemia THP-1 cells is reactive oxygen dependent. , 2005, Leukemia research.

[64]  B. Teh,et al.  Functional Characterization of JMJD2A, a Histone Deacetylase- and Retinoblastoma-binding Protein* , 2005, Journal of Biological Chemistry.

[65]  Charles Auffray,et al.  Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces , 2005, Nucleic acids research.

[66]  J. Hess.  MLL: a histone methyltransferase disrupted in leukemia. , 2004, Trends in molecular medicine.

[67]  A. Ross,et al.  Retinoic acid regulates cell cycle progression and cell differentiation in human monocytic THP-1 cells. , 2004, Experimental cell research.

[68]  L. Pattacini,et al.  MLL-AF9 oncogene expression affects cell growth but not terminal differentiation and is downregulated during monocyte–macrophage maturation in AML-M5 THP-1 cells , 2003, Oncogene.

[69]  R. Verdun,et al.  p53 functions through stress- and promoter-specific recruitment of transcription initiation components before and after DNA damage. , 2003, Molecular cell.

[70]  A. Karginov,et al.  The association of ASAP1, an ADP ribosylation factor-GTPase activating protein, with focal adhesion kinase contributes to the process of focal adhesion assembly. , 2002, Molecular biology of the cell.

[71]  J. Holik,et al.  Signaling Complexes of the FERM Domain-containing Protein GRSP1 Bound to ARF Exchange Factor GRP1* , 2001, The Journal of Biological Chemistry.

[72]  H. Koeffler,et al.  p21WAF1 expression by an activator of protein kinase C is regulated mainly at the post-transcriptional level in cells lacking p53: important role of RNA stabilization. , 1999, The Biochemical journal.

[73]  A. Saunders,et al.  Divergent effects of bryostatin 1 and phorbol myristate acetate on cell cycle arrest and maturation in human myelomonocytic leukemia cells (U937). , 1998, Differentiation; research in biological diversity.

[74]  E. Reddy,et al.  cAMP-induced NF-κB (p50/relB) binding to a c-myb intronic enhancer correlates with c-myb up-regulation and inhibition of erythroleukemia cell differentiation , 1997, Oncogene.

[75]  D. Kufe,et al.  Functional expression of the macrophage colony-stimulating factor receptor in human THP-1 monocytic leukemia cells. , 1992, Blood.

[76]  R. Ulevitch,et al.  CD14, a receptor for complexes of lipopolysaccharide (LPS) and LPS binding protein. , 1990, Science.

[77]  E. Vellenga,et al.  Expression of the macrophage colony-stimulating factor and c-fms genes in human acute myeloblastic leukemia cells. , 1988, The Journal of clinical investigation.

[78]  J. Horiguchi,et al.  Expression of the macrophage specific colony-stimulating factor (CSF-1) during human monocytic differentiation. , 1986, Biochemical and biophysical research communications.

[79]  K. Tada,et al.  Induction of maturation in cultured human monocytic leukemia cells by a phorbol diester. , 1982, Cancer research.

[80]  Shigeru Tsuchiya,et al.  Establishment and characterization of a human acute monocytic leukemia cell line (THP‐1) , 1980, International journal of cancer.

[81]  A. Mandoli,et al.  MLL-AF 9 and MLL-AF 4 oncofusion proteins bind a distinct enhancer repertoire and target the RUNX 1 program in 11 q 23 acute myeloid leukemia , 2017 .

[82]  S. Ness,et al.  Myb proteins: angels and demons in normal and transformed cells. , 2011, Frontiers in bioscience.

[83]  T. Mak,et al.  p 53-dependent inhibition of FKHRL 1 in response to DNA damage through protein kinase SGK 1 , 2004 .

[84]  G. Stark,et al.  Analyzing the G2/M checkpoint. , 2004, Methods in molecular biology.

[85]  J V Watson,et al.  A pragmatic approach to the analysis of DNA histograms with a definable G1 peak. , 1987, Cytometry.

[86]  L. Sachs.  Control of growth and normal differentiation in leukemic cells: Regulation of the developmental program and restoration of the normal phenotype in myeloid leukemia , 1982, Journal of cellular physiology. Supplement.