PHAGOCYTES, GRANULOCYTES, AND MYELOPOIESIS Transcription and enhancer pro fi ling in human monocyte subsets

Human blood monocytes comprise at least 3 subpopulations that differ in phenotype and function. Here, we present the first in-depth regulome analysis of human classical (CD14(++)CD16(-)), intermediate (CD14(+)CD16(+)), and nonclassical (CD14(dim)CD16(+)) monocytes. Cap analysis of gene expression adapted to Helicos single-molecule sequencing was used to map transcription start sites throughout the genome in all 3 subsets. In addition, global maps of H3K4me1 and H3K27ac deposition were generated for classical and nonclassical monocytes defining enhanceosomes of the 2 major subsets. We identified differential regulatory elements (including promoters and putative enhancers) that were associated with subset-specific motif signatures corresponding to different transcription factor activities and exemplarily validated novel downstream enhancer elements at the CD14 locus. In addition to known subset-specific features, pathway analysis revealed marked differences in metabolic gene signatures. Whereas classical monocytes expressed higher levels of genes involved in carbohydrate metabolism, priming them for anaerobic energy production, nonclassical monocytes expressed higher levels of oxidative pathway components and showed a higher mitochondrial routine activity. Our findings describe promoter/enhancer landscapes and provide novel insights into the specific biology of human monocyte subsets.

[1]  Piotr J. Balwierz,et al.  The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations. , 2014, Blood.

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

[3]  J. Wysocka,et al.  Modification of enhancer chromatin: what, how, and why? , 2013, Molecular cell.

[4]  D. Hume,et al.  The Function of the Conserved Regulatory Element within the Second Intron of the Mammalian Csf1r Locus , 2013, PloS one.

[5]  C. Benner,et al.  Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states. , 2012, Blood.

[6]  R. Xavier,et al.  Regulation of monocyte functional heterogeneity by miR-146a and Relb. , 2012, Cell reports.

[7]  Stefan Schewe,et al.  Transcript profiling of CD16‐positive monocytes reveals a unique molecular fingerprint , 2012, European journal of immunology.

[8]  S. Wong,et al.  The three human monocyte subsets: implications for health and disease , 2012, Immunologic Research.

[9]  D. Hume,et al.  Therapeutic applications of macrophage colony-stimulating factor-1 (CSF-1) and antagonists of CSF-1 receptor (CSF-1R) signaling. , 2012, Blood.

[10]  Björn Rotter,et al.  SuperSAGE evidence for CD14++CD16+ monocytes as a third monocyte subset. , 2011, Blood.

[11]  Wing-Cheong Wong,et al.  Gene expression profiling reveals the defining features of the classical, intermediate, and nonclassical human monocyte subsets. , 2011, Blood.

[12]  P. Scacheri,et al.  Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. , 2011, Genome research.

[13]  F. Geissmann,et al.  The transcription factor NR4A1 (Nur77) controls bone marrow differentiation and the survival of Ly6C− monocytes , 2011, Nature Immunology.

[14]  Y. Hayashizaki,et al.  Unamplified cap analysis of gene expression on a single-molecule sequencer. , 2011, Genome Research.

[15]  Ryan A. Flynn,et al.  A unique chromatin signature uncovers early developmental enhancers in humans , 2011, Nature.

[16]  R. Young,et al.  Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.

[17]  Damian Szklarczyk,et al.  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored , 2010, Nucleic Acids Res..

[18]  S. Wong,et al.  The CD14+/lowCD16+ monocyte subset is more susceptible to spontaneous and oxidant-induced apoptosis than the CD14+CD16− subset , 2010, Cell Death and Disease.

[19]  R. Kaiser,et al.  Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models , 2010, PloS one.

[20]  Silvano Sozzani,et al.  Nomenclature of monocytes and dendritic cells in blood. , 2010, Blood.

[21]  Jie Dong,et al.  Hfq Is a Global Regulator That Controls the Pathogenicity of Staphylococcus aureus , 2010, PloS one.

[22]  P. Geurts,et al.  Inferring Regulatory Networks from Expression Data Using Tree-Based Methods , 2010, PloS one.

[23]  J. Casanova,et al.  Human CD14dim Monocytes Patrol and Sense Nucleic Acids and Viruses via TLR7 and TLR8 Receptors , 2010, Immunity.

[24]  S. Akira,et al.  Myeloid Differentiation Factor 88 (MyD88)-Deficiency Increases Risk of Diabetes in Mice , 2010, PloS one.

[25]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[26]  Steffen Jung,et al.  Development of Monocytes, Macrophages, and Dendritic Cells , 2010, Science.

[27]  Claudio Lottaz,et al.  Comparison of gene expression profiles between human and mouse monocyte subsets. , 2010, Blood.

[28]  Steffen Jung,et al.  Monocytes: subsets, origins, fates and functions , 2010, Current opinion in hematology.

[29]  David J. Adams,et al.  The IFITM Proteins Mediate Cellular Resistance to Influenza A H1N1 Virus, West Nile Virus, and Dengue Virus , 2009, Cell.

[30]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[31]  Kuang-Yu Liu,et al.  Transcriptional profiling reveals developmental relationship and distinct biological functions of CD16+ and CD16- monocyte subsets , 2009, BMC Genomics.

[32]  Piotr J. Balwierz,et al.  Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data , 2009, Genome Biology.

[33]  Christian Schmidl,et al.  Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity. , 2009, Genome research.

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

[35]  F. Geissmann,et al.  Blood monocytes: development, heterogeneity, and relationship with dendritic cells. , 2009, Annual review of immunology.

[36]  Nathaniel D. Heintzman,et al.  Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.

[37]  D. Hume,et al.  Differentiation and heterogeneity in the mononuclear phagocyte system , 2008, Mucosal Immunology.

[38]  L. Schwarzfischer,et al.  CCAAT Enhancer-binding Protein β Regulates Constitutive Gene Expression during Late Stages of Monocyte to Macrophage Differentiation* , 2007, Journal of Biological Chemistry.

[39]  L. Ziegler‐Heitbrock,et al.  The CD14+ CD16+ blood monocytes: their role in infection and inflammation , 2007, Journal of leukocyte biology.

[40]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[41]  S Miyano,et al.  Open source clustering software. , 2004, Bioinformatics.

[42]  R. Kofler,et al.  Changes of mitochondrial respiration, mitochondrial content and cell size after induction of apoptosis in leukemia cells. , 2003, Biochimica et biophysica acta.

[43]  R. Margreiter,et al.  Evaluation of mitochondrial respiratory function in small biopsies of liver. , 2002, Analytical biochemistry.

[44]  K. Akashi,et al.  Regulation of the PU.1 gene by distal elements. , 2001, Blood.

[45]  M. Ernst,et al.  Heterogeneity of human peripheral blood monocyte subsets , 2001, Journal of leukocyte biology.

[46]  Dong-er Zhang,et al.  Hepatocytes Contribute to Soluble CD14 Production, and CD14 Expression Is Differentially Regulated in Hepatocytes and Monocytes* , 2000, The Journal of Biological Chemistry.

[47]  C. Weber,et al.  Differential chemokine receptor expression and function in human monocyte subpopulations , 2000, Journal of leukocyte biology.

[48]  L. Schwarzfischer,et al.  PU.1 and Interferon Consensus Sequence-binding Protein Regulate the Myeloid Expression of the Human Toll-like Receptor 4 Gene* , 2000, The Journal of Biological Chemistry.

[49]  P. Kingsley,et al.  Characterization of human endotoxin lipopolysaccharide receptor CD14 expression in transgenic mice. , 1999, Journal of immunology.

[50]  D. Pette,et al.  Chronic stimulation of rat skeletal muscle induces coordinate increases in mitochondrial and nuclear mRNAs of cytochrome-c-oxidase subunits. , 1989, European journal of biochemistry.

[51]  J. Holloszy,et al.  Mitochondrial citric acid cycle and related enzymes: adaptive response to exercise. , 1970, Biochemical and biophysical research communications.

[52]  Claudio Lottaz,et al.  Comparison of gene expression profiles between human and mouse monocyte , 2016 .

[53]  D. Hume,et al.  The transcriptional regulation of the Colony-Stimulating Factor 1 Receptor (csf1r) gene during hematopoiesis. , 2008, Frontiers in bioscience : a journal and virtual library.

[54]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[55]  L. Schwarzfischer,et al.  CCAAT Enhancer-binding Protein Regulates Constitutive Gene Expression during Late Stages of Monocyte to Macrophage Differentiation* , 2007 .

[56]  F. Offner,et al.  Preserved coupling of oxidative phosphorylation but decreased mitochondrial respiratory capacity in IL-1β-treated human peritoneal mesothelial cells , 2006, Cell Biochemistry and Biophysics.

[57]  Piero Carninci,et al.  Unamplified Cap Analysis of Gene Expression on a Single-molecule Sequencer , 2022 .