Transcriptomic analysis of mononuclear phagocyte differentiation and activation

Immunological Reviews

Volumn 262, Issue 1, 2014, Pages 74-84

  Hume, David A ^a   Freeman, Tom C ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

CSF1; Dendritic cell; Macrophage; Transcriptome

Indexed keywords

TRANSCRIPTOME;

ANIMAL; ANTIBODY SPECIFICITY; CELL DIFFERENTIATION; CYTOLOGY; DENDRITIC CELL; FACTUAL DATABASE; GENE REGULATORY NETWORK; GENOMICS; HUMAN; IMMUNOLOGY; MACROPHAGE; MACROPHAGE ACTIVATION; METABOLISM; MONOCYTE; MONONUCLEAR PHAGOCYTE; PHYSIOLOGY; SIGNAL TRANSDUCTION; WEB BROWSER;

ANIMALS; CELL DIFFERENTIATION; DATABASES, FACTUAL; DENDRITIC CELLS; GENE REGULATORY NETWORKS; GENOMICS; HUMANS; MACROPHAGE ACTIVATION; MACROPHAGES; MONOCYTES; MONONUCLEAR PHAGOCYTE SYSTEM; ORGAN SPECIFICITY; SIGNAL TRANSDUCTION; TRANSCRIPTOME; WEB BROWSER;

EID: 84911126794     PISSN: 01052896     EISSN: 1600065X     Source Type: Journal    
DOI: 10.1111/imr.12211     Document Type: Article

References (108)

1. Geissmann F, Manz MG, Jung S, Sieweke MH, Merad M, Ley K. Development of monocytes, macrophages, and dendritic cells. Science 2010;327:656-661.
2. Gordon S, Taylor PR. Monocyte and macrophage heterogeneity. Nat Rev Immunol 2005;5:953-964.
3. Hume DA. The mononuclear phagocyte system. Curr Opin Immunol 2006;18:49-53.
4. Hume DA. Differentiation and heterogeneity in the mononuclear phagocyte system. Mucosal Immunol 2008;1:432-441.
5. Hume DA, MacDonald KP. Therapeutic applications of macrophage colony-stimulating factor-1 (CSF-1) and antagonists of CSF-1 receptor (CSF-1R) signaling. Blood 2012;119:1810-1820.
6. Wynn TA, Chawla A, Pollard JW. Macrophage biology in development, homeostasis and disease. Nature 2013;496:445-455.
7. Jenkins SJ, Hume DA. Homeostasis in the mononuclear phagocyte system. Trends Immunol 2014. doi: 10.1016/j.it.2014.06.006. [Epub ahead of print].
8. Sasmono RT, et al. Mouse neutrophilic granulocytes express mRNA encoding the macrophage colony-stimulating factor receptor (CSF-1R) as well as many other macrophage-specific transcripts and can transdifferentiate into macrophages in vitro in response to CSF-1. J Leukoc Biol 2007;82:111-123.
9. Ginhoux F, et al. Fate mapping analysis reveals that adult microglia derive from primitive macrophages. Science 2010;330:841-845.
10. Chorro L, et al. Langerhans cell (LC) proliferation mediates neonatal development, homeostasis, and inflammation-associated expansion of the epidermal LC network. J Exp Med 2009;206:3089-3100.
11. Hoeffel G, et al. Adult Langerhans cells derive predominantly from embryonic fetal liver monocytes with a minor contribution of yolk sac-derived macrophages. J Exp Med 2012;209:1167-1181.
12. Hashimoto D, et al. Tissue-resident macrophages self-maintain locally throughout adult life with minimal contribution from circulating monocytes. Immunity 2013;38:792-804.
13. Schulz C, et al. A lineage of myeloid cells independent of Myb and hematopoietic stem cells. Science 2012;336:86-90.
14. Yona S, et al. Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis. Immunity 2013;38:79-91.
15. Jenkins SJ, et al. IL-4 directly signals tissue-resident macrophages to proliferate beyond homeostatic levels controlled by CSF-1. J Exp Med 2013;210:2477-2491.
16. Davies LC, Jenkins SJ, Allen JE, Taylor PR. Tissue-resident macrophages. Nat Immunol 2013;14:986-995.
17. Nakamichi Y, Udagawa N, Takahashi N. IL-34 and CSF-1: similarities and differences. J Bone Mineral Metab 2013;31:486-495.
18. Garceau V, et al. Pivotal advance: avian colony-stimulating factor 1 (CSF-1), interleukin-34 (IL-34), and CSF-1 receptor genes and gene products. J Leukoc Biol 2010;87:753-764.
19. Liu H, et al. The mechanism of shared but distinct CSF-1R signaling by the non-homologous cytokines IL-34 and CSF-1. Biochim Biophys Acta 2012;1824:938-945.
20. Ma X, et al. Structural basis for the dual recognition of helical cytokines IL-34 and CSF-1 by CSF-1R. Structure 2012;20:676-687.
21. Pollard JW. Trophic macrophages in development and disease. Nat Rev Immunol 2009;9:259-270.
22. Nandi S, et al. The CSF-1 receptor ligands IL-34 and CSF-1 exhibit distinct developmental brain expression patterns and regulate neural progenitor cell maintenance and maturation. Dev Biol 2012;367:100-113.
23. Pridans C, Sauter KA, Baer K, Kissel H, Hume DA. CSF1R mutations in hereditary diffuse leukoencephalopathy with spheroids are loss of function. Scientific Rep 2013;3:3013.
24. MacDonald KP, et al. An antibody against the colony-stimulating factor 1 receptor depletes the resident subset of monocytes and tissue- and tumor-associated macrophages but does not inhibit inflammation. Blood 2010;116:3955-3963.
25. Sauter KA, et al. Pleiotropic effects of extended blockade of CSF1R signaling in adult mice. J Leukoc Biol 2014; doi: jlb.2A0114-006R.
26. Sasmono RT, et al. A macrophage colony-stimulating factor receptor-green fluorescent protein transgene is expressed throughout the mononuclear phagocyte system of the mouse. Blood 2003;101:1155-1163.
27. Hume DA. Applications of myeloid-specific promoters in transgenic mice support in vivo imaging and functional genomics but do not support the concept of distinct macrophage and dendritic cell lineages or roles in immunity. J Leukoc Biol 2010;89:525-538.
28. Ovchinnikov DA, van Zuylen WJ, DeBats CE, Alexander KA, Kellie S, Hume DA. Expression of Gal4-dependent transgenes in cells of the mononuclear phagocyte system labeled with enhanced cyan fluorescent protein using Csf1r-Gal4VP16/UAS-ECFP double-transgenic mice. J Leukoc Biol 2008;83:430-433.
29. van Zuylen WJ, et al. Macrophage activation and differentiation signals regulate schlafen-4 gene expression: evidence for Schlafen-4 as a modulator of myelopoiesis. PLoS ONE 2011;6:e15723.
30. Jacquelin S, et al. CX3CR1 reduces Ly6Chigh-monocyte motility within, and release from the bone marrow after chemotherapy in mice. Blood 2013;122:674-683.
31. Varol C, Zigmond E, Jung S. Securing the immune tightrope: mononuclear phagocytes in the intestinal lamina propria. Nat Rev Immunol 2010;10:415-426.
32. Pridans CE, Lillico S, Whitelaw CBA, Hume DA. Lentiviral vectors containing mouse Csf1r control elements direct macrophage-restricted expression in multiple species of birds and mammals. Mol Ther Methods Clin Dev 2014;1:14010.
33. Balic A, et al. Visualisation of the avian mononuclear phagocyte system using novel transgenic reporter genes based upon conserved elements of the CSF1R locus. Development 2014. [Epub ahead of print].
34. Ala U, et al. Prediction of human disease genes by human-mouse conserved coexpression analysis. PLoS Comput Biol 2008;4:e1000043.
35. Hume DA, Summers KM, Raza S, Baillie JK, Freeman TC. Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations. Genomics 2010;95:328-338.
36. Piro RM, et al. An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction. Eur J Hum Genet 2011;19:1173-1180.
37. Su AI, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004;101:6062-6067.
38. Theocharidis A, van Dongen S, Enright AJ, Freeman TC. Network visualization and analysis of gene expression data using BioLayout Express(3D). Nat Protoc 2009;4:1535-1550.
39. Freeman TC, et al. Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol 2007;3:2032-2042.
40. Mabbott NA, Baillie JK, Hume DA, Freeman TC. Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations. Immunobiology 2010;215:724-736.
41. Mabbott NA, Baillie JK, Brown H, Freeman TC, Hume DA. An expression atlas of human primary cells: inference of gene function from coexpression networks. BMC Genomics 2013;14:632.
42. Freeman TC, et al. A gene expression atlas of the domestic pig. BMC Biol 2012;10:90.
43. Andersson R, et al. Systematic in vivo characterization of the active enhancers across the human body. Nature 2014;507:455-461.
44. FANTOM Consortium and the RIKEN PMI and CLST (DGT), et al. A human gene expression atlas based upon promoter activity. Nature 2014;507:462-470.
45. Feng R, et al. PU.1 and C/EBPalpha/beta convert fibroblasts into macrophage-like cells. Proc Natl Acad Sci USA 2008;105:6057-6062.
46. Settembre C, et al. TFEB links autophagy to lysosomal biogenesis. Science 2011;332:1429-1433.
47. Rehli M, Lichanska A, Cassady AI, Ostrowski MC, Hume DA. TFEC is a macrophage-restricted member of the microphthalmia-TFE subfamily of basic helix-loop-helix leucine zipper transcription factors. J Immunol 1999;162:1559-1565.
48. Luchin A, et al. Genetic and physical interactions between Microphthalmia transcription factor and PU.1 are necessary for osteoclast gene expression and differentiation. J Biol Chem 2011;276:36703-36710.
49. Merad M, Sathe P, Helft J, Miller J, Mortha A. The dendritic cell lineage: ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting. Annu Rev Immunol 2013;31:563-604.
50. Liu K, Nussenzweig MC. Origin and development of dendritic cells. Immunol Rev 2010;234:45-54.
51. Mildner A, Jung S. Development and function of dendritic cell subsets. Immunity 2014;40:642-656.
52. Hume DA. Macrophages as APC and the dendritic cell myth. J Immunol 2008;181:5829-5835.
53. Hume DA, Mabbott N, Raza S, Freeman TC. Can DCs be distinguished from macrophages by molecular signatures? Nat Immunol 2013;14:187-189.
54. Miller JC, et al. Deciphering the transcriptional network of the dendritic cell lineage. Nat Immunol 2012;13:888-899.
55. Gautier EL, et al. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat Immunol 2012;13:1118-1128.
56. Inaba K, Swiggard WJ, Steinman RM, Romani N, Schuler G, Brinster C. Isolation of dendritic cells. Curr Protoc Immunol 2009;3:3.7.
57. Steinman RM, Cohn ZA. Identification of a novel cell type in peripheral lymphoid organs of mice. I. Morphology, quantitation, tissue distribution. J Exp Med 1973;137:1142-1162.
58. Belz GT, Nutt SL. Transcriptional programming of the dendritic cell network. Nat Rev Immunol 2012;12:101-113.
59. Hume DA. Plenary perspective: the complexity of constitutive and inducible gene expression in mononuclear phagocytes. J Leukoc Biol 2012;92:433-444.
60. Raza S, Barnett MW, Barnett-Itzhaki Z, Amit I, Hume DA, Freeman TC. Analysis of the transcriptional networks underpinning the activation of murine macrophages by inflammatory mediators. J Leukoc Biol 2014; doi:jlb.6HI0313-169R.
61. Butovsky O, et al. Identification of a unique TGF-beta-dependent molecular and functional signature in microglia. Nat Neurosci 2014;17:131-143.
62. Geissmann F, Jung S, Littman DR. Blood monocytes consist of two principal subsets with distinct migratory properties. Immunity 2003;19:71-82.
63. Ziegler-Heitbrock L. Monocyte subsets in man and other species. Cell Immunol 2014;289:135-139.
64. Zigmond E, Jung S. Intestinal macrophages: well educated exceptions from the rule. Trends Immunol 2013;34:162-168.
65. Cros J, et al. Human CD14dim monocytes patrol and sense nucleic acids and viruses via TLR7 and TLR8 receptors. Immunity 2010;33:375-386.
66. Ingersoll MA, et al. Comparison of gene expression profiles between human and mouse monocyte subsets. Blood 2010;115:e10-e19.
67. Fairbairn L, et al. Comparative analysis of monocyte subsets in the pig. J Immunol 2013;190:6389-6396.
68. Schmidl C, et al. Transcription and enhancer profiling in human monocyte subsets. Blood 2014;123:e90-e99.
69. Carlin LM, et al. Nr4a1-dependent Ly6C(low) monocytes monitor endothelial cells and orchestrate their disposal. Cell 2013;153:362-375.
70. Gordon S, Martinez FO. Alternative activation of macrophages: mechanism and functions. Immunity 2010;32:593-604.
71. Taylor PR, Gordon S. Monocyte heterogeneity and innate immunity. Immunity 2003;19:2-4.
72. Sica A, Mantovani A. Macrophage plasticity and polarization: in vivo veritas. J Clin Invest 2012;122:787-795.
73. Schroder K, Hertzog PJ, Ravasi T, Hume DA. Interferon-gamma: an overview of signals, mechanisms and functions. J Leukoc Biol 2004;75:163-189.
74. Lawrence T, Natoli G. Transcriptional regulation of macrophage polarization: enabling diversity with identity. Nat Rev Immunol 2011;11:750-761.
75. Martinez FO, Sica A, Mantovani A, Locati M. Macrophage activation and polarization. Front Biosci 2008;13:453-461.
76. Bhatt DM, et al. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 2012;150:279-290.
77. Ghisletti S, et al. Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 2010;32:317-328.
78. Gilchrist M, et al. Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 2006;441:173-178.
79. Kaikkonen MU, et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell 2013;51:310-325.
80. Nilsson R, et al. Transcriptional network dynamics in macrophage activation. Genomics 2006;88:133-142.
81. Ostuni R, et al. Latent enhancers activated by stimulation in differentiated cells. Cell 2013;152:157-171.
82. Wells CA, Ravasi T, Hume DA. Inflammation suppressor genes: please switch out all the lights. J Leukoc Biol 2005;78:9-13.
83. Nguyen KD, et al. Alternatively activated macrophages produce catecholamines to sustain adaptive thermogenesis. Nature 2012;480:104-108.
84. Rehli M, et al. Transcription factor Tfec contributes to the IL-4-inducible expression of a small group of genes in mouse macrophages including the granulocyte colony-stimulating factor receptor. J Immunol 2005;174:7111-7122.
85. Schroder K, et al. Conservation and divergence in toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proc Natl Acad Sci USA 2012;109:E944-E953.
86. Kapetanovic R, et al. Pig bone marrow-derived macrophages resemble human macrophages in their response to bacterial lipopolysaccharide. J Immunol 2012;188:3382-3394.
87. Mosser DM, Edwards JP. Exploring the full spectrum of macrophage activation. Nat Rev Immunol 2008;8:958-969.
88. Xue J, et al. Transcriptome-based network analysis reveals a spectrum model of human macrophage activation. Immunity 2014;40:274-288.
89. Qian BZ, Pollard JW. Macrophage diversity enhances tumor progression and metastasis. Cell 2010;141:39-51.
90. Doig TN, Hume DA, Theocharidis T, Goodlad JR, Gregory CD, Freeman TC. Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment. BMC Genomics 2013;14:469.
91. Kapetanovic R, et al. The impact of breed and tissue compartment on the response of pig macrophages to lipopolysaccharide. BMC Genomics 2013;14:581.
92. Fairfax BP, et al. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science 2014;343:1246949.
93. Everitt AR, et al. IFITM3 restricts the morbidity and mortality associated with influenza. Nature 2012;484:519-523.
94. Ramilo O, et al. Gene expression patterns in blood leukocytes discriminate patients with acute infections. Blood 2007;109:2066-2077.
95. Chaussabel D, Baldwin N. Democratizing systems immunology with modular transcription repertoire analysis. Nat Rev Immunol 2014;14:271-280.
96. Li H, Ice JA, Lessard CJ, Sivils KL. Interferons in Sjogren's syndrome: genes, mechanisms, and effects. Front Immunol 2013;4:290.
97. Ronnblom L, Eloranta ML. The interferon signature in autoimmune diseases. Curr Opin Rheumatol 2013;25:248-253.
98. Medzhitov R, Horng T. Transcriptional control of the inflammatory response. Nat Rev Immunol 2009;9:692-703.
99. Hargreaves DC, Horng T, Medzhitov R. Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 2009;138:129-145.
100. Carninci P, et al. The transcriptional landscape of the mammalian genome. Science 2005;309:1559-1563.
101. Carninci P, et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 2006;38:626-635.
102. Balwierz PJ, et al. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol 2009;10:R79.
103. Takeuchi O, Akira S. Pattern recognition receptors and inflammation. Cell 2010;140:805-820.
104. Amit I, et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 2009;326:257-263.
105. Hume DA. Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood 2000;96:2323-2328.
106. Suzuki H, et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 2009;41:553-562.
107. Reddy MA, et al. Opposing actions of c-ets/PU.1 and c-myb protooncogene products in regulating the macrophage-specific promoters of the human and mouse colony-stimulating factor-1 receptor (c-fms) genes. J Exp Med 1994;180:2309-2319.
108. Robert C, Lu X, Law A, Freeman TC, Hume DA. Macrophages.com: an on-line community resource for innate immunity research. Immunobiology 2011;216:1203-1211.