Transcriptional and epigenetic networks in the development and maturation of dendritic cells

Epigenomics

Volumn 5, Issue 2, 2013, Pages 195-204

  Kim, Hyoung Pyo ^a   Lee, Yeon Su ^b   Park, Jong Hoon ^c   Kim, Young Joon ^d  

^a Yonsei University College of Medicine   (South Korea)

^b National Cancer Center   (South Korea)

^c Sookmyung Women's University   (South Korea)

^d Yonsei University   (South Korea)

Author keywords

chromatin; dendritic cells; DNA methylation; epigenetic; histone; lineage; transcriptional network

Indexed keywords

CYTOKINE; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ANTIGEN PRESENTATION; CELL DIFFERENTIATION; CELL FUNCTION; CELL HETEROGENEITY; CELL LINEAGE; CELL MATURATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; DENDRITIC CELL; DNA METHYLATION; EPIGENETICS; GENE EXPRESSION; HEMATOPOIETIC STEM CELL; HISTONE MODIFICATION; HUMAN; MACROPHAGE; MONOCYTE; PHENOTYPE; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

ADAPTIVE IMMUNITY; CELL DIFFERENTIATION; CELL LINEAGE; CHROMATIN; CYTOKINES; DENDRITIC CELLS; EPIGENESIS, GENETIC; GENE REGULATORY NETWORKS; HUMANS; IMMUNITY, INNATE; SIGNAL TRANSDUCTION;

EID: 84876154364     PISSN: 17501911     EISSN: 1750192X     Source Type: Journal    
DOI: 10.2217/epi.13.14     Document Type: Review

References (77)

1. Kanno Y, Vahedi G, Hirahara K, Singleton K, O'Shea JJ. Transcriptional and epigenetic control of T helper cell specification: molecular mechanisms underlying commitment and plasticity. Ann. Rev. Immunol. 30, 707-731 (2012).
2. Fisher CL, Fisher AG. Chromatin states in pluripotent, differentiated, and reprogrammed cells. Curr. Opin. Genet. Dev. 21(2), 140-146 (2011).
3. Miller JC, Brown BD, Shay T et al. Deciphering the transcriptional network of the dendritic cell lineage. Nat. Rev. Immunol. 13(9), 888-899 (2012).
4. Steinman RM. Decisions about dendritic cells: past, present, and future. Ann. Rev. Immunol. 30, 1-22 (2012).
5. Geissmann F, Manz MG, Jung S, Sieweke MH, Merad M, Ley K. Development of monocytes, macrophages, and dendritic cells. Science 327(5966), 656-661 (2010).
6. Trombetta ES, Mellman I. Cell biology of antigen processing in vitro and in vivo. Ann. Rev. Immunol. 23, 975-1028 (2005). (Pubitemid 40563191)
7. Randolph GJ, Angeli V, Swartz MA. Dendritic-cell trafficking to lymph nodes through lymphatic vessels. Nat. Rev. Immunol. 5(8), 617-628 (2005). (Pubitemid 41113193)
8. Morelli AE, Thomson AW. Tolerogenic dendritic cells and the quest for transplant tolerance. Nat. Rev. Immunol. 7(8), 610-621 (2007). (Pubitemid 47123548)
9. Heath WR, Carbone FR. Dendritic cell subsets in primary and secondary T cell responses at body surfaces. Nat. Rev. Immunol. 10(12), 1237-1244 (2009).
10. Shortman K, Liu YJ. Mouse and human dendritic cell subtypes. Nat. Rev. Immunol. 2(3), 151-161 (2002). (Pubitemid 37336516)
11. Steinman RM, Cohn ZA. Identif?ication of a novel cell type in peripheral lymphoid organs of mice. I. Morphology, quantitation, tissue distribution. J. Exp. Med. 137(5), 1142-1162 (1973).
12. Den Haan JM, Lehar SM, Bevan MJ. CD8(+) but not CD8(-) dendritic cells crossprime cytotoxic T cells in vivo. J. Exp. Med. 192(12), 1685-1696 (2000).
13. Pooley JL, Heath WR, Shortman K. Cutting edge: intravenous soluble antigen is presented to CD4 T cells by CD8- dendritic cells, but cross-presented to CD8 T cells by CD8+ dendritic cells. J. Immunol. 166(9), 5327-5330 (2001). (Pubitemid 32374150)
14. Dudziak D, Kamphorst AO, Heidkamp GF et al. Differential antigen processing by dendritic cell subsets in vivo. Science 315(5808), 107-111 (2007). (Pubitemid 46196991)
15. Kamphorst AO, Guermonprez P, Dudziak D, Nussenzweig MC. Route of antigen uptake differentially impacts presentation by dendritic cells and activated monocytes. J. Immunol. 185(6), 3426-3435 (2010).
16. Helft J, Ginhoux F, Bogunovic M, Merad M. Origin and functional heterogeneity of nonlymphoid tissue dendritic cells in mice. Immunol. Rev. 234(1), 55-75 (2010).
17. Liu K, Nussenzweig MC. Origin and development of dendritic cells. Immunol. Rev. 234(1), 45-54 (2010).
18. Belz GT, Smith CM, Kleinert L et al. Distinct migrating and nonmigrating dendritic cell populations are involved in MHC class I-restricted antigen presentation after lung infection with virus. Proc. Natl Acad. Sci. USA 101(23), 8670-8675 (2004).
19. Bedoui S, Whitney PG, Waithman J et al. Cross-presentation of viral and self antigens by skin-derived CD103+ dendritic cells. Nat. Rev. Immunol. 10(5), 488-495 (2009).
20. Reizis B, Bunin A, Ghosh HS, Lewis KL, Sisirak V. Plasmacytoid dendritic cells: recent progress and open questions. Ann. Rev. Immunol. 29, 163-183 (2011).
21. Reizis B, Colonna M, Trinchieri G, Barrat F, Gilliet M. Plasmacytoid dendritic cells: onetrick ponies or workhorses of the immune system? Nat. Rev. Immunol. 11(8), 558-565 (2011).
22. Grouard G, Rissoan MC, Filgueira L, Durand I, Banchereau J, Liu YJ. The enigmatic plasmacytoid T cells develop into dendritic cells with interleukin (IL)-3 and CD40- ligand. J. Exp. Med. 185(6), 1101-1111 (1997). (Pubitemid 27136802)
23. Blasius AL, Giurisato E, Cella M, Schreiber RD, Shaw AS, Colonna M. Bone marrow stromal cell antigen 2 is a specific marker of type I IFN-producing cells in the naive mouse, but a promiscuous cell surface antigen following IFN stimulation. J. Immunol. 177(5), 3260-3265 (2006). (Pubitemid 44277845)
24. Zhang J, Raper A, Sugita N et al. Characterization of Siglec-H as a novel endocytic receptor expressed on murine plasmacytoid dendritic cell precursors. Blood 107(9), 3600-3608 (2006).
25. Dzionek A, Sohma Y, Nagafune J et al. BDCA-2, a novel plasmacytoid dendritic cellspecific type II C-type lectin, mediates antigen capture and is a potent inhibitor of interferon alpha/beta induction. J. Exp. Med. 194(12), 1823-1834 (2001). (Pubitemid 34028661)
26. Auffray C, Sieweke MH, Geissmann F. Blood monocytes: development, heterogeneity, and relationship with dendritic cells. Ann. Rev. Immunol. 27, 669-692 (2009).
27. Inaba K, Inaba M, Romani N et al. Generation of large numbers of dendritic cells from mouse bone marrow cultures supplemented with granulocyte/macrophage colony-stimulating factor. J. Exp. Med. 176(6), 1693-1702 (1992).
28. Sallusto F, Lanzavecchia A. Efficient presentation of soluble antigen by cultured human dendritic cells is maintained by granulocyte/macrophage colony-stimulating factor plus interleukin 4 and downregulated by tumor necrosis factor alpha. J. Exp. Med. 179(4), 1109-1118 (1994).
29. Cheong C, Matos I, Choi JH et al. Microbial stimulation fully differentiates monocytes to DC-SIGN/CD209(+) dendritic cells for immune T cell areas. Cell 143(3), 416-429 (2010).
30. D'amico A, Wu L. The early progenitors of mouse dendritic cells and plasmacytoid predendritic cells are within the bone marrow hemopoietic precursors expressing Flt3. J. Exp. Med. 198(2), 293-303 (2003). (Pubitemid 36987854)
31. Fogg DK, Sibon C, Miled C et al. A clonogenic bone marrow progenitor specific for macrophages and dendritic cells. Science 311(5757), 83-87 (2006). (Pubitemid 43063063)
32. Onai N, Obata-Onai A, Schmid MA, Ohteki T, Jarrossay D, Manz MG. Identification of clonogenic common Flt3+M-CSFR+ plasmacytoid and conventional dendritic cell progenitors in mouse bone marrow. Nat. Immunol. 8(11), 1207-1216 (2007). (Pubitemid 350011759)
33. Naik SH, Sathe P, Park HY et al. Development of plasmacytoid and conventional dendritic cell subtypes from single precursor cells derived in vitro and in vivo. Nat. Immunol. 8(11), 1217-1226 (2007). (Pubitemid 350011760)
34. Naik SH, Metcalf D, Van Nieuwenhuijze A et al. Intrasplenic steady-state dendritic cell precursors that are distinct from monocytes. Nat. Immunol. 7(6), 663-671 (2006). (Pubitemid 43797348)
35. Liu K, Victora GD, Schwickert TA et al. In vivo analysis of dendritic cell development and homeostasis. Science 324(5925), 392-397 (2009).
36. Bogunovic M, Ginhoux F, Helft J et al. Origin of the lamina propria dendritic cell network. Immunity 31(3), 513-525 (2009).
37. Amit I, Garber M, Chevrier N et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 326(5950), 257-263 (2009).
38. Garber M, Yosef N, Goren A et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47(5), 810-822 (2012).
39. Bennett CL, Clausen BE. DC ablation in mice: promises, pitfalls, and challenges. Trends Immunol. 28(12), 525-531 (2007).
40. Probst HC, Tschannen K, Odermatt B, Schwendener R, Zinkernagel RM, Van Den Broek M. Histological analysis of CD11c- DTR/GFP mice after in vivo depletion of dendritic cells. Clin. Exp. Immunol. 141(3), 398-404 (2005). (Pubitemid 41075862)
41. 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. Leukocyte Biol. 89(4), 525-538 (2011).
42. Van Rijt LS, Jung S, Kleinjan A et al. In vivo depletion of lung CD11c+ dendritic cells during allergen challenge abrogates the characteristic features of asthma. J. Exp. Med. 201(6), 981- 991 (2005). (Pubitemid 40524467)
43. Reizis B. Regulation of plasmacytoid dendritic cell development. Curr. Opin. Immunol. 22(2), 206-211 (2010).
44. Meredith MM, Liu K, Darrasse-Jeze G et al. Expression of the zinc finger transcription factor zDC (Zbtb46, Btbd4) defines the classical dendritic cell lineage. J. Exp. Med. 209(6), 1153-1165 (2012).
45. Satpathy AT, Kc W, Albring JC et al. Zbtb46 expression distinguishes classical dendritic cells and their committed progenitors from other immune lineages. J. Exp. Med. 209(6), 1135- 1152 (2012).
46. Waskow C, Liu K, Darrasse-Jeze G et al. The receptor tyrosine kinase Flt3 is required for dendritic cell development in peripheral lymphoid tissues. Nat. Immunol. 9(6), 676-683 (2008). (Pubitemid 351712638)
47. Lyman SD, James L, Escobar S et al. Identification of soluble and membrane-bound isoforms of the murine flt3 ligand generated by alternative splicing of mRNAs. Oncogene 10(1), 149-157 (1995).
48. Ohl L, Mohaupt M, Czeloth N et al. CCR7 governs skin dendritic cell migration under inflammatory and steady-state conditions. Immunity 21(2), 279-288 (2004). (Pubitemid 39094056)
49. Jelinek I, Leonard JN, Price GE et al. TLR3- specific double-stranded RNA oligonucleotide adjuvants induce dendritic cell cross-presentation, CTL responses, and antiviral protection. J. Immunol. 186(4), 2422-2429 (2011).
50. Dorner BG, Dorner MB, Zhou X et al. Selective expression of the chemokine receptor XCR1 on cross-presenting dendritic cells determines cooperation with CD8+ T cells. Immunity 31(5), 823-833 (2009).
51. Sharpe AH, Wherry EJ, Ahmed R, Freeman GJ. The function of programmed cell death 1 and its ligands in regulating autoimmunity and infection. Nat. Immunol. 8(3), 239-245 (2007). (Pubitemid 46745373)
52. Travis MA, Reizis B, Melton AC et al. Loss of integrin alpha(v)beta8 on dendritic cells causes autoimmunity and colitis in mice. Nature 449(7160), 361-365 (2007). (Pubitemid 47443473)
53. Posselt G, Schwarz H, Duschl A, Horejs- Hoeck J. Suppressor of cytokine signaling 2 is a feedback inhibitor of TLR-induced activation in human monocyte-derived dendritic cells. J. Immunol. 187(6), 2875-2884 (2011).
54. Yagil Z, Nechushtan H, Kay G, Yang CM, Kemeny DM, Razin E. The enigma of the role of protein inhibitor of activated STAT3 (PIAS3) in the immune response. Trends Immunol. 31(5), 199-204 (2010).
55. Minas K, Liversidge J. Is the CD200/CD200 receptor interaction more than just a myeloid cell inhibitory signal? Crit. Rev. Immunol. 26(3), 213-230 (2006). (Pubitemid 44079772)
56. Chen M, Wang YH, Wang Y et al. Dendritic cell apoptosis in the maintenance of immune tolerance. Science 311(5764), 1160-1164 (2006).
57. Qi R, Liu M, Gao XH et al. Histone deacetylase activity is required for skin Langerhans cell maturation and phagocytosis. J. Dermatol. Sci. 65(2), 152-155 (2012).
58. Nencioni A, Beck J, Werth D et al. Histone deacetylase inhibitors affect dendritic cell differentiation and immunogenicity. Clin. Cancer. Res. 13(13), 3933-3941 (2007). (Pubitemid 47037601)
59. Frikeche J, Simon T, Brissot E, Gregoire M, Gaugler B, Mohty M. Impact of valproic acid on dendritic cells function. Immunobiology 217(7), 704-710 (2012).
60. Jung ID, Lee JS, Jeong YI et al. Apicidin, the histone deacetylase inhibitor, suppresses Th1 polarization of murine bone marrow-derived dendritic cells. Int. J. Immunopathol. Pharmacol. 22(2), 501-515 (2009).
61. Reddy P, Sun Y, Toubai T et al. Histone deacetylase inhibition modulates indoleamine 2,3-dioxygenase-dependent DC functions and regulates experimental graft-versus-host disease in mice. J. Clin. Invest. 118(7), 2562-2573 (2008). (Pubitemid 351949783)
62. Bode KA, Schroder K, Hume DA et al. Histone deacetylase inhibitors decrease Toll-like receptor-mediated activation of proinflammatory gene expression by impairing transcription factor recruitment. Immunology 122(4), 596-606 (2007). (Pubitemid 350075958)
63. Brogdon JL, Xu Y, Szabo SJ et al. Histone deacetylase activities are required for innate immune cell control of Th1 but not Th2 effector cell function. Blood 109(3), 1123-1130 (2007). (Pubitemid 46220659)
64. Song W, Tai YT, Tian Z et al. HDAC inhibition by LBH589 affects the phenotype and function of human myeloid dendritic cells. Leukemia 25(1), 161-168 (2011).
65. Reddy P, Maeda Y, Hotary K et al. Histone deacetylase inhibitor suberoylanilide hydroxamic acid reduces acute graft-versus-host disease and preserves graft-versus-leukemia effect. Proc. Natl Acad. Sci. USA 101(11), 3921-3926 (2004). (Pubitemid 38381078)
66. Leoni F, Zaliani A, Bertolini G et al. The antitumor histone deacetylase inhibitor suberoylanilide hydroxamic acid exhibits antiinflammatory properties via suppression of cytokines. Proc. Natl Acad. Sci. USA 99(5), 2995-3000 (2002). (Pubitemid 34240574)
67. Wen H, Dou Y, Hogaboam CM, Kunkel SL. Epigenetic regulation of dendritic cell-derived interleukin-12 facilitates immunosuppression after a severe innate immune response. Blood 111(4), 1797-1804 (2008). (Pubitemid 351451484)
68. Bluml S, Zupkovitz G, Kirchberger S et al. Epigenetic regulation of dendritic cell differentiation and function by oxidized phospholipids. Blood 114(27), 5481-5489 (2009).
69. Tserel L, Kolde R, Rebane A et al. Genome-wide promoter analysis of histone modifications in human monocyte-derived antigen presenting cells. BMC Genomics 11, 642 (2010).
70. Tian Y, Jia Z, Wang J et al. Global mapping of H3K4me1 and H3K4me3 reveals the chromatin state-based cell type-specific gene regulation in human Treg cells. PloS One 6(11), e27770 (2011).
71. Huang Y, Min S, Lui Y et al. Global mapping of H3K4me3 and H3K27me3 reveals chromatin state-based regulation of human monocyte-derived dendritic cells in different environments. Genes Immun. 13(4), 311-320 (2012).
72. Fang TC, Schaefer U, Mecklenbrauker I et al. Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response. J. Exp. Med. 209(4), 661-669 (2012).
73. Zhu Y, Van Essen D, Saccani S. Cell-type-specific control of enhancer activity by H3K9 trimethylation. Mol. Cell 46(4), 408-423 (2012).
74. Deaton AM, Webb S, Kerr AR et al. Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res. 21(7), 1074-1086 (2011).
75. Illingworth RS, Gruenewald-Schneider U, Webb S et al. Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 6(9), pii: e1001134 (2010).
76. Frikeche J, Clavert A, Delaunay J et al. Impact of the hypomethylating agent 5-azacytidine on dendritic cells function. Exp. Hematol. 39(11), 1056-1063 (2011).
77. Fedulov AV, Kobzik L. Allergy risk is mediated by dendritic cells with congenital epigenetic changes. Am. J. Respir. Cell Mol. Biol. 44(3), 285-292 (2011).