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Emerging Roles for Epigenetic Programming in the Control of Inflammatory Signaling Integration in Heath and Disease

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Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1024))

Abstract

Macrophages and dendritic cells initiate the innate immune response to infection and injury and contribute to inflammatory signaling to maintain the homeostasis of various tissues, which includes resident macrophages for the elimination of invading microorganisms and tissue damage. Inappropriate inflammatory signaling can lead to persistent inflammation and further develop into autoimmune and inflammation-associated diseases. Inflammatory signaling pathways have been well characterized, but how these signaling pathways are converted into sustained and diverse patterns of expression of cytokines, chemokines, and other genes in response to environmental challenges is unclear. Emerging evidence suggests the important role of epigenetic mechanisms in finely tuning the outcome of the host innate immune response. An understanding of epigenetic regulation of innate immune cell identity and function will enable the identification of the mechanism between gene-specific host defenses and inflammatory disease and will also allow for exploration of the program of innate immune memory in health and disease. This information could be used to develop therapeutic agents to enhance the host response, preventing chronic inflammation through preserving tissues and signaling integrity.

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References

  1. Asgari E, Zhou W, Sacks S (2010) Complement in organ transplantation. Curr Opin Organ Transplant 15(4):486–491

    PubMed  Google Scholar 

  2. Iwasaki A, Medzhitov R (2010) Regulation of adaptive immunity by the innate immune system. Science 327(5963):291–295

    PubMed  PubMed Central  Google Scholar 

  3. Barton GM (2008) A calculated response: control of inflammation by the innate immune system. J Clin Invest 118(2):413–420

    PubMed  PubMed Central  Google Scholar 

  4. Markiewski MM, Lambris JD (2007) The role of complement in inflammatory diseases from behind the scenes into the spotlight. Am J Pathol 171(3):715–727

    PubMed  PubMed Central  Google Scholar 

  5. Kolaczkowska E, Kubes P (2013) Neutrophil recruitment and function in health and inflammation. Nat Rev Immunol 13(3):159–175

    PubMed  Google Scholar 

  6. O’Neill LA, Golenbock D, Bowie AG (2013) The history of toll-like receptors – redefining innate immunity. Nat Rev Immunol 13(6):453–460

    PubMed  Google Scholar 

  7. Chen KW, Schroder K (2013) Antimicrobial functions of inflammasomes. Curr Opin Microbiol 16(3):311–318

    PubMed  Google Scholar 

  8. Schroder K, Tschopp J (2010) The inflammasomes. Cell 140(6):821–832

    PubMed  Google Scholar 

  9. Franklin BS, Mangan MS, Latz E (2016) Crystal formation in inflammation. Annu Rev Immunol 34:173–202

    PubMed  Google Scholar 

  10. Heneka MT, Golenbock DT, Latz E (2015) Innate immunity in Alzheimer’s disease. Nat Immunol 16(3):229–236

    PubMed  Google Scholar 

  11. Zimmer S, Grebe A, Latz E (2015) Danger signaling in atherosclerosis. Circ Res 116(2):323–340

    PubMed  Google Scholar 

  12. Broderick L, De Nardo D, Franklin BS, Hoffman HM, Latz E (2015) The inflammasomes and autoinflammatory syndromes. Annu Rev Pathol 10:395–424

    PubMed  Google Scholar 

  13. Kono H, Kimura Y, Latz E (2014) Inflammasome activation in response to dead cells and their metabolites. Curr Opin Immunol 30:91–98

    PubMed  Google Scholar 

  14. Heneka MT, Kummer MP, Latz E (2014) Innate immune activation in neurodegenerative disease. Nat Rev Immunol 14(7):463–477

    PubMed  Google Scholar 

  15. Meng G, Zhang F, Fuss I, Kitani A, Strober W (2009) A mutation in the Nlrp3 gene causing inflammasome hyperactivation potentiates Th17 cell-dominant immune responses. Immunity 30(6):860–874

    PubMed  PubMed Central  Google Scholar 

  16. Iwasaki A, Medzhitov R (2004) Toll-like receptor control of the adaptive immune responses. Nat Immunol 5(10):987–995

    PubMed  Google Scholar 

  17. Kawai T, Akira S (2011) Toll-like receptors and their crosstalk with other innate receptors in infection and immunity. Immunity 34(5):637–650

    PubMed  Google Scholar 

  18. Cao X (2016) Self-regulation and cross-regulation of pattern-recognition receptor signalling in health and disease. Nat Rev Immunol 16(1):35–50

    PubMed  Google Scholar 

  19. Foster SL, Hargreaves DC, Medzhitov R (2007) Gene-specific control of inflammation by TLR-induced chromatin modifications. Nature 447(7147):972–978

    PubMed  Google Scholar 

  20. Stender JD, Glass CK (2013) Epigenomic control of the innate immune response. Curr Opin Pharmacol 13(4):582–587

    PubMed  PubMed Central  Google Scholar 

  21. Maciejewska Rodrigues H, Jungel A, Gay RE, Gay S (2009) Innate immunity, epigenetics and autoimmunity in rheumatoid arthritis. Mol Immunol 47(1):12–18

    PubMed  Google Scholar 

  22. Biggar KK, Li SS (2015) Non-histone protein methylation as a regulator of cellular signalling and function. Nat Rev Mol Cell Biol 16(1):5–17

    PubMed  Google Scholar 

  23. Xue J, Schmidt SV, Sander J, Draffehn A, Krebs W, Quester I, De Nardo D, Gohel TD, Emde M, Schmidleithner L, Ganesan H, Nino-Castro A, Mallmann MR, Labzin L, Theis H, Kraut M et al (2014) Transcriptome-based network analysis reveals a spectrum model of human macrophage activation. Immunity 40(2):274–288

    PubMed  PubMed Central  Google Scholar 

  24. Winter DR, Jung S, Amit I (2015) Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape. Nat Rev Immunol 15(9):585–594

    PubMed  Google Scholar 

  25. Baylin SB, Jones PA (2016, September 1) Epigenetic determinants of cancer. Cold Spring Harb Perspect Biol 8(9). pii: a019505 doi:10.1101/cshperspect.a019505

    Article  PubMed  PubMed Central  Google Scholar 

  26. Kouzarides T (2007) Chromatin modifications and their function. Cell 128(4):693–705

    PubMed  Google Scholar 

  27. Kouzarides T (2007) SnapShot: histone-modifying enzymes. Cell 131(4):822

    PubMed  Google Scholar 

  28. Stricker SH, Koferle A, Beck S (2017) From profiles to function in epigenomics. Nat Rev Genet 18(1):51–66

    PubMed  Google Scholar 

  29. Liu F, Wang L, Perna F, Nimer SD (2016) Beyond transcription factors: how oncogenic signalling reshapes the epigenetic landscape. Nat Rev Cancer 16(6):359–372

    PubMed  PubMed Central  Google Scholar 

  30. Bell O, Tiwari VK, Thoma NH, Schubeler D (2011) Determinants and dynamics of genome accessibility. Nat Rev Genet 12(8):554–564

    PubMed  Google Scholar 

  31. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389(6648):251–260

    PubMed  Google Scholar 

  32. Jiang C, Pugh BF (2009) Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 10(3):161–172

    PubMed  PubMed Central  Google Scholar 

  33. Ehrlich M (2003) Expression of various genes is controlled by DNA methylation during mammalian development. J Cell Biochem 88(5):899–910

    PubMed  Google Scholar 

  34. Wu H, Zhang Y (2014) Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 156(1–2):45–68

    PubMed  PubMed Central  Google Scholar 

  35. Lin JC, Jeong S, Liang G, Takai D, Fatemi M, Tsai YC, Egger G, Gal-Yam EN, Jones PA (2007) Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. Cancer Cell 12(5):432–444

    PubMed  PubMed Central  Google Scholar 

  36. Wade PA (2001) Methyl CpG-binding proteins and transcriptional repression. BioEssays 23(12):1131–1137

    PubMed  Google Scholar 

  37. Okano M, Bell DW, Haber DA, Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99(3):247–257

    PubMed  Google Scholar 

  38. Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y (2011) Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333(6047):1300–1303

    PubMed  PubMed Central  Google Scholar 

  39. Rivera CM, Ren B (2013) Mapping human epigenomes. Cell 155(1):39–55

    PubMed  Google Scholar 

  40. Sadler AJ, Rossello FJ, Yu L, Deane JA, Yuan X, Wang D, Irving AT, Kaparakis-Liaskos M, Gantier MP, Ying H, Yim HC, Hartland EL, Notini AJ, de Boer S, White SJ, Mansell A et al (2015) BTB-ZF transcriptional regulator PLZF modifies chromatin to restrain inflammatory signaling programs. Proc Natl Acad Sci U S A 112(5):1535–1540

    PubMed  PubMed Central  Google Scholar 

  41. Schmidt SV, Krebs W, Ulas T, Xue J, Bassler K, Gunther P, Hardt AL, Schultze H, Sander J, Klee K, Theis H, Kraut M, Beyer M, Schultze JL (2016) The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin. Cell Res 26(2):151–170

    PubMed  PubMed Central  Google Scholar 

  42. Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S et al (2015) Population variation and genetic control of modular chromatin architecture in humans. Cell 162(5):1039–1050

    PubMed  Google Scholar 

  43. Calo E, Wysocka J (2013) Modification of enhancer chromatin: what, how, and why? Mol Cell 49(5):825–837

    PubMed  Google Scholar 

  44. Nagy G, Daniel B, Jonas D, Nagy L, Barta E (2013) A novel method to predict regulatory regions based on histone mark landscapes in macrophages. Immunobiology 218(11):1416–1427

    PubMed  Google Scholar 

  45. Falkenberg KJ, Johnstone RW (2014) Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders. Nat Rev Drug Discov 13(9):673–691

    PubMed  Google Scholar 

  46. Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21(3):381–395

    PubMed  PubMed Central  Google Scholar 

  47. Pasini D, Hansen KH, Christensen J, Agger K, Cloos PA, Helin K (2008) Coordinated regulation of transcriptional repression by the RBP2 H3K4 demethylase and polycomb-repressive complex 2. Genes Dev 22(10):1345–1355

    PubMed  PubMed Central  Google Scholar 

  48. Yang SH, Sharrocks AD (2004) SUMO promotes HDAC-mediated transcriptional repression. Mol Cell 13(4):611–617

    PubMed  Google Scholar 

  49. Pflum MK, Tong JK, Lane WS, Schreiber SL (2001) Histone deacetylase 1 phosphorylation promotes enzymatic activity and complex formation. J Biol Chem 276(50):47733–47741

    PubMed  Google Scholar 

  50. Kung JT, Colognori D, Lee JT (2013) Long noncoding RNAs: past, present, and future. Genetics 193(3):651–669

    PubMed  PubMed Central  Google Scholar 

  51. Wang KC, Chang HY (2011) Molecular mechanisms of long noncoding RNAs. Mol Cell 43(6):904–914

    PubMed  PubMed Central  Google Scholar 

  52. Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D et al (2014) An atlas of active enhancers across human cell types and tissues. Nature 507(7493):455–461

    PubMed  PubMed Central  Google Scholar 

  53. FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF et al (2014) A promoter-level mammalian expression atlas. Nature 507(7493):462–470

    Google Scholar 

  54. Boguski MS (2004) ENCODE and ChIP-chip in the genome era. Genomics 83(3):347–348

    PubMed  Google Scholar 

  55. Consortium EP (2004) The ENCODE (ENCyclopedia Of DNA elements) project. Science 306(5696):636–640

    Google Scholar 

  56. Alvarez-Errico D, Vento-Tormo R, Sieweke M, Ballestar E (2015) Epigenetic control of myeloid cell differentiation, identity and function. Nat Rev Immunol 15(1):7–17

    PubMed  Google Scholar 

  57. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D’Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM et al (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466(7303):253–257

    PubMed  PubMed Central  Google Scholar 

  58. Zilbauer M, Rayner TF, Clark C, Coffey AJ, Joyce CJ, Palta P, Palotie A, Lyons PA, Smith KG (2013) Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type-specific hypomethylated regions. Blood 122(25):e52–e60

    PubMed  PubMed Central  Google Scholar 

  59. Feng J, Zhou Y, Campbell SL, Le T, Li E, Sweatt JD, Silva AJ, Fan G (2010) Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci 13(4):423–430

    PubMed  PubMed Central  Google Scholar 

  60. Cheng C, Huang C, Ma TT, Bian EB, He Y, Zhang L, Li J (2014) SOCS1 hypermethylation mediated by DNMT1 is associated with lipopolysaccharide-induced inflammatory cytokines in macrophages. Toxicol Lett 225(3):488–497

    PubMed  Google Scholar 

  61. Yang X, Wang X, Liu D, Yu L, Xue B, Shi H (2014) Epigenetic regulation of macrophage polarization by DNA methyltransferase 3b. Mol Endocrinol 28(4):565–574

    PubMed  PubMed Central  Google Scholar 

  62. Babu M, Durga Devi T, Makinen P, Kaikkonen M, Lesch HP, Junttila S, Laiho A, Ghimire B, Gyenesei A, Yla-Herttuala S (2015) Differential promoter methylation of macrophage genes is associated with impaired vascular growth in ischemic muscles of hyperlipidemic and type 2 diabetic mice: genome-wide promoter methylation study. Circ Res 117(3):289–299

    PubMed  Google Scholar 

  63. Teles FR, Teles RP, Uzel NG, Song XQ, Torresyap G, Socransky SS, Haffajee AD (2012) Early microbial succession in redeveloping dental biofilms in periodontal health and disease. J Periodontal Res 47(1):95–104

    PubMed  Google Scholar 

  64. Burns E, Bachrach G, Shapira L, Nussbaum G (2006) Cutting Edge: TLR2 is required for the innate response to Porphyromonas gingivalis: activation leads to bacterial persistence and TLR2 deficiency attenuates induced alveolar bone resorption. J Immunol 177(12):8296–8300

    PubMed  Google Scholar 

  65. Benakanakere M, Abdolhosseini M, Hosur K, Finoti LS, Kinane DF (2015) TLR2 promoter hypermethylation creates innate immune dysbiosis. J Dent Res 94(1):183–191

    PubMed  PubMed Central  Google Scholar 

  66. de Faria Amormino SA, Arao TC, Saraiva AM, Gomez RS, Dutra WO, da Costa JE, de Fatima Correia Silva J, Moreira PR (2013) Hypermethylation and low transcription of TLR2 gene in chronic periodontitis. Hum Immunol 74(9):1231–1236

    PubMed  Google Scholar 

  67. Feinberg AP (2007) Phenotypic plasticity and the epigenetics of human disease. Nature 447(7143):433–440

    PubMed  Google Scholar 

  68. Ruthenburg AJ, Li H, Patel DJ, Allis CD (2007) Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol 8(12):983–994

    PubMed  PubMed Central  Google Scholar 

  69. Del Rizzo PA, Trievel RC (2011) Substrate and product specificities of SET domain methyltransferases. Epigenetics 6(9):1059–1067

    PubMed  PubMed Central  Google Scholar 

  70. Vedadi M, Blazer L, Eram MS, Barsyte-Lovejoy D, Arrowsmith CH, Hajian T (2017) Targeting human SET1/MLL family of proteins. Protein Sci 26(4):662–676

    PubMed  PubMed Central  Google Scholar 

  71. Zhang Y, Mittal A, Reid J, Reich S, Gamblin SJ, Wilson JR (2015) Evolving catalytic properties of the MLL family SET domain. Structure 23(10):1921–1933

    PubMed  PubMed Central  Google Scholar 

  72. Krivtsov AV, Hoshii T, Armstrong SA (2017, February 27) Mixed-lineage leukemia fusions and chromatin in leukemia. Cold Spring Harb Perspect Med. pii: a026658 doi:10.1101/cshperspect.a026658

    Article  PubMed  PubMed Central  Google Scholar 

  73. Shilatifard A (2012) The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis. Annu Rev Biochem 81:65–95

    PubMed  PubMed Central  Google Scholar 

  74. Rousseau M, Ferraiuolo MA, Crutchley JL, Wang XQ, Miura H, Blanchette M, Dostie J (2014) Classifying leukemia types with chromatin conformation data. Genome Biol 15(4):R60

    PubMed  PubMed Central  Google Scholar 

  75. Krivtsov AV, Armstrong SA (2007) MLL translocations, histone modifications and leukaemia stem-cell development. Nat Rev Cancer 7(11):823–833

    PubMed  Google Scholar 

  76. Austenaa L, Barozzi I, Chronowska A, Termanini A, Ostuni R, Prosperini E, Stewart AF, Testa G, Natoli G (2012) The histone methyltransferase Wbp7 controls macrophage function through GPI glycolipid anchor synthesis. Immunity 36(4):572–585

    PubMed  Google Scholar 

  77. Wang X, Zhu K, Li S, Liao Y, Du R, Zhang X, Shu HB, Guo AY, Li L, Wu M (2012) MLL1, a H3K4 methyltransferase, regulates the TNFalpha-stimulated activation of genes downstream of NF-kappaB. J Cell Sci 125(Pt 17):4058–4066

    PubMed  Google Scholar 

  78. Xia M, Liu J, Wu X, Liu S, Li G, Han C, Song L, Li Z, Wang Q, Wang J, Xu T, Cao X (2013) Histone methyltransferase Ash1l suppresses interleukin-6 production and inflammatory autoimmune diseases by inducing the ubiquitin-editing enzyme A20. Immunity 39(3):470–481

    PubMed  Google Scholar 

  79. De Santa F, Totaro MG, Prosperini E, Notarbartolo S, Testa G, Natoli G (2007) The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. Cell 130(6):1083–1094

    PubMed  Google Scholar 

  80. Ishii M, Wen H, Corsa CA, Liu T, Coelho AL, Allen RM, Carson WF, Cavassani KA, Li X, Lukacs NW, Hogaboam CM, Dou Y, Kunkel SL (2009) Epigenetic regulation of the alternatively activated macrophage phenotype. Blood 114(15):3244–3254

    PubMed  PubMed Central  Google Scholar 

  81. Satoh T, Takeuchi O, Vandenbon A, Yasuda K, Tanaka Y, Kumagai Y, Miyake T, Matsushita K, Okazaki T, Saitoh T, Honma K, Matsuyama T, Yui K, Tsujimura T, Standley DM, Nakanishi K et al (2010) The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nat Immunol 11(10):936–944

    PubMed  Google Scholar 

  82. Liu Y, Zhang Q, Ding Y, Li X, Zhao D, Zhao K, Guo Z, Cao X (2015) Histone lysine methyltransferase Ezh1 promotes TLR-triggered inflammatory cytokine production by suppressing Tollip. J Immunol 194(6):2838–2846

    PubMed  Google Scholar 

  83. Fang TC, Schaefer U, Mecklenbrauker I, Stienen A, Dewell S, Chen MS, Rioja I, Parravicini V, Prinjha RK, Chandwani R, MacDonald MR, Lee K, Rice CM, Tarakhovsky A (2012) Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response. J Exp Med 209(4):661–669

    PubMed  PubMed Central  Google Scholar 

  84. Schliehe C, Flynn EK, Vilagos B, Richson U, Swaminathan S, Bosnjak B, Bauer L, Kandasamy RK, Griesshammer IM, Kosack L, Schmitz F, Litvak V, Sissons J, Lercher A, Bhattacharya A, Khamina K et al (2015) The methyltransferase Setdb2 mediates virus-induced susceptibility to bacterial superinfection. Nat Immunol 16(1):67–74

    PubMed  Google Scholar 

  85. Zhang Q, Zhao K, Shen Q, Han Y, Gu Y, Li X, Zhao D, Liu Y, Wang C, Zhang X, Su X, Liu J, Ge W, Levine RL, Li N, Cao X (2015) Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6. Nature 525(7569):389–393

    PubMed  PubMed Central  Google Scholar 

  86. Li X, Zhang Q, Ding Y, Liu Y, Zhao D, Zhao K, Shen Q, Liu X, Zhu X, Li N, Cheng Z, Fan G, Wang Q, Cao X (2016) Methyltransferase Dnmt3a upregulates HDAC9 to deacetylate the kinase TBK1 for activation of antiviral innate immunity. Nat Immunol 17(7):806–815

    PubMed  Google Scholar 

  87. Li Y, Seto E (2016) HDACs and HDAC inhibitors in cancer development and therapy. Cold Spring Harb Perspect Med 6(10):a026831

    PubMed  PubMed Central  Google Scholar 

  88. Lee KK, Workman JL (2007) Histone acetyltransferase complexes: one size doesn’t fit all. Nat Rev Mol Cell Biol 8(4):284–295

    PubMed  Google Scholar 

  89. Chauhan A, Quenum FZ, Abbas A, Bradley DS, Nechaev S, Singh BB, Sharma J, Mishra BB (2015) Epigenetic modulation of microglial inflammatory gene loci in helminth-induced immune suppression: implications for immune regulation in neurocysticercosis. ASN Neuro 7(4):1–12

    Google Scholar 

  90. Feng D, Sangster-Guity N, Stone R, Korczeniewska J, Mancl ME, Fitzgerald-Bocarsly P, Barnes BJ (2010) Differential requirement of histone acetylase and deacetylase activities for IRF5-mediated proinflammatory cytokine expression. J Immunol 185(10):6003–6012

    PubMed  Google Scholar 

  91. Kawahara TL, Michishita E, Adler AS, Damian M, Berber E, Lin M, McCord RA, Ongaigui KC, Boxer LD, Chang HY, Chua KF (2009) SIRT6 links histone H3 lysine 9 deacetylation to NF-kappaB-dependent gene expression and organismal life span. Cell 136(1):62–74

    PubMed  PubMed Central  Google Scholar 

  92. Sadler AJ, Suliman BA, Yu L, Yuan X, Wang D, Irving AT, Sarvestani ST, Banerjee A, Mansell AS, Liu JP, Gerondakis S, Williams BR, Xu D (2015) The acetyltransferase HAT1 moderates the NF-kappaB response by regulating the transcription factor PLZF. Nat Commun 6:6795

    PubMed  Google Scholar 

  93. Alam MM, O’Neill LA (2011) MicroRNAs and the resolution phase of inflammation in macrophages. Eur J Immunol 41(9):2482–2485

    PubMed  Google Scholar 

  94. O’Neill LA, Sheedy FJ, McCoy CE (2011) MicroRNAs: the fine-tuners of Toll-like receptor signalling. Nat Rev Immunol 11(3):163–175

    PubMed  Google Scholar 

  95. Hangauer MJ, Vaughn IW, McManus MT (2013) Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet 9(6):e1003569

    PubMed  PubMed Central  Google Scholar 

  96. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25(18):1915–1927

    PubMed  PubMed Central  Google Scholar 

  97. Guttman M, Rinn JL (2012) Modular regulatory principles of large non-coding RNAs. Nature 482(7385):339–346

    PubMed  PubMed Central  Google Scholar 

  98. Wang P, Xue Y, Han Y, Lin L, Wu C, Xu S, Jiang Z, Xu J, Liu Q, Cao X (2014) The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science 344(6181):310–313

    PubMed  Google Scholar 

  99. Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL, Byron M, Monks B, Henry-Bezy M, Lawrence JB, O’Neill LA, Moore MJ, Caffrey DR, Fitzgerald KA (2013) A long noncoding RNA mediates both activation and repression of immune response genes. Science 341(6147):789–792

    PubMed  PubMed Central  Google Scholar 

  100. Hu G, Gong AY, Wang Y, Ma S, Chen X, Chen J, Su CJ, Shibata A, Strauss-Soukup JK, Drescher KM, Chen XM (2016) LincRNA-Cox2 promotes late inflammatory gene transcription in macrophages through modulating SWI/SNF-mediated chromatin remodeling. J Immunol 196(6):2799–2808

    PubMed  Google Scholar 

  101. Tong Q, Gong AY, Zhang XT, Lin C, Ma S, Chen J, Hu G, Chen XM (2016) LincRNA-Cox2 modulates TNF-alpha-induced transcription of Il12b gene in intestinal epithelial cells through regulation of Mi-2/NuRD-mediated epigenetic histone modifications. FASEB J 30(3):1187–1197

    PubMed  Google Scholar 

  102. Rapicavoli NA, Qu K, Zhang J, Mikhail M, Laberge RM, Chang HY (2013) A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. eLife 2:e00762

    PubMed  PubMed Central  Google Scholar 

  103. Li Z, Chao TC, Chang KY, Lin N, Patil VS, Shimizu C, Head SR, Burns JC, Rana TM (2014) The long noncoding RNA THRIL regulates TNFalpha expression through its interaction with hnRNPL. Proc Natl Acad Sci U S A 111(3):1002–1007

    PubMed  Google Scholar 

  104. Ma S, Ming Z, Gong AY, Wang Y, Chen X, Hu G, Zhou R, Shibata A, Swanson PC, Chen XM (2017) A long noncoding RNA, lincRNA-tnfaip3, acts as a coregulator of NF-kappaB to modulate inflammatory gene transcription in mouse macrophages. FASEB J 31(3):1215–1225

    PubMed  Google Scholar 

  105. Atianand MK, Hu W, Satpathy AT, Shen Y, Ricci EP, Alvarez-Dominguez JR, Bhatta A, Schattgen SA, McGowan JD, Blin J, Braun JE, Gandhi P, Moore MJ, Chang HY, Lodish HF, Caffrey DR et al (2016) A Long Noncoding RNA lincRNA-EPS Acts as a transcriptional brake to restrain inflammation. Cell 165(7):1672–1685

    PubMed  PubMed Central  Google Scholar 

  106. Medzhitov R, Horng T (2009) Transcriptional control of the inflammatory response. Nat Rev Immunol 9(10):692–703

    PubMed  Google Scholar 

  107. Medzhitov R, Schneider DS, Soares MP (2012) Disease tolerance as a defense strategy. Science 335(6071):936–941

    PubMed  PubMed Central  Google Scholar 

  108. Witteveldt J, Cifuentes CC, Vlak JM, van Hulten MC (2004) Protection of Penaeus monodon against white spot syndrome virus by oral vaccination. J Virol 78(4):2057–2061

    PubMed  PubMed Central  Google Scholar 

  109. Saeed S, Quintin J, Kerstens HH, Rao NA, Aghajanirefah A, Matarese F, Cheng SC, Ratter J, Berentsen K, van der Ent MA, Sharifi N, Janssen-Megens EM, Ter Huurne M, Mandoli A, van Schaik T, Ng A et al (2014) Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science 345(6204):1251086

    PubMed  PubMed Central  Google Scholar 

  110. Zhang X, Morrison DC (1993) Lipopolysaccharide-induced selective priming effects on tumor necrosis factor alpha and nitric oxide production in mouse peritoneal macrophages. J Exp Med 177(2):511–516

    PubMed  Google Scholar 

  111. Hirohashi N, Morrison DC (1996) Low-dose lipopolysaccharide (LPS) pretreatment of mouse macrophages modulates LPS-dependent interleukin-6 production in vitro. Infect Immun 64(3):1011–1015

    PubMed  PubMed Central  Google Scholar 

  112. Quintin J, Saeed S, Martens JH, Giamarellos-Bourboulis EJ, Ifrim DC, Logie C, Jacobs L, Jansen T, Kullberg BJ, Wijmenga C, Joosten LA, Xavier RJ, van der Meer JW, Stunnenberg HG, Netea MG (2012) Candida albicans infection affords protection against reinfection via functional reprogramming of monocytes. Cell Host Microbe 12(2):223–232

    PubMed  Google Scholar 

  113. Ostuni R, Piccolo V, Barozzi I, Polletti S, Termanini A, Bonifacio S, Curina A, Prosperini E, Ghisletti S, Natoli G (2013) Latent enhancers activated by stimulation in differentiated cells. Cell 152(1–2):157–171

    PubMed  Google Scholar 

  114. Bhatt D, Ghosh S (2014) Regulation of the NF-kappaB-mediated transcription of inflammatory genes. Front Immunol 5:71

    PubMed  PubMed Central  Google Scholar 

  115. Cheng SC, Quintin J, Cramer RA, Shepardson KM, Saeed S, Kumar V, Giamarellos-Bourboulis EJ, Martens JH, Rao NA, Aghajanirefah A, Manjeri GR, Li Y, Ifrim DC, Arts RJ, van der Veer BM, Deen PM et al (2014) mTOR- and HIF-1alpha-mediated aerobic glycolysis as metabolic basis for trained immunity. Science 345(6204):1250684

    PubMed  PubMed Central  Google Scholar 

  116. Rajaiah R, Perkins DJ, Polumuri SK, Zhao A, Keegan AD, Vogel SN (2013) Dissociation of endotoxin tolerance and differentiation of alternatively activated macrophages. J Immunol 190(9):4763–4772

    PubMed  Google Scholar 

  117. Adib-Conquy M, Cavaillon JM (2009) Compensatory anti-inflammatory response syndrome. Thromb Haemost 101(1):36–47

    PubMed  Google Scholar 

  118. Ivashkiv LB, Park SH (2016, June) Epigenetic regulation of myeloid cells. Microbiol Spectr 4(3). doi:10.1128/microbiolspec.MCHD-0010-2015

  119. Takeuch O, Akira S (2011) Epigenetic control of macrophage polarization. Eur J Immunol 41(9):2490–2493

    PubMed  Google Scholar 

  120. Dandona P, Ghanim H, Green K, Sia CL, Abuaysheh S, Kuhadiya N, Batra M, Dhindsa S, Chaudhuri A (2013) Insulin infusion suppresses while glucose infusion induces Toll-like receptors and high-mobility group-B1 protein expression in mononuclear cells of type 1 diabetes patients. Am J Physiol Endocrinol Metab 304(8):E810–E818

    PubMed  Google Scholar 

  121. Shanmugam N, Reddy MA, Guha M, Natarajan R (2003) High glucose-induced expression of proinflammatory cytokine and chemokine genes in monocytic cells. Diabetes 52(5):1256–1264

    PubMed  Google Scholar 

  122. Yun JM, Jialal I, Devaraj S (2011) Epigenetic regulation of high glucose-induced proinflammatory cytokine production in monocytes by curcumin. J Nutr Biochem 22(5):450–458

    PubMed  Google Scholar 

  123. Maslowski KM, Vieira AT, Ng A, Kranich J, Sierro F, Yu D, Schilter HC, Rolph MS, Mackay F, Artis D, Xavier RJ, Teixeira MM, Mackay CR (2009) Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature 461(7268):1282–1286

    PubMed  PubMed Central  Google Scholar 

  124. Ey B, Eyking A, Klepak M, Salzman NH, Gothert JR, Runzi M, Schmid KW, Gerken G, Podolsky DK, Cario E (2013) Loss of TLR2 worsens spontaneous colitis in MDR1A deficiency through commensally induced pyroptosis. J Immunol 190(11):5676–5688

    PubMed  PubMed Central  Google Scholar 

  125. Huang E, Wells CA (2014) The ground state of innate immune responsiveness is determined at the interface of genetic, epigenetic, and environmental influences. J Immunol 193(1):13–19

    PubMed  Google Scholar 

  126. Yanez A, Hassanzadeh-Kiabi N, Ng MY, Megias J, Subramanian A, Liu GY, Underhill DM, Gil ML, Goodridge HS (2013) Detection of a TLR2 agonist by hematopoietic stem and progenitor cells impacts the function of the macrophages they produce. Eur J Immunol 43(8):2114–2125

    PubMed  PubMed Central  Google Scholar 

  127. Consortium EP (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74

    Google Scholar 

  128. Ricano-Ponce I, Wijmenga C (2013) Mapping of immune-mediated disease genes. Annu Rev Genomics Hum Genet 14:325–353

    PubMed  Google Scholar 

  129. Kumar V, Westra HJ, Karjalainen J, Zhernakova DV, Esko T, Hrdlickova B, Almeida R, Zhernakova A, Reinmaa E, Vosa U, Hofker MH, Fehrmann RS, Fu J, Withoff S, Metspalu A, Franke L et al (2013) Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. PLoS Genet 9(1):e1003201

    PubMed  PubMed Central  Google Scholar 

  130. Kent OA, McCall MN, Cornish TC, Halushka MK (2014) Lessons from miR-143/145: the importance of cell-type localization of miRNAs. Nucleic Acids Res 42(12):7528–7538

    PubMed  PubMed Central  Google Scholar 

  131. Zhang DD, Wang WT, Xiong J, Xie XM, Cui SS, Zhao ZG, Li MJ, Zhang ZQ, Hao DL, Zhao X, Li YJ, Wang J, Chen HZ, Lv X, Liu DP (2017) Long noncoding RNA LINC00305 promotes inflammation by activating the AHRR-NF-kappaB pathway in human monocytes. Sci Rep 7:46204

    PubMed  PubMed Central  Google Scholar 

  132. Liu CC, Fang TJ, Ou TT, Wu CC, Li RN, Lin YC, Lin CH, Tsai WC, Liu HW, Yen JH (2011) Global DNA methylation, DNMT1, and MBD2 in patients with rheumatoid arthritis. Immunol Lett 135(1–2):96–99

    PubMed  Google Scholar 

  133. Martin P, McGovern A, Orozco G, Duffus K, Yarwood A, Schoenfelder S, Cooper NJ, Barton A, Wallace C, Fraser P, Worthington J, Eyre S (2015) Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci. Nat Commun 6:10069

    PubMed  Google Scholar 

  134. Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Varnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnstrom K, Downes K, Grassi L et al (2016) Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters. Cell 167(5):1369–1384. e1319

    PubMed  PubMed Central  Google Scholar 

  135. Peters JE, Lyons PA, Lee JC, Richard AC, Fortune MD, Newcombe PJ, Richardson S, Smith KG (2016) Insight into genotype-phenotype associations through eQTL mapping in multiple cell types in health and immune-mediated disease. PLoS Genet 12(3):e1005908

    PubMed  PubMed Central  Google Scholar 

  136. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN et al (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462(7269):58–64

    PubMed  PubMed Central  Google Scholar 

  137. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950):289–293

    PubMed  PubMed Central  Google Scholar 

  138. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398):376–380

    PubMed  PubMed Central  Google Scholar 

  139. Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian SZ, Penrad-Mobayed M et al (2015) CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell 163(7):1611–1627

    PubMed  PubMed Central  Google Scholar 

  140. Laird PW (2010) Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 11(3):191–203

    PubMed  Google Scholar 

  141. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669–680

    PubMed  PubMed Central  Google Scholar 

  142. Yong WS, Hsu FM, Chen PY (2016) Profiling genome-wide DNA methylation. Epigenetics Chromatin 9:26

    PubMed  PubMed Central  Google Scholar 

  143. De Nardo D, Labzin LI, Kono H, Seki R, Schmidt SV, Beyer M, Xu D, Zimmer S, Lahrmann C, Schildberg FA, Vogelhuber J, Kraut M, Ulas T, Kerksiek A, Krebs W, Bode N et al (2014) High-density lipoprotein mediates anti-inflammatory reprogramming of macrophages via the transcriptional regulator ATF3. Nat Immunol 15(2):152–160

    PubMed  Google Scholar 

  144. Stelzer Y, Shivalila CS, Soldner F, Markoulaki S, Jaenisch R (2015) Tracing dynamic changes of DNA methylation at single-cell resolution. Cell 163(1):218–229

    PubMed  PubMed Central  Google Scholar 

  145. Sasaki K, Ito T, Nishino N, Khochbin S, Yoshida M (2009) Real-time imaging of histone H4 hyperacetylation in living cells. Proc Natl Acad Sci U S A 106(38):16257–16262

    PubMed  PubMed Central  Google Scholar 

  146. Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32(4):347–355

    PubMed  PubMed Central  Google Scholar 

  147. Tough DF, Tak PP, Tarakhovsky A, Prinjha RK (2016) Epigenetic drug discovery: breaking through the immune barrier. Nat Rev Drug Discov 15(12):835–853

    PubMed  Google Scholar 

  148. Leoni F, Zaliani A, Bertolini G, Porro G, Pagani P, Pozzi P, Dona G, Fossati G, Sozzani S, Azam T, Bufler P, Fantuzzi G, Goncharov I, Kim SH, Pomerantz BJ, Reznikov LL et al (2002) The antitumor histone deacetylase inhibitor suberoylanilide hydroxamic acid exhibits antiinflammatory properties via suppression of cytokines. Proc Natl Acad Sci U S A 99(5):2995–3000

    PubMed  PubMed Central  Google Scholar 

  149. Leoni F, Fossati G, Lewis EC, Lee JK, Porro G, Pagani P, Modena D, Moras ML, Pozzi P, Reznikov LL, Siegmund B, Fantuzzi G, Dinarello CA, Mascagni P (2005) The histone deacetylase inhibitor ITF2357 reduces production of pro-inflammatory cytokines in vitro and systemic inflammation in vivo. Mol Med 11(1–12):1–15

    PubMed  PubMed Central  Google Scholar 

  150. Grabiec AM, Krausz S, de Jager W, Burakowski T, Groot D, Sanders ME, Prakken BJ, Maslinski W, Eldering E, Tak PP, Reedquist KA (2010) Histone deacetylase inhibitors suppress inflammatory activation of rheumatoid arthritis patient synovial macrophages and tissue. J Immunol 184(5):2718–2728

    PubMed  Google Scholar 

  151. Gillespie J, Savic S, Wong C, Hempshall A, Inman M, Emery P, Grigg R, McDermott MF (2012) Histone deacetylases are dysregulated in rheumatoid arthritis and a novel histone deacetylase 3-selective inhibitor reduces interleukin-6 production by peripheral blood mononuclear cells from rheumatoid arthritis patients. Arthritis Rheum 64(2):418–422

    PubMed  Google Scholar 

  152. Belkina AC, Denis GV (2012) BET domain co-regulators in obesity, inflammation and cancer. Nat Rev Cancer 12(7):465–477

    PubMed  PubMed Central  Google Scholar 

  153. Khan YM, Kirkham P, Barnes PJ, Adcock IM (2014) Brd4 is essential for IL-1beta-induced inflammation in human airway epithelial cells. PLoS One 9(4):e95051

    PubMed  PubMed Central  Google Scholar 

  154. Wang CY, Filippakopoulos P (2015) Beating the odds: BETs in disease. Trends Biochem Sci 40(8):468–479

    PubMed  Google Scholar 

  155. Nicodeme E, Jeffrey KL, Schaefer U, Beinke S, Dewell S, Chung CW, Chandwani R, Marazzi I, Wilson P, Coste H, White J, Kirilovsky J, Rice CM, Lora JM, Prinjha RK, Lee K et al (2010) Suppression of inflammation by a synthetic histone mimic. Nature 468(7327):1119–1123

    PubMed  PubMed Central  Google Scholar 

  156. Belkina AC, Nikolajczyk BS, Denis GV (2013) BET protein function is required for inflammation: Brd2 genetic disruption and BET inhibitor JQ1 impair mouse macrophage inflammatory responses. J Immunol 190(7):3670–3678

    PubMed  Google Scholar 

  157. Kruidenier L, Chung CW, Cheng Z, Liddle J, Che K, Joberty G, Bantscheff M, Bountra C, Bridges A, Diallo H, Eberhard D, Hutchinson S, Jones E, Katso R, Leveridge M, Mander PK et al (2012) A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response. Nature 488(7411):404–408

    PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (81273247, 81472655 and 31670905) and the Shanghai Municipal Education Commission key discipline support project 2015-10101001-1.

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Correspondence to Dakang Xu .

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Hu, Y., Yan, F., Ying, L., Xu, D. (2017). Emerging Roles for Epigenetic Programming in the Control of Inflammatory Signaling Integration in Heath and Disease. In: Xu, D. (eds) Regulation of Inflammatory Signaling in Health and Disease. Advances in Experimental Medicine and Biology, vol 1024. Springer, Singapore. https://doi.org/10.1007/978-981-10-5987-2_3

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