Newborn

Register      Login

VOLUME 4 , ISSUE 1 ( January-March, 2025 ) > List of Articles

REVIEW ARTICLE

Epigenetic Regulation of Macrophage Polarization

Srijan Singh, Akhil Maheshwari

Keywords : Epigenetics, Hematopoiesis, Hematopoietic stem cells, Infant, Lineage-determining transcription factors, Macrophages, Macrophage polarization states, Monocytes, Neonate, Newborn

Citation Information : Singh S, Maheshwari A. Epigenetic Regulation of Macrophage Polarization. 2025; 4 (1):36-48.

DOI: 10.5005/jp-journals-11002-0118

License: CC BY-NC 4.0

Published Online: 25-03-2025

Copyright Statement:  Copyright © 2025; The Author(s).


Abstract

Increasing data shows that macrophages, the primary immune cells in the growing fetus/neonate, retain an innate immune memory of prior stimuli. This memory is rooted in epigenetic regulation of lineage- and tissue-specific transcription either to enhance the responses or to induce tolerance to repeated exposures to a stimulus. As we understand, epigenetics refers to the study of heritable information transmitted during cell divisions that can alter gene expression via inclusion of chemical tags but no changes in the DNA sequence. We now recognize the lineage-determining transcription factors as important mediators that can make the local chromatin more accessible to other factors; one example is the erythroblast transformation-specific gene PU.1 (purine-rich sequence binding protein 1). The PU.1 can upregulate the basal activation state of many promoters by increasing histone H3 lysine 4 trimethylation (H3K4me3). There are several other newly discovered regulators that perform similar regulatory roles. These mediators enhance macrophage differentiation into several phenotypes essential for host defense or tissue homeostasis in response to environmental stimuli. The two ends of this polarization spectrum include the classically-activated (M1) macrophages induced by interferon-γ and microbial products; and the alternatively-activated (M2) macrophages induced by the T-helper 2 cytokines interleukin (IL)-4 and IL-13. The M1 macrophages participate in host defense and clearing pathogens, whereas all the known subtypes of M2 cells promote resolution of inflammation and tissue repair. Maladaptive changes in macrophages can disrupt the normal sequence of immune/inflammatory responses and predispose to disease states. The review summarizes our current understanding of the involved mechanisms; this information can help understand the immune responses in neonates who are yet to develop mature neutrophil function or adaptive immunity and are largely dependent on mononuclear cells for immune defenses.


PDF Share
  1. van Furth R, Cohn ZA. The origin and kinetics of mononuclear phagocytes. J Exp Med 1968;128(3):415−435. DOI: 10.1084/JEM.128.3.415.
  2. Chen S, Yang J, Wei Y, et al. Epigenetic regulation of macrophages: From homeostasis maintenance to host defense. Cell Mol Immunol 2020;17(1):36−49. DOI: 10.1038/S41423-019-0315-0.
  3. Mezu-Ndubuisi OJ, Maheshwari A. Role of macrophages in fetal development and perinatal disorders. Pediatr Res 2021;90(3):513−523. DOI: 10.1038/S41390-020-01209-4.
  4. Maheshwari A. Innate immune memory in macrophages. Newborn (Clarksville) 2023;2(1):60−79. DOI: 10.5005/JP-JOURNALS-11002-0058.
  5. Hoeffel G, Chen J, Lavin Y, et al. C-Myb(+) erythro-myeloid progenitor-derived fetal monocytes give rise to adult tissue-resident macrophages. Immunity 2015;42(4):665−678. DOI: 10.1016/J.IMMUNI.2015.03.011.
  6. Perdiguero EG, Geissmann F. The development and maintenance of resident macrophages. Nat Immunol 2016;17:12−18. DOI: 10.1038/ni.3341.
  7. Goldmann T, Wieghofer P, Jordão MJC, et al. Origin, fate and dynamics of macrophages at central nervous system interfaces. Nat Immunol 2016;17(7):797−805. DOI: 10.1038/ni.3423.
  8. Spangrude G, Smith L, Uchida N, et al. Mouse hematopoietic stem cells. Blood 1991;78(6):1395−1402. DOI: 10.1182/BLOOD.V78.6.1395.1395.
  9. Flot JF, Marie-Nelly H, Koszul R. Contact genomics: Scaffolding and phasing (meta)genomes using chromosome 3D physical signatures. FEBS Lett 2015;589(20):2966−2974. DOI: 10.1016/J.FEBSLET.2015.04.034.
  10. Netea MG, Joosten LAB. Master and commander: Epigenetic regulation of macrophages. Cell Res 2016;26(2):145−146. DOI: 10.1038/CR.2016.5.
  11. Luger K, Mäder AW, Richmond RK, et al. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997;389(6648):251−260. DOI: 10.1038/38444.
  12. Wilson NK, Schoenfelder S, Hannah R, et al. Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model. Blood 2016;127(13):e12−e23. DOI: 10.1182/BLOOD-2015-10-677393.
  13. Parelho V, Hadjur S, Spivakov M, et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 2008;132(3):422−433. DOI: 10.1016/J.CELL.2008.01.011.
  14. Wendt KS, Yoshida K, Itoh T, et al. Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 2008;451(7180):796−801. DOI: 10.1038/nature06634.
  15. Sofueva S, Yaffe E, Chan WC, et al. Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J 2013;32(24):3119−3129. DOI: 10.1038/EMBOJ.2013.237.
  16. Ong CT, Corces VG. CTCF: An architectural protein bridging genome topology and function. Nat Rev Genet 2014;15(4):234−246. DOI: 10.1038/nrg3663.
  17. Liu M, Maurano MT, Wang H, et al. Genomic discovery of potent chromatin insulators for human gene therapy. Nat Biotechnol 2015;33(2):198−203. DOI: 10.1038/nbt.3062.
  18. Joshi O, Wang SY, Kuznetsova T, et al. Dynamic reorganization of extremely long-range promoter-promoter interactions between two states of pluripotency. Cell Stem Cell 2015;17(6):748−757. DOI: 10.1016/J.STEM.2015.11.010.
  19. Schoenfelder S, Furlan-Magaril M, Mifsud B, et al. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res 2015;25(4):582−597. DOI: 10.1101/GR.185272.114.
  20. Vieux-Rochas M, Fabre PJ, Leleu M, et al. Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain. Proc Natl Acad Sci USA 2015;112(15):4672−4677. DOI: 10.1073/PNAS.1504783112/SUPPL_FILE/PNAS.1504783112.SD05.TXT.
  21. Kind J, Pagie L, De Vries SS, et al. Genome-wide maps of nuclear lamina interactions in single human cells. Cell 2015;163(1):134−147. DOI: 10.1016/J.CELL.2015.08.040.
  22. Romanoski CE, Link VM, Heinz S, et al. Exploiting genomics and natural genetic variation to decode macrophage enhancers. Trends Immunol 2015;36(9):507−518. DOI: 10.1016/J.IT.2015.07.006.
  23. Zaret KS, Carroll JS. Pioneer transcription factors: Establishing competence for gene expression. Genes Dev 2011;25(21):2227−2241. DOI: 10.1101/GAD.176826.111.
  24. Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 2010;38(4):576−589. DOI: 10.1016/J.MOLCEL.2010.05.004.
  25. Heinz S, Romanoski CE, Benner C, et al. Effect of natural genetic variation on enhancer selection and function. Nature 2013;503(7477):487−492. DOI: 10.1038/NATURE12615.
  26. Gosselin D, Link VM, Romanoski CE, et al. Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell 2014;159(6):1327−1340. DOI: 10.1016/J.CELL.2014.11.023.
  27. Ginhoux F, Jung S. Monocytes and macrophages: Developmental pathways and tissue homeostasis. Nat Rev Immunol 2014;14(6):392−404. DOI: 10.1038/nri3671.
  28. Murray PJ, Allen JE, Biswas SK, et al. Macrophage activation and polarization: Nomenclature and experimental guidelines. Immunity 2014;41(1):14−20. DOI: 10.1016/J.IMMUNI.2014.06.008.
  29. Ivashkiv LB. Epigenetic regulation of macrophage polarization and function. Trends Immunol 2013;34(5):216−223. DOI: 10.1016/J.IT.2012.11.001.
  30. Smale ST. Selective transcription in response to an inflammatory stimulus. Cell 2010;140(6):833−844. DOI: 10.1016/J.CELL.2010.01.037.
  31. Medzhitov R, Horng T. Transcriptional control of the inflammatory response. Nat Rev Immunol 2009;9(10):692−703. DOI: 10.1038/NRI2634.
  32. Glass CK, Saijo K. Nuclear receptor transrepression pathways that regulate inflammation in macrophages and T cells. Nat Rev Immunol 2010;10(5):365−376. DOI: 10.1038/NRI2748.
  33. Natoli G, Ghisletti S, Barozzi I. The genomic landscapes of inflammation. Genes Dev 2011;25(2):101−106. DOI: 10.1101/GAD.2018811.
  34. Natoli G. Maintaining cell identity through global control of genomic organization. Immunity 2010;33(1):12−24. DOI: 10.1016/J.IMMUNI.2010.07.006.
  35. Buecker C, Wysocka J. Enhancers as information integration hubs in development: Lessons from genomics. Trends Genet 2012;28(6):276−284. DOI: 10.1016/J.TIG.2012.02.008.
  36. Sica A, Mantovani A. Macrophage plasticity and polarization: In vivo veritas. J Clin Invest 2012;122(3):787−795. DOI: 10.1172/JCI59643.
  37. Mosser DM, Edwards JP. Exploring the full spectrum of macrophage activation. Nat Rev Immunol 2008;8(12):958−969. DOI: 10.1038/NRI2448.
  38. Lawrence T, Natoli G. Transcriptional regulation of macrophage polarization: Enabling diversity with identity. Nat Rev Immunol 2011;11(11):750−761. DOI: 10.1038/NRI3088.
  39. Gordon S, Martinez FO. Alternative activation of macrophages: Mechanism and functions. Immunity 2010;32(5):593−604. DOI: 10.1016/J.IMMUNI.2010.05.007.
  40. Murray PJ, Wynn TA. Obstacles and opportunities for understanding macrophage polarization. J Leukoc Biol 2011;89(4):557−563. DOI: 10.1189/JLB.0710409.
  41. Kim S-J, Chang HJ, Volin MV, et al. Macrophages are the primary effector cells in IL-7-induced arthritis. Cell Mol Immunol 2020;17(7):728−740. DOI: 10.1038/S41423-019-0235-Z.
  42. Kumar KM, Namachivayam K, Cheng F, et al. Trinitrobenzene sulfonic acid-induced intestinal injury in neonatal mice activates transcriptional networks similar to those seen in human necrotizing enterocolitis. Pediatr Res 2016;81(1):99−112. DOI: 10.1038/pr.2016.189.
  43. MohanKumar K, Namachivayam K, Song T, et al. A murine neonatal model of necrotizing enterocolitis caused by anemia and red blood cell transfusions. Nat Commun 2019;10(1):1−17. DOI: 10.1038/s41467-019-11199-5.
  44. Hamilton JA. Colony-stimulating factors in inflammation and autoimmunity. Nat Rev Immunol 2008;8(7):533−544. DOI: 10.1038/NRI2356.
  45. Hume DA, MacDonald KPA. Therapeutic applications of macrophage colony-stimulating factor-1 (CSF-1) and antagonists of CSF-1 receptor (CSF-1R) signaling. Blood 2012;119(8):1810−1820. DOI: 10.1182/BLOOD-2011-09-379214.
  46. Laskin DL, Sunil VR, Gardner CR, et al. Macrophages and tissue injury: Agents of defense or destruction? Annu Rev Pharmacol Toxicol 2011;51:267−288. DOI: 10.1146/ANNUREV.PHARMTOX.010909.105812.
  47. Wang L-X, Zhang S-X, Wu H-J, et al. M2b macrophage polarization and its roles in diseases. J Leukoc Biol 2019;106(2):345−358. DOI: 10.1002/JLB.3RU1018-378RR.
  48. Duque GA, Descoteaux A. Macrophage cytokines: Involvement in immunity and infectious diseases. Front Immunol 2014;5:491. DOI: 10.3389/FIMMU.2014.00491.
  49. Huang S, Yue Y, Feng K, et al. Conditioned medium from M2b macrophages modulates the proliferation, migration, and apoptosis of pulmonary artery smooth muscle cells by deregulating the PI3K/Akt/FoxO3a pathway. PeerJ 2020;8(3):e9110. DOI: 10.7717/PEERJ.9110.
  50. Pérez S, Rius-Pérez S. Macrophage polarization and reprogramming in acute inflammation: A redox perspective. Antioxidants (Basel) 2022;11(7):1394. DOI: 10.3390/ANTIOX11071394.
  51. Pilling D, Galvis-Carvajal E, Karhadkar TR, et al. Monocyte differentiation and macrophage priming are regulated differentially by pentraxins and their ligands. BMC Immunol 2017;18(1):30. DOI: 10.1186/S12865-017-0214-Z.
  52. Spiller KL, Anfang RR, Spiller KJ, et al. The role of macrophage phenotype in vascularization of tissue engineering scaffolds. Biomaterials 2014;35(15):4477−4488. DOI: 10.1016/J.BIOMATERIALS.2014.02.012.
  53. Viola A, Munari F, Sánchez-Rodríguez R, et al. The metabolic signature of macrophage responses. Front Immunol 2019;10:1462. DOI: 10.3389/FIMMU.2019.01462.
  54. Ferrante CJ, Pinhal-Enfield G, Elson G, et al. The adenosine-dependent angiogenic switch of macrophages to an M2-like phenotype is independent of interleukin-4 receptor alpha (IL-4Rα) signaling. Inflammation 2013;36(4):921−931. DOI: 10.1007/S10753-013-9621-3.
  55. Atri C, Guerfali FZ, Laouini D. Role of human macrophage polarization in inflammation during infectious diseases. Int J Mol Sci 2018;19(6):1801. DOI: 10.3390/IJMS19061801.
  56. Yao Y, Xu XH, Jin L. Macrophage polarization in physiological and pathological pregnancy. Front Immunol 2019;10:792. DOI: 10.3389/FIMMU.2019.00792.
  57. Sapudom J, Karaman S, Mohamed WKE, et al. 3D in vitro M2 macrophage model to mimic modulation of tissue repair. NPJ Regen Med 2021;6(1):83. DOI: 10.1038/S41536-021-00193-5.
  58. Graney PL, Ben-Shaul S, Landau S, et al. Macrophages of diverse phenotypes drive vascularization of engineered tissues. Sci Adv 2020;6(18):eaay6391. DOI: 10.1126/SCIADV.AAY6391.
  59. Beyer M, Mallmann MR, Xue J, et al. High-resolution transcriptome of human macrophages. PLoS One 2012;7(9):e45466. DOI: 10.1371/JOURNAL.PONE.0045466.
  60. Jetten N, Verbruggen S, Gijbels MJ, et al. Anti-inflammatory M2, but not pro-inflammatory M1 macrophages promote angiogenesis in vivo. Angiogenesis 2014;17(1):109−118. DOI: 10.1007/S10456-013-9381-6.
  61. Zajac E, Schweighofer B, Kupriyanova TA, et al. Angiogenic capacity of M1- and M2-polarized macrophages is determined by the levels of TIMP-1 complexed with their secreted proMMP-9. Blood 2013;122(25):4054–4067. DOI: 10.1182/BLOOD-2013-05-501494.
  62. Corliss BA, Azimi MS, Munson JM, et al. Macrophages: An inflammatory link between angiogenesis and lymphangiogenesis. Microcirculation 2016;23(2):95−121. DOI: 10.1111/MICC.12259.
  63. Netea MG, Joosten LAB, Latz E, et al. Trained immunity: A program of innate immune memory in health and disease. Science 2016;352(6284):427. DOI: 10.1126/SCIENCE.AAF1098.
  64. Hajishengallis G, Li X, Mitroulis I, et al. Trained innate immunity and its implications for mucosal immunity and inflammation. Adv Exp Med Biol 2019;1197:11−26. DOI: 10.1007/978-3-030-28524-1_2.
  65. Zhou H, Lu X, Huang J, et al. Induction of trained immunity protects neonatal mice against microbial sepsis by boosting both the inflammatory response and antimicrobial activity. J Inflamm Res 2022;15:3829−3845. DOI: 10.2147/JIR.S363995.
  66. Netea MG, Domínguez-Andrés J, Barreiro LB, et al. Defining trained immunity and its role in health and disease. Nat Rev Immunol 2020;20(6):375−388. DOI: 10.1038/S41577-020-0285-6.
  67. Stender JD, Pascual G, Liu W, et al. Control of proinflammatory gene programs by regulated trimethylation and demethylation of histone H4K20. Mol Cell 2012;48(1):28−38. DOI: 10.1016/J.MOLCEL.2012.07.020.
  68. Ramirez-Carrozzi VR, Nazarian AA, Li CC, et al. Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response. Genes Dev 2006;20(3):282−296. DOI: 10.1101/GAD.1383206.
  69. Ramirez-Carrozzi VR, Braas D, Bhatt DM, et al. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 2009;138(1):114−128. DOI: 10.1016/J.CELL.2009.04.020.
  70. Levy D, Kuo AJ, Chang Y, et al. Ly sine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling. Nat Immunol 2011;12(1):29−36. DOI: 10.1038/NI.1968.
  71. Hargreaves DC, Horng T, Medzhitov R. Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 2009;138(1):129−145. DOI: 10.1016/J.CELL.2009.05.047.
  72. Escoubet-Lozach L, Benner C, Kaikkonen MU, et al. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS Genet 2011;7(12):1002401. DOI: 10.1371/JOURNAL.PGEN.1002401.
  73. De Santa F, Narang V, Yap ZH, et al. Jmjd3 contributes to the control of gene expression in LPS-activated macrophages. EMBO J 2009;28(21):3341−3352. DOI: 10.1038/EMBOJ.2009.271.
  74. Barish GD, Yu RT, Karunasiri M, et al. Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. Genes Dev 2010;24(24):2760−2765. DOI: 10.1101/GAD.1998010.
  75. Adelman K, Kennedy MA, Nechaev S, et al. Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling. Proc Natl Acad Sci USA 2009;106(43):18207−18212. DOI: 10.1073/PNAS.0910177106.
  76. Ganal SC, Sanos SL, Kallfass C, et al. Priming of natural killer cells by nonmucosal mononuclear phagocytes requires instructive signals from commensal microbiota. Immunity 2012;37(1):171−186. DOI: 10.1016/J.IMMUNI.2012.05.020.
  77. Chen X, Barozzi I, Termanini A, et al. Requirement for the histone deacetylase Hdac3 for the inflammatory gene expression program in macrophages. Proc Natl Acad Sci USA 2012;109(42):E2865−E2874. DOI: 10.1073/PNAS.1121131109.
  78. Wen H, Dou Y, Hogaboam CM, et al. Epigenetic regulation of dendritic cell-derived interleukin-12 facilitates immunosuppression after a severe innate immune response. Blood 2008;111(4):1797−1804. DOI: 10.1182/BLOOD-2007-08-106443.
  79. Park SH, Park-Min KH, Chen J, et al. Tumor necrosis factor induces GSK3 kinase-mediated cross-tolerance to endotoxin in macrophages. Nat Immunol 2011;12(7):607−615. DOI: 10.1038/NI.2043.
  80. Liu TF, Yoza BK, El Gazzar M, et al. NAD+-dependent SIRT1 deacetylase participates in epigenetic reprogramming during endotoxin tolerance. J Biol Chem 2011;286(11):9856−9864. DOI: 10.1074/JBC.M110.196790.
  81. Foster SL, Hargreaves DC, Medzhitov R. Gene-specific control of inflammation by TLR-induced chromatin modifications. Nature 2007;447(7147):972−978. DOI: 10.1038/NATURE05836.
  82. Chen J, Ivashkiv LB. IFN-γ abrogates endotoxin tolerance by facilitating Toll-like receptor-induced chromatin remodeling. Proc Natl Acad Sci USA 2010;107(45):19438−19443. DOI: 10.1073/PNAS.1007816107.
  83. Kobayashi T, Matsuoka K, Sheikh SZ, et al. IL-10 regulates Il12b expression via histone deacetylation: Implications for intestinal macrophage homeostasis. J Immunol 2012;189(4):1792−1799. DOI: 10.4049/JIMMUNOL.1200042.
  84. Ishii M, Wen H, Corsa CAS, et al. Epigenetic regulation of the alternatively activated macrophage phenotype. Blood 2009;114(15):3244−3254. DOI: 10.1182/BLOOD-2009-04-217620.
  85. Mullican SE, Gaddis CA, Alenghat T, et al. Histone deacetylase 3 is an epigenomic brake in macrophage alternative activation. Genes Dev 2011;25(23):2480−2488. DOI: 10.1101/GAD.175950.111.
  86. Satoh T, Takeuchi O, Vandenbon A, et al. The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nat Immunol 2010;11(10):936−944. DOI: 10.1038/NI.1920.
  87. Yasui T, Hirose J, Tsutsumi S, et al. Epigenetic regulation of osteoclast differentiation: Possible involvement of Jmjd3 in the histone demethylation of Nfatc1. J Bone Miner Res 2011;26(11):2665−2671. DOI: 10.1002/JBMR.464.
  88. Levy O. Innate immunity of the newborn: Basic mechanisms and clinical correlates. Nat Rev Immunol 2007;7(5):379−390. DOI: 10.1038/nri2075.
  89. Namachivayam K, MohanKumar K, Arbach D, et al. All-trans retinoic acid induces TGF-β2 in intestinal epithelial cells via RhoA- and p38α MAPK-mediated activation of the transcription factor ATF2. PLoS One 2015;10(7):e0134003. DOI: 10.1371/JOURNAL.PONE.0134003.
  90. MohanKumar K, Namachivayam K, Chapalamadugu KC, et al. Smad7 interrupts TGF-β signaling in intestinal macrophages and promotes inflammatory activation of these cells during necrotizing enterocolitis. Pediatr Res 2016;79(6):951−961. DOI: 10.1038/pr.2016.18.
  91. Maheshwari A, Voitenok NN, Akalovich S, et al. Developmental changes in circulating IL-8/CXCL8 isoforms in neonates. Cytokine 2009;46(1):12−16. DOI: 10.1016/J.CYTO.2008.12.022.
  92. 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 2012;209(4):661−669. DOI: 10.1084/JEM.20112343.
  93. van Essen D, Zhu Y, Saccani S. A feed-forward circuit controlling inducible NF-κB target gene activation by promoter histone demethylation. Mol Cell 2010;39(5):750−760. DOI: 10.1016/J.MOLCEL.2010.08.010.
  94. Zhu Y, van Essen D, Saccani S. Cell-type-specific control of enhancer activity by H3K9 trimethylation. Mol Cell 2012;46(4):408−423. DOI: 10.1016/J.MOLCEL.2012.05.011.
  95. Kruidenier L, Chung CW, Cheng Z, et al. A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response. Nature 2012;488(7411):404−408. DOI: 10.1038/NATURE11262.
  96. Ghisletti S, Barozzi I, Mietton F, et al. Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 2010;32(3):317−328. DOI: 10.1016/J.IMMUNI.2010.02.008.
  97. Jin F, Li Y, Ren B, et al. PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers. Proc Natl Acad Sci USA 2011;108(13):5290−5295. DOI: 10.1073/PNAS.1017214108.
  98. De Santa F, Barozzi I, Mietton F, et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 2010;8(5). DOI: 10.1371/JOURNAL.PBIO.1000384.
  99. Nicodeme E, Jeffrey KL, Schaefer U, et al. Suppression of inflammation by a synthetic histone mimic. Nature 2010;468(7327):1119−1123. DOI: 10.1038/NATURE09589.
  100. Delmore JE, Issa GC, Lemieux ME, et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 2011;146(6):904−917. DOI: 10.1016/J.CELL.2011.08.017.
  101. Schenk T, Chen WC, Göllner S, et al. Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia. Nat Med 2012;18(4):605−611. DOI: 10.1038/NM.2661.
  102. Chinenov Y, Gupte R, Dobrovolna J, et al. Role of transcriptional coregulator GRIP1 in the anti-inflammatory actions of glucocorticoids. Proc Natl Acad Sci USA 2012;109(29):11776−11781. DOI: 10.1073/PNAS.1206059109/-/DCSUPPLEMENTAL/PNAS.201206059SI.PDF.
  103. Gilchrist M, Thorsson V, Li B, et al. Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 2006;441(7090):173−178. DOI: 10.1038/NATURE04768.
  104. Hu X, Chung AY, Wu I, et al. Integrated regulation of Toll-like receptor responses by Notch and interferon-gamma pathways. Immunity 2008;29(5):691−703. DOI: 10.1016/J.IMMUNI.2008.08.016.
  105. Saijo K, Collier JG, Li AC, et al. An ADIOL-ERβ-CtBP transrepression pathway negatively regulates microglia-mediated inflammation. Cell 2011;145(4):584−595. DOI: 10.1016/J.CELL.2011.03.050.
  106. Yan Q, Carmody RJ, Qu Z, et al. Nuclear factor-κB binding motifs specify Toll-like receptor-induced gene repression through an inducible repressosome. Proc Natl Acad Sci USA 2012;109(35):14140−14145. DOI: 10.1073/PNAS.1119842109.
  107. Gough DJ, Messina NL, Clarke CJP, et al. Constitutive type I interferon modulates homeostatic balance through tonic signaling. Immunity 2012;36(2):166−174. DOI: 10.1016/J.IMMUNI.2012.01.011.
  108. Yarilina A, Park-Min KH, Antoniv T, et al. TNF activates an IRF1-dependent autocrine loop leading to sustained expression of chemokines and STAT1-dependent type I interferon-response genes. Nat Immunol 2008;9(4):378−387. DOI: 10.1038/NI1576.
  109. Chi T. A BAF-centred view of the immune system. Nat Rev Immunol 2004;4(12):965−977. DOI: 10.1038/NRI1501.
  110. Ivashkiv LB. IFNγ: Signalling, epigenetics and roles in immunity, metabolism, disease and cancer immunotherapy. Nat Rev Immunol 2018;18(9):545–558. DOI: 10.1038/s41577-018-0029-z.
  111. Shakespear MR, Halili MA, Irvine KM, et al. Histone deacetylases as regulators of inflammation and immunity. Trends Immunol 2011;32(7):335−343. DOI: 10.1016/J.IT.2011.04.001.
  112. Ivashkiv LB. Inflammatory signaling in macrophages: Transitions from acute to tolerant and alternative activation states. Eur J Immunol 2011;41(9):2477−2481. DOI: 10.1002/EJI.201141783.
  113. Ho PC, Tsui YC, Feng X, et al. NF-κB-mediated degradation of the coactivator RIP140 regulates inflammatory responses and contributes to endotoxin tolerance. Nat Immunol 2012;13(4):379−386. DOI: 10.1038/NI.2238.
  114. Abt MC, Osborne LC, Monticelli LA, et al. Commensal bacteria calibrate the activation threshold of innate antiviral immunity. Immunity 2012;37(1):158−170. DOI: 10.1016/J.IMMUNI.2012.04.011.
  115. Patel DJ. A structural perspective on readout of epigenetic histone and DNA methylation marks. Cold Spring Harb Perspect Biol 2016;8(3):a018754. DOI: 10.1101/CSHPERSPECT.A018754.
  116. Lavin Y, Winter D, Blecher-Gonen R, et al. Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment. Cell 2014;159(6):1312−1326. DOI: 10.1016/J.CELL.2014.11.018.
  117. Buttgereit A, Lelios I, Yu X, et al. Sall1 is a transcriptional regulator defining microglia identity and function. Nat Immunol 2016;17(12):1397−1406. DOI: 10.1038/NI.3585.
  118. Bain CC, Mowat AM. Macrophages in intestinal homeostasis and inflammation. Immunol Rev 2014;260(1):102−117. DOI: 10.1111/IMR.12192.
  119. Bain CC, Bravo-Blas A, Scott CL, et al. Constant replenishment from circulating monocytes maintains the macrophage pool in the intestine of adult mice. Nat Immunol 2014;15(10):929−937. DOI: 10.1038/NI.2967.
  120. Schneider C, Nobs SP, Kurrer M, et al. Induction of the nuclear receptor PPAR-γ by the cytokine GM-CSF is critical for the differentiation of fetal monocytes into alveolar macrophages. Nat Immunol 2014;15(11):1026−1037. DOI: 10.1038/NI.3005.
  121. Guilliams M, De Kleer I, Henri S, et al. Alveolar macrophages develop from fetal monocytes that differentiate into long-lived cells in the first week of life via GM-CSF. J Exp Med 2013;210(10):1977−1992. DOI: 10.1084/JEM.20131199.
  122. Ebina-Shibuya R, Watanabe-Matsui M, Matsumoto M, et al. The double knockout of Bach1 and Bach2 in mice reveals shared compensatory mechanisms in regulating alveolar macrophage function and lung surfactant t homeostasis. J Biochem 2016;160(6):333−344. DOI: 10.1093/JB/MVW041.
  123. Li R, Fang L, Pu Q, et al. MEG3-4 is a miRNA decoy that regulates IL-1β abundance to initiate and then limit inflammation to prevent sepsis during lung infection. Sci Signal 2018;11(536):eaao2387. DOI: 10.1126/SCISIGNAL.AAO2387.
  124. Mebius RE, Kraal G. Structure and function of the spleen. Nat Rev Immunol 2005;5(8):606−616. DOI: 10.1038/NRI1669.
  125. A-Gonzalez N, Guillen JA, Gallardo G, et al. The nuclear receptor LXRα controls the functional specialization of splenic macrophages. Nat Immunol 2013;14(8):831−839. DOI: 10.1038/NI.2622.
  126. Miyake Y, Asano K, Kaise H, et al. Critical role of macrophages in the marginal zone in the suppression of immune responses to apoptotic cell-associated antigens. J Clin Invest 2007;117(8):2268−2278. DOI: 10.1172/JCI31990.
  127. Kohyama M, Ise W, Edelson BT, et al. Role for Spi-C in the development of red pulp macrophages and splenic iron homeostasis. Nature 2009;457(7227):318−321. DOI: 10.1038/NATURE07472.
  128. Bain CC, Jenkins SJ. The biology of serous cavity macrophages. Cell Immunol 2018;330:126−135. DOI: 10.1016/J.CELLIMM.2018.01.003.
  129. Rosas M, Davies LC, Giles PJ, et al. The transcription factor Gata6 links tissue macrophage phenotype and proliferative renewal. Science 2014;344(6184):645−648. DOI: 10.1126/SCIENCE.1251414.
  130. Okabe Y, Medzhitov R. Tissue-specific signals control reversible program of localization and functional polarization of macrophages. Cell 2014;157(4):832−844. DOI: 10.1016/J.CELL.2014.04.016.
  131. Wynn TA, Chawla A, Pollard JW. Macrophage biology in development, homeostasis and disease. Nature 2013;496(7446):445−455. DOI: 10.1038/NATURE12034.
  132. Li Y, Zhao T, Liu B, et al. Inhibition of histone deacetylase 6 improves long-term survival in a lethal septic model. J Trauma Acute Care Surg 2015;78(2):378. DOI: 10.1097/TA.0000000000000510.
  133. How CK, Hou SK, Shih HC, et al. Expression profile of MicroRNAs in gram-negative bacterial sepsis. Shock 2015;43(2):121−127. DOI: 10.1097/SHK.0000000000000282.
  134. Wang X, Cao Q, Yu L, et al. Epigenetic regulation of macrophage polarization and inflammation by DNA methylation in obesity. JCI Insight 2016;1(19):87748. DOI: 10.1172/JCI.INSIGHT.87748.
  135. Bowes AJ, Khan MI, Shi Y, et al. Valproate attenuates accelerated atherosclerosis in hyperglycemic ApoE-deficient mice: Evidence in support of a role for endoplasmic reticulum stress and glycogen synthase kinase-3 in lesion development and hepatic steatosis. Am J Pathol 2009;174(1):330. DOI: 10.2353/AJPATH.2009.080385.
  136. Wendeln AC, Degenhardt K, Kaurani L, et al. Innate immune memory in the brain shapes neurological disease hallmarks. Nature 2018;556(7701):332−338. DOI: 10.1038/S41586-018-0023-4.
  137. Rodriguez RM, Suarez-Alvarez B, Lopez-Larrea C. Therapeutic epigenetic reprogramming of trained immunity in myeloid cells. Trends Immunol 2019;40(1):66−80. DOI: 10.1016/J.IT.2018.11.006.
  138. Chen X, El Gazzar M, Yoza BK, et al. The NF-κB factor RelB and histone H3 lysine methyltransferase G9a directly interact to generate epigenetic silencing in endotoxin tolerance. J Biol Chem 2009;284(41):27857. DOI: 10.1074/JBC.M109.000950.
  139. Nahid MA, Benso LM, Shin JD, et al. TLR4, TLR7/8 agonist-induced miR-146a promotes macrophage tolerance to MyD88-dependent TLR agonists. J Leukoc Biol 2016;100(2):339−349. DOI: 10.1189/JLB.2A0515-197R.
  140. Seeley JJ, Baker RG, Mohamed G, et al. Induction of innate immune memory via microRNA targeting of chromatin remodelling factors. Nature 2018;559(7712):114−119. DOI: 10.1038/S41586-018-0253-5.
  141. Norouzitallab P, Baruah K, Biswas P, et al. Probing the phenomenon of trained immunity in invertebrates during a transgenerational study, using brine shrimp Artemia as a model system. Sci Rep 2016;6:21166. DOI: 10.1038/SREP21166.
  142. Haley MJ, Brough D, Quintin J, et al. Microglial priming as trained immunity in the brain. Neuroscience 2019;405:47−54. DOI: 10.1016/J.NEUROSCIENCE.2017.12.039.
  143. Ostuni R, Piccolo V, Barozzi I, et al. Latent enhancers activated by stimulation in differentiated cells. Cell 2013;152(1−2):157−171. DOI: 10.1016/J.CELL.2012.12.018.
  144. Fanucchi S, Mhlanga MM. Lnc-ing trained immunity to chromatin architecture. Front Cell Dev Biol 2019;7:2. DOI: 10.3389/FCELL.2019.00002.
  145. Brown GD, Taylor PR, Reid DM, et al. Dectin-1 is a major beta-glucan receptor on macrophages. J Exp Med 2002;196(3):407−412. DOI: 10.1084/JEM.20020470.
  146. Kasivajjula H, Maheshwari A. Pathophysiology and current management of necrotizing enterocolitis. Indian J Pediatr 2014;81(5):489−497. DOI: 10.1007/S12098-014-1388-5/TABLES/3.
  147. Saeed S, Quintin J, Kerstens HHD, et al. Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science 2014;345(6204):1251086. DOI: 10.1126/SCIENCE.1251086.
  148. Benjaskulluecha S, Boonmee A, Pattarakankul T, et al. Screening of compounds to identify novel epigenetic regulatory factors that affect innate immune memory in macrophages. Sci Rep 2022;12(1):1−13. DOI: 10.1038/s41598-022-05929-x.
  149. Fang XH, Li ZJ, Liu CY, et al. Macrophage memory: Types, mechanisms, and its role in health and disease. Immunology 2024;171(1):18−30. DOI: 10.1111/IMM.13697.
  150. Quintin J, Saeed S, Martens JHA, et al. Candida albicans infection affords protection against reinfection via functional reprogramming of monocytes. Cell Host Microbe 2012;12(2):223−232. DOI: 10.1016/J.CHOM.2012.06.006.
  151. Arts RJW, Moorlag SJCFM, Novakovic B, et al. BCG vaccination protects against experimental viral infection in humans through the induction of cytokines associated with trained immunity. Cell Host Microbe 2018;23(1):89.e5−100.e5. DOI: 10.1016/J.CHOM.2017.12.010.
  152. Kleinnijenhuis J, Quintin J, Preijers F, et al. Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes. Proc Natl Acad Sci USA 2012;109(43):17537−17542. DOI: 10.1073/PNAS.1202870109.
  153. Bekkering S, Quintin J, Joosten LAB, et al. Oxidized low-density lipoprotein induces long-term proinflammatory cytokine production and foam cell formation via epigenetic reprogramming of monocytes. Arterioscler Thromb Vasc Biol 2014;34(8):1731−1738. DOI: 10.1161/ATVBAHA.114.303887.
  154. Verma D, Parasa VR, Raffetseder J, et al. Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects. Sci Rep 2017;7(1):12305. DOI: 10.1038/S41598-017-12110-2.
  155. Das J, Verma D, Gustafsson M, et al. Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects. Epigenetics 2019;14(6):589−601. DOI: 10.1080/15592294.2019.1603963.
  156. Madden K, Liang YC, Rajabalee N, et al. Surveying the epigenetic landscape of tuberculosis in alveolar macrophages. Infect Immun 2022;90(5):0052221. DOI: 10.1128/IAI.00522-21.
  157. Karlsson L, Das J, Nilsson M, et al. A differential DNA methylome signature of pulmonary immune cells from individuals converting to latent tuberculosis infection. Sci Rep 2021;11(1):19418. DOI: 10.1038/S41598-021-98542-3.
  158. Leonhardt J, Große S, Marx C, et al. Candida albicans β-glucan differentiates human monocytes into a specific subset of macrophages. Front Immunol 2018;9:2818. DOI: 10.3389/fimmu.2018.02818.
  159. Goodridge HS, Ahmed SS, Curtis N, et al. Harnessing the beneficial heterologous effects of vaccination. Nat Rev Immunol 2016;16(6):392−400. DOI: 10.1038/nri.2016.43.
  160. Mylonas KJ, Nair MG, Prieto-Lafuente L, et al. Alternatively activated macrophages elicited by helminth infection can be reprogrammed to enable microbial killing. J Immunol 2009;182(5):3084−3094. DOI: 10.4049/JIMMUNOL.0803463.
  161. Rückerl D, Campbell SM, Duncan S, et al. Macrophage origin limits functional plasticity in helminth-bacterial co-infection. PLoS Pathog 2017;13(3):e1006233. DOI: 10.1371/JOURNAL.PPAT.1006233.
  162. Li P, Spann NJ, Kaikkonen MU, et al. NCoR repression of LXRs restricts macrophage biosynthesis of insulin-sensitizing omega 3 fatty acids. Cell 2013;155(1):200−214. DOI: 10.1016/J.CELL.2013.08.054.
  163. Menzies KJ, Zhang H, Katsyuba E, et al. Protein acetylation in metabolism — Metabolites and cofactors. Nat Rev Endocrinol 2015;12(1):43−60. DOI: 10.1038/nrendo.2015.181.
  164. Baardman J, Licht I, De Winther MPJ, et al. Metabolic–epigenetic crosstalk in macrophage activation. Epigenomics 2015;7(7):1155−1164. DOI: 10.2217/EPI.15.71.
  165. Kaikkonen MU, Spann NJ, Heinz S, et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell 2013;51(3):310−325. DOI: 10.1016/J.MOLCEL.2013.07.010.
  166. Nair J, Maheshwari A. Non-coding RNAs in necrotizing enterocolitis − A new frontier? Curr Pediatr Rev 2021;18(1):25−32. DOI: 10.2174/1573396317666211102093646.
  167. Nair J, Maheshwari A. Epigenetics in necrotizing enterocolitis. Curr Pediatr Rev 2021;17(3):172−184. DOI: 10.2174/1573396317666210421110608.
  168. Donda K, Bose T, Dame C, et al. The impact of microRNAs in neonatal necrotizing enterocolitis and other inflammatory conditions of intestine: A review. Curr Pediatr Rev 2022;19(1):5−14. DOI: 10.2174/1573396318666220117102119.
  169. Donda KT,
PDF Share
PDF Share

© Jaypee Brothers Medical Publishers (P) LTD.