REFERENCES
1. Kettenmann H, Hanisch UK, Noda M, Verkhratsky A. Physiology of microglia. Physiol Rev 2011;91:461-553.
2. Nimmerjahn A, Kirchhoff F, Helmchen F. Resting microglial cells are highly dynamic surveillants of brain parenchyma in vivo. Science 2005;308:1314-8.
3. Parkhurst CN, Gan WB. Microglia dynamics and function in the CNS. Curr Opin Neurobiol 2010;20:595-600.
4. Ransohoff RM, Perry VH. Microglial physiology: unique stimuli, specialized responses. Ann Rev Immunol 2009;27:119-45.
5. Saijo K, Glass CK. Microglial cell origin and phenotypes in health and disease. Nat Rev Immunol 2011;11:775-87.
6. Wake H, Moorhouse AJ, Miyamoto A, Nabekura J. Microglia: actively surveying and shaping neuronal circuit structure and function. Trends Neurosci 2013;36:209-17.
7. Hanisch UK, Kettenmann H. Microglia: active sensor and versatile effector cells in the normal and pathologic brain. Nat Neurosci 2007;10:1387-94.
8. Saijo K, Winner B, Carson CT, Collier JG, Boyer L, et al. A Nurr1/CoREST pathway in microglia and astrocytes protects dopaminergic neurons from inflammation-induced death. Cell 2009;137:47-59.
9. Mosher KI, Wyss-Coray T. Microglial dysfunction in brain aging and Alzheimer’s disease. Biochem Pharmacol 2014;88:594-604.
10. Hickman S, Izzy S, Sen P, Morsett L, El Khoury J. Microglia in neurodegeneration. Nat Neurosci 2018;21:1359-69.
11. Salter MW, Stevens B. Microglia emerge as central players in brain disease. Nat Med 2017;23:1018-27.
12. Glass CK, Saijo K, Winner B, Marchetto MC, Gage FH. Mechanisms underlying inflammation in neurodegeneration. Cell 2010;140:918-34.
13. McCoy MK. Blocking soluble tumor necrosis factor signaling with dominant-negative tumor necrosis factor inhibitor attenuates loss of dopaminergic neurons in models of Parkinson’s disease. J Neurosci 2006;26:9365-75.
14. Sriram K, Matheson JM, Benkovic SA, Miller DB, Luster MI, et al. Mice deficient in TNF receptors are protected against dopaminergic neurotoxicity: implications for Parkinson’s disease. FASEB J 2002;16:1474-6.
15. Glass CK, Ogawa S. Combinatorial roles of nuclear receptors in inflammation and immunity. Nat Rev Immunol 2005;6:44-55.
16. Glass CK, Saijo K. Nuclear receptor transrepression pathways that regulate inflammation in macrophages and T cells. Nat Rev Immunol 2010;10:365-76.
17. Medzhitov R, Horng T. Transcriptional control of the inflammatory response. Nat Rev Immunol 2009;9:692-703.
18. Smale ST, Natoli G. Transcriptional control of inflammatory responses. Cold Spring Harb Perspect Biol 2014;6:a016261.
20. Smale ST, Tarakhovsky A, Natoli G. Chromatin contributions to the regulation of innate immunity. Ann Rev Immunol 2014;32:489-511.
21. Soreq L, Rose J, Soreq E, Hardy J, Trabzuni D, et al. Major shifts in glial regional identity are a transcriptional hallmark of human brain aging. Cell Rep 2017;18:557-70.
22. Han X, Gui B, Xiong C, Zhao L, Liang J, et al. Destabilizing LSD1 by Jade-2 promotes neurogenesis: an antibraking system in neural development. Mol Cell 2014;55:482-94.
23. Baruch K, Deczkowska A, David E, Castellano JM, Miller O, et al. Aging. Aging-induced type I interferon response at the choroid plexus negatively affects brain function. Science 2014;346:89-93.
24. Gabuzda D, Yankner BA. Physiology: inflammation links ageing to the brain. Nature 2013;497:197-8.
25. Godbout JP, Chen J, Abraham J, Richwine AF, Berg BM, et al. Exaggerated neuroinflammation and sickness behavior in aged mice following activation of the peripheral innate immune system. FASEB J 2005;19:1329-31.
26. Sparkman NL, Johnson RW. Neuroinflammation associated with aging sensitizes the brain to the effects of infection or stress. Neuroimmunomodulation 2008;15:323-30.
27. Stewart SA. Lentivirus-delivered stable gene silencing by RNAi in primary cells. RNA 2003;9:493-501.
28. Sena-Esteves M, Tebbets JC, Steffens S, Crombleholme T, Flake AW. Optimized large-scale production of high titer lentivirus vector pseudotypes. J Virol Methods 2004;122:131-9.
29. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2012;29:15-21.
30. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014;15:31-21.
31. Blighe K, Rana S, Lewis M. emphEnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling n.d. Available from: https://doi.org/10.18129/B9.bioc.EnhancedVolcano [Last accessed on 6 Mar 2020].
32. Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10:1523.
33. Craik FIM, Salthouse TA. The handbook of aging and cognition. 1st ed. Psychology Press; 2011.
34. Simen AA, Bordner KA, Martin MP, Moy LA, Barry LC. Cognitive dysfunction with aging and the role of inflammation. Ther Adv Chronic Dis 2011;2:175-95.
35. Nagamoto-Combs K, Kulas J, Combs CK. A novel cell line from spontaneously immortalized murine microglia. J Neurosci Methods 2014;233:187-98.
36. Zhao J, Bi W, Xiao S, Lan X, Cheng X, et al. Neuroinflammation induced by lipopolysaccharide causes cognitive impairment in mice. Sci Rep 2019;9:5790.
37. Glaros TG, Chang S, Gilliam EA, Maitra U, Deng H, et al. Causes and consequences of low grade endotoxemia and inflammatory diseases. Front Biosci (Schol Ed) 2013;5:754-65.
38. Sandiego CM, Gallezot JD, Pittman B, Nabulsi N, Lim K, et al. Imaging robust microglial activation after lipopolysaccharide administration in humans with PET. Proc Natl Acad Sci U S A 2015;112:12468-73.
40. Chen YC, Yip PK, Huang YL, Sun Y, Wen LL, et al. Sequence variants of toll like receptor 4 and late-onset Alzheimer’s disease. PLoS One 2012;7:e50771.
41. Perez-Pardo P, Dodiya HB, Engen PA, Forsyth CB, Huschens AM, et al. Role of TLR4 in the gut-brain axis in Parkinson’s disease: a translational study from men to mice. Gut 2019;68:829-43.
45. McDonald PP. Transcriptional regulation in neutrophils: teaching old cells new tricks. Adv Immunol 2004;82:1-48.
46. Zheng S, Hedl M, Abraham C. Twist1 and Twist2 contribute to cytokine downregulation following chronic NOD2 stimulation of human macrophages through the coordinated regulation of transcriptional repressors and activators. J Immunol 2015;195:217-26.
47. Lo HYG, Jin RU, Sibbel G, Liu D, Karki A, et al. A single transcription factor is sufficient to induce and maintain secretory cell architecture. Genes Dev 2017;31:154-71.
48. Kaminska B, Mota M, Pizzi M. Signal transduction and epigenetic mechanisms in the control of microglia activation during neuroinflammation. Biochim Biophys Acta 2016;1862:339-51.
49. Nagatsu T, Sawada M. Inflammatory process in Parkinson’s disease: role for cytokines. Curr Pharm Des 2005;11:999-1016.
50. Boka G, Anglade P, Wallach D, Javoy-Agid F, Agid Y, et al. Immunocytochemical analysis of tumor necrosis factor and its receptors in Parkinson’s disease. Neurosci Lett 1994;172:151-4.
51. Mogi M, Harada M, Riederer P, Narabayashi H, Fujita K, et al. Tumor necrosis factor-alpha (TNF-alpha) increases both in the brain and in the cerebrospinal fluid from parkinsonian patients. Neurosci Lett 1994;165:208-10.
52. Qin XY, Zhang SP, Cao C, Loh YP, Cheng Y. Aberrations in peripheral inflammatory cytokine levels in Parkinson disease. JAMA Neurol 2016;73:1316-9.
53. Rizzo FR, Musella A, De Vito F, Fresegna D, Bullitta S, et al. Tumor necrosis factor and interleukin-1β modulate synaptic plasticity during neuroinflammation. Neural Plast 2018;2018:1-12.
55. Takeuchi H, Jin S, Wang J, Zhang G, Kawanokuchi J, et al. Tumor necrosis factor-alpha induces neurotoxicity via glutamate release from hemichannels of activated microglia in an autocrine manner. J Biol Chem 2006;281:21362-8.
56. Ye L, Huang Y, Zhao L, Li Y, Sun L, et al. IL-1β and TNF-α induce neurotoxicity through glutamate production: a potential role for neuronal glutaminase. J Neurochem 2013;125:897-908.
57. Denver P, McClean P. Distinguishing normal brain aging from the development of Alzheimer’s disease: inflammation, insulin signaling and cognition. Neural Regen Res 2018;13:1719-12.
58. Njie eMalick G, Boelen E, Stassen FR, Steinbusch HWM, Borchelt DR, et al. Ex vivo cultures of microglia from young and aged rodent brain reveal age-related changes in microglial function. Neurobiol Aging 2012;33:195.e1-12.
59. Foster CT, Dovey OM, Lezina L, Luo JL, Gant TW, et al. Lysine-specific demethylase 1 regulates the embryonic transcriptome and CoREST stability. Mol Cell Biol 2010;30:4851-63.
60. Lee MG, Wynder C, Cooch N, Shiekhattar R. An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 2005;437:432-5.
61. Grabert K, Michoel T, Karavolos MH, Clohisey S, Baillie JK, et al. Microglial brain region-dependent diversity and selective regional sensitivities to aging. Nat Neurosci 2016;19:504-16.
62. Hammond TR, Dufort C, Dissing-Olesen L, Giera S, Young A, et al. Single-cell RNA sequencing of microglia throughout the mouse lifespan and in the injured brain reveals complex cell-state changes. Immunity 2019;50:253-71.e6.
63. Deczkowska A, Matcovitch-Natan O, Tsitsou-Kampeli A, Ben-Hamo S, Dvir-Szternfeld R, et al. Mef2C restrains microglial inflammatory response and is lost in brain ageing in an IFN-I-dependent manner. Nat Commun 2017;8:717.
64. The Tabula Muris Consortium, Pisco AO, McGeever A, Schaum N, Karkanias J, Neff NF, et al. A single cell transcriptomic atlas characterizes aging tissues in the mouse. bioRxiv; 2019. Available from: https://doi.org/10.1101/661728 [Last accessed on 6 Mar 2020].
65. Deczkowska A, Amit I, Schwartz M. Microglial immune checkpoint mechanisms. Nat Neurosci 2018;21:779-86.
66. Readhead B, Haure-Mirande JV, Funk CC, Richards MA, Shannon P, et al. Multiscale analysis of independent Alzheimer’s cohorts finds disruption of molecular, genetic, and clinical networks by human herpesvirus. Neuron 2018;99:64-82.e7.
68. Vijaya Kumar DK, Choi SH, Washicosky KJ, Eimer WA, Tucker S, et al. Amyloid-β peptide protects against microbial infection in mouse and worm models of Alzheimer’s disease. Sci Transl Med 2016;8:340ra72.