{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T18:06:20Z","timestamp":1790791580276,"version":"4.1.0"},"reference-count":70,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,7,26]],"date-time":"2021-07-26T00:00:00Z","timestamp":1627257600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,7,26]],"date-time":"2021-07-26T00:00:00Z","timestamp":1627257600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["1088242"],"award-info":[{"award-number":["1088242"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"crossref","award":["1030897"],"award-info":[{"award-number":["1030897"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Merridew Foundation","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Neuroinflammation"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Differentiating infiltrating myeloid cells from resident microglia in neuroinflammatory disease is challenging, because bone marrow-derived inflammatory monocytes infiltrating the inflamed brain adopt a \u2018microglia-like\u2019 phenotype. This precludes the accurate identification of either cell type without genetic manipulation, which is important to understand their temporal contribution to disease and inform effective intervention in its pathogenesis. During West Nile virus (WNV) encephalitis, widespread neuronal infection drives substantial CNS infiltration of inflammatory monocytes, causing severe immunopathology and\/or death, but the role of microglia in this remains unclear.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Using high-parameter cytometry and dimensionality-reduction, we devised a simple, novel gating strategy to identify microglia and infiltrating myeloid cells during WNV-infection. Validating our strategy, we (1) blocked the entry of infiltrating myeloid populations from peripheral blood using monoclonal blocking antibodies, (2) adoptively transferred BM-derived monocytes and tracked their phenotypic changes after infiltration and (3) labelled peripheral leukocytes that infiltrate into the brain with an intravenous dye. We demonstrated that myeloid immigrants populated only the identified macrophage gates, while PLX5622 depletion reduced all 4 subsets defined by the microglial gates.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Using this gating approach, we identified four consistent microglia subsets in the homeostatic and WNV-infected brain. These were P2RY12\n                      <jats:sup>hi<\/jats:sup>\n                      CD86\n                      <jats:sup>\u2212<\/jats:sup>\n                      , P2RY12\n                      <jats:sup>hi<\/jats:sup>\n                      CD86\n                      <jats:sup>+<\/jats:sup>\n                      and P2RY12\n                      <jats:sup>lo<\/jats:sup>\n                      CD86\n                      <jats:sup>\u2212<\/jats:sup>\n                      P2RY12\n                      <jats:sup>lo<\/jats:sup>\n                      CD86\n                      <jats:sup>+<\/jats:sup>\n                      . During infection, 2 further populations were identified as 'inflammatory' and 'microglia-like' macrophages, recruited from the bone marrow. Detailed kinetic analysis showed significant increases in the proportions of both P2RY12\n                      <jats:sup>lo<\/jats:sup>\n                      microglia subsets in all anatomical areas, largely at the expense of the P2RY12\n                      <jats:sup>hi<\/jats:sup>\n                      CD86\n                      <jats:sup>\u2212<\/jats:sup>\n                      subset, with the latter undergoing compensatory proliferation, suggesting replenishment of, and differentiation from this subset in response to infection. Microglia altered their morphology early in infection, with all cells adopting temporal and regional disease-specific phenotypes. Late in disease, microglia produced IL-12, downregulated CX3CR1, F4\/80 and TMEM119 and underwent apoptosis. Infiltrating macrophages expressed both TMEM119 and P2RY12 de novo, with the microglia-like subset notably exhibiting the highest proportional myeloid population death.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our approach enables detailed kinetic analysis of resident vs infiltrating myeloid cells in a wide range of neuroinflammatory models without non-physiological manipulation. This will more clearly inform potential therapeutic approaches that specifically modulate these cells.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12974-021-02214-y","type":"journal-article","created":{"date-parts":[[2021,7,26]],"date-time":"2021-07-26T09:02:58Z","timestamp":1627290178000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["High-parameter cytometry unmasks microglial cell spatio-temporal response kinetics in severe neuroinflammatory disease"],"prefix":"10.1186","volume":"18","author":[{"given":"Alanna G.","family":"Spiteri","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel L.","family":"Terry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire L.","family":"Wishart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas M.","family":"Ashhurst","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iain L.","family":"Campbell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus J.","family":"Hofer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3877-9772","authenticated-orcid":false,"given":"Nicholas J. C.","family":"King","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,7,26]]},"reference":[{"issue":"10","key":"2214_CR1","doi-asserted-by":"publisher","first-page":"2319","DOI":"10.1084\/jem.20080421","volume":"205","author":"DR Getts","year":"2008","unstructured":"Getts DR, Terry RL, Getts MT, M\u00fcller M, Rana S, Shrestha B, et al. Ly6c+ \u201cinflammatory monocytes\u201d are microglial precursors recruited in a pathogenic manner in West Nile virus encephalitis. J Expe Med. 2008;205(10):2319\u201337. https:\/\/doi.org\/10.1084\/jem.20080421.","journal-title":"J Expe Med"},{"issue":"219","key":"2214_CR2","doi-asserted-by":"publisher","first-page":"219ra7","DOI":"10.1126\/scitranslmed.3007563","volume":"6","author":"DR Getts","year":"2014","unstructured":"Getts DR, Terry RL, Getts MT, Deffrasnes C, M\u00fcller M, van Vreden C, et al. Therapeutic inflammatory monocyte modulation using immune-modifying microparticles. Science Transl Med. 2014;6(219):219ra7.","journal-title":"Science Transl Med"},{"issue":"1","key":"2214_CR3","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1186\/1742-2094-9-246","volume":"9","author":"DR Getts","year":"2012","unstructured":"Getts DR, Terry RL, Getts MT, M\u00fcller M, Rana S, Deffrasnes C, et al. Targeted blockade in lethal West Nile virus encephalitis indicates a crucial role for very late antigen (VLA)-4-dependent recruitment of nitric oxide-producing macrophages. J Neuroinflam. 2012;9(1):246.","journal-title":"J Neuroinflam"},{"key":"2214_CR4","first-page":"25","volume-title":"Prague: InTech","author":"NJC King","year":"2011","unstructured":"King NJC, Van Vreden C, Terry RL, Getts DR, Yeung AWS, Teague-Getts M, et al. The immunopathogenesis of neurotropic flavivirus infection. In: R\u016f\u017eek D, editor. Prague: InTech; 2011. p. 25\u201352."},{"issue":"6005","key":"2214_CR5","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1126\/science.1194637","volume":"330","author":"F Ginhoux","year":"2010","unstructured":"Ginhoux F, Greter M, Leboeuf M, Nandi S, See P, Gokhan S, et al. Fate mapping analysis reveals that adult microglia derive from primitive macrophages. Science. 2010;330(6005):841\u20135. https:\/\/doi.org\/10.1126\/science.1194637.","journal-title":"Science."},{"issue":"3","key":"2214_CR6","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1038\/nn.3318","volume":"16","author":"K Kierdorf","year":"2013","unstructured":"Kierdorf K, Erny D, Goldmann T, Sander V, Schulz C, Perdiguero EG, et al. Microglia emerge from erythromyeloid precursors via Pu.1- and Irf8-dependent pathways. Nat Neurosci. 2013;16(3):273\u201380. https:\/\/doi.org\/10.1038\/nn.3318.","journal-title":"Nat Neurosci."},{"issue":"12","key":"2214_CR7","doi-asserted-by":"publisher","first-page":"1538","DOI":"10.1038\/nn2014","volume":"10","author":"B Ajami","year":"2007","unstructured":"Ajami B, Bennett JL, Krieger C, Tetzlaff W, Rossi FM. Local self-renewal can sustain CNS microglia maintenance and function throughout adult life. Nature neuroscience. 2007;10(12):1538\u201343. https:\/\/doi.org\/10.1038\/nn2014.","journal-title":"Nature neuroscience."},{"issue":"6","key":"2214_CR8","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1038\/nn.4547","volume":"20","author":"TL Tay","year":"2017","unstructured":"Tay TL, Mai D, Dautzenberg J, Fernandez-Klett F, Lin G. Sagar, et al. A new fate mapping system reveals context-dependent random or clonal expansion of microglia. Nat Neurosci. 2017;20(6):793\u2013803. https:\/\/doi.org\/10.1038\/nn.4547.","journal-title":"Nat Neurosci."},{"issue":"2","key":"2214_CR9","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1016\/j.celrep.2016.12.041","volume":"18","author":"K Askew","year":"2017","unstructured":"Askew K, Li K, Olmos-Alonso A, Garcia-Moreno F, Liang Y, Richardson P, et al. Coupled proliferation and apoptosis maintain the rapid turnover of microglia in the adult brain. Cell reports. 2017;18(2):391\u2013405. https:\/\/doi.org\/10.1016\/j.celrep.2016.12.041.","journal-title":"Cell reports."},{"key":"2214_CR10","doi-asserted-by":"publisher","first-page":"600822","DOI":"10.3389\/fimmu.2020.600822","volume":"11","author":"AG Spiteri","year":"2020","unstructured":"Spiteri AG, Wishart CL, King NJC. Immovable object meets unstoppable force? dialogue between resident and peripheral myeloid cells in the inflamed brain. Front Immunol. 2020;11:600822. https:\/\/doi.org\/10.3389\/fimmu.2020.600822","journal-title":"Front Immunol."},{"issue":"1","key":"2214_CR11","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1038\/nn.3599","volume":"17","author":"O Butovsky","year":"2014","unstructured":"Butovsky O, Jedrychowski MP, Moore CS, Cialic R, Lanser AJ, Gabriely G, et al. Identification of a unique TGF-\u03b2-dependent molecular and functional signature in microglia. Nature neuroscience. 2014;17(1):131\u201343. https:\/\/doi.org\/10.1038\/nn.3599.","journal-title":"Nature neuroscience."},{"issue":"11","key":"2214_CR12","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1016\/j.tins.2007.08.007","volume":"30","author":"K Biber","year":"2007","unstructured":"Biber K, Neumann H, Inoue K, Boddeke HW. Neuronal \u2018On\u2019 and \u2018Off\u2019 signals control microglia. Trends Neurosci. 2007;30(11):596\u2013602. https:\/\/doi.org\/10.1016\/j.tins.2007.08.007.","journal-title":"Trends Neurosci"},{"issue":"6","key":"2214_CR13","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1016\/j.neuron.2018.05.014","volume":"98","author":"FC Bennett","year":"2018","unstructured":"Bennett FC, Bennett ML, Yaqoob F, Mulinyawe SB, Grant GA, Hayden Gephart M, et al. A Combination of ontogeny and CNS environment establishes microglial identity. Neuron. 2018;98(6):1170\u201383.e8.","journal-title":"Neuron"},{"key":"2214_CR14","doi-asserted-by":"publisher","unstructured":"Gosselin D, Skola D, Coufal NG, Holtman IR, Schlachetzki JCM, Sajti E, et al. An environment-dependent transcriptional network specifies human microglia identity. Science. 2017;356(6344):eaal3222. https:\/\/doi.org\/10.1126\/science.aal3222.","DOI":"10.1126\/science.aal3222"},{"issue":"5448","key":"2214_CR15","doi-asserted-by":"publisher","first-page":"2333","DOI":"10.1126\/science.286.5448.2333","volume":"286","author":"RS Lanciotti","year":"1999","unstructured":"Lanciotti RS, Roehrig JT, Deubel V, Smith J, Parker M, Steele K, et al. Origin of the West Nile virus responsible for an outbreak of encephalitis in the northeastern United States. Science. 1999;286(5448):2333\u20137. https:\/\/doi.org\/10.1126\/science.286.5448.2333.","journal-title":"Science."},{"issue":"8","key":"2214_CR16","doi-asserted-by":"publisher","first-page":"1519","DOI":"10.1016\/j.clinthera.2017.07.001","volume":"39","author":"MH Collins","year":"2017","unstructured":"Collins MH, Metz SW. Progress and works in progress: update on flavivirus vaccine development. Clin Ther. 2017;39(8):1519\u201336. https:\/\/doi.org\/10.1016\/j.clinthera.2017.07.001.","journal-title":"Clin Ther."},{"key":"2214_CR17","doi-asserted-by":"publisher","unstructured":"Ulbert S. West Nile virus vaccines - current situation and future directions.\u00a0Hum Vaccin Immunother. 2019;15(10):2337\u201342. https:\/\/doi.org\/10.1080\/21645515.2019.1621149.","DOI":"10.1080\/21645515.2019.1621149"},{"issue":"5","key":"2214_CR18","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1038\/ncpneuro0176","volume":"2","author":"RL Debiasi","year":"2006","unstructured":"Debiasi RL, Tyler KL. West Nile virus meningoencephalitis. Nat Clin Pract Neurol. 2006;2(5):264\u201375. https:\/\/doi.org\/10.1038\/ncpneuro0176.","journal-title":"Nat Clin Pract Neurol."},{"issue":"7","key":"2214_CR19","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.3201\/eid1107.040991","volume":"11","author":"JJ Sejvar","year":"2005","unstructured":"Sejvar JJ, Bode AV, Marfin AA, Campbell GL, Ewing D, Mazowiecki M, et al. West Nile virus-associated flaccid paralysis. Emerg Infect Dis. 2005;11(7):1021\u20137. https:\/\/doi.org\/10.3201\/eid1107.040991.","journal-title":"Emerg Infect Dis."},{"issue":"5","key":"2214_CR20","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1212\/WNL.0000000000000086","volume":"82","author":"NM Vora","year":"2014","unstructured":"Vora NM, Holman RC, Mehal JM, Steiner CA, Blanton J, Sejvar J. Burden of encephalitis-associated hospitalizations in the United States, 1998-2010. Neurology. 2014;82(5):443\u201351. https:\/\/doi.org\/10.1212\/WNL.0000000000000086.","journal-title":"Neurology."},{"issue":"6","key":"2214_CR21","doi-asserted-by":"publisher","first-page":"768","DOI":"10.4269\/ajtmh.2005.72.768","volume":"72","author":"GD Huhn","year":"2005","unstructured":"Huhn GD, Austin C, Langkop C, Kelly K, Lucht R, Lampman R, et al. The emergence of West Nile virus during a large outbreak in Illinois in 2002. Am J Trop Med Hyg. 2005;72(6):768\u201376. https:\/\/doi.org\/10.4269\/ajtmh.2005.72.768.","journal-title":"Am J Trop Med Hyg."},{"issue":"24","key":"2214_CR22","doi-asserted-by":"publisher","first-page":"1807","DOI":"10.1056\/NEJM200106143442401","volume":"344","author":"D Nash","year":"2001","unstructured":"Nash D, Mostashari F, Fine A, Miller J, O'Leary D, Murray K, et al. The outbreak of West Nile virus infection in the New York City area in 1999. N Engl J Med. 2001;344(24):1807\u201314. https:\/\/doi.org\/10.1056\/NEJM200106143442401.","journal-title":"N Engl J Med."},{"issue":"1","key":"2214_CR23","doi-asserted-by":"publisher","first-page":"3758","DOI":"10.1038\/s41467-019-11674-z","volume":"10","author":"E Spangenberg","year":"2019","unstructured":"Spangenberg E, Severson PL, Hohsfield LA, Crapser J, Zhang J, Burton EA, et al. Sustained microglial depletion with CSF1R inhibitor impairs parenchymal plaque development in an Alzheimer\u2019s disease model. Nat Commun. 2019;10(1):3758. https:\/\/doi.org\/10.1038\/s41467-019-11674-z.","journal-title":"Nat Commun."},{"issue":"3","key":"2214_CR24","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1007\/s00401-018-1885-0","volume":"136","author":"R Fekete","year":"2018","unstructured":"Fekete R, Cserep C, Lenart N, Toth K, Orsolits B, Martinecz B, et al. Microglia control the spread of neurotropic virus infection via P2Y12 signalling and recruit monocytes through P2Y12-independent mechanisms. Acta Neuropathol. 2018;136(3):461\u201382. https:\/\/doi.org\/10.1007\/s00401-018-1885-0.","journal-title":"Acta Neuropathol"},{"key":"2214_CR25","doi-asserted-by":"publisher","unstructured":"Seitz S, Clarke P, Tyler KL. Pharmacologic Depletion of Microglia Increases Viral Load in the Brain and Enhances Mortality in Murine Models of Flavivirus-Induced Encephalitis.\u00a0J Virol. 2018;92(16):e00525-18. https:\/\/doi.org\/10.1128\/JVI.00525-18.","DOI":"10.1128\/JVI.00525-18"},{"key":"2214_CR26","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1016\/j.bbi.2018.09.006","volume":"74","author":"I Waltl","year":"2018","unstructured":"Waltl I, K\u00e4ufer C, Gerhauser I, et al. Microglia have a protective role in viral encephalitis-induced seizure development and hippocampal damage. Brain Behav Immun. 2018;74:186\u2013204. https:\/\/doi.org\/10.1016\/j.bbi.2018.09.006.","journal-title":"Brain Behav Immun."},{"issue":"3","key":"2214_CR27","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1172\/JCI97229","volume":"128","author":"DL Wheeler","year":"2018","unstructured":"Wheeler DL, Sariol A, Meyerholz DK, Perlman S. Microglia are required for protection against lethal coronavirus encephalitis in mice. J Clin Invest. 2018;128(3):931\u201343. https:\/\/doi.org\/10.1172\/JCI97229.","journal-title":"J Clin Invest."},{"issue":"3","key":"2214_CR28","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1007\/s13365-019-00740-3","volume":"25","author":"J Sanchez","year":"2019","unstructured":"Sanchez J, DePaula-Silva A, Doty D, Truong A, Libbey J, Fujinami R. Microglial cell depletion is fatal with low level picornavirus infection of the central nervous system. J NeuroVirol. 2019;25(3):415\u201321. https:\/\/doi.org\/10.1007\/s13365-019-00740-3.","journal-title":"J NeuroVirol"},{"issue":"1","key":"2214_CR29","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/s12974-019-1397-4","volume":"16","author":"KE Funk","year":"2019","unstructured":"Funk KE, Klein RS. CSF1R antagonism limits local restimulation of antiviral CD8+ T cells during viral encephalitis. Journal of Neuroinflammation. 2019;16(1):22. https:\/\/doi.org\/10.1186\/s12974-019-1397-4.","journal-title":"Journal of Neuroinflammation."},{"issue":"38","key":"2214_CR30","doi-asserted-by":"publisher","first-page":"23336","DOI":"10.1073\/pnas.1922788117","volume":"117","author":"F Lei","year":"2020","unstructured":"Lei F, Cui N, Zhou C, Chodosh J, Vavvas DG, Paschalis EI. CSF1R inhibition by a small-molecule inhibitor is not microglia specific; affecting hematopoiesis and the function of macrophages. Proc Natl Acad Sci U S A. 2020;117(38):23336\u20138. https:\/\/doi.org\/10.1073\/pnas.1922788117.","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"1","key":"2214_CR31","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1016\/j.celrep.2018.09.003","volume":"25","author":"C Chhatbar","year":"2018","unstructured":"Chhatbar C, Detje CN, Grabski E, Borst K, Spanier J, Ghita L, et al. Type I interferon receptor signaling of neurons and astrocytes regulates microglia activation during viral encephalitis. Cell Rep. 2018;25(1):118\u201329 e4. https:\/\/doi.org\/10.1016\/j.celrep.2018.09.003.","journal-title":"Cell Rep"},{"key":"2214_CR32","doi-asserted-by":"publisher","unstructured":"Moseman EA, Blanchard AC, Nayak D, McGavern DB. T cell engagement of cross-presenting microglia protects the brain from a nasal virus infection.\u00a0Sci Immunol. 2020;5(48):eabb1817. https:\/\/doi.org\/10.1126\/sciimmunol.abb1817.","DOI":"10.1126\/sciimmunol.abb1817"},{"issue":"8","key":"2214_CR33","doi-asserted-by":"publisher","first-page":"1276","DOI":"10.1038\/s41593-019-0427-y","volume":"22","author":"C Garber","year":"2019","unstructured":"Garber C, Soung A, Vollmer LL, Kanmogne M, Last A, Brown J, et al. T cells promote microglia-mediated synaptic elimination and cognitive dysfunction during recovery from neuropathogenic flaviviruses. Nat Neurosci. 2019;22(8):1276\u201388. https:\/\/doi.org\/10.1038\/s41593-019-0427-y.","journal-title":"Nat Neurosci."},{"issue":"7608","key":"2214_CR34","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1038\/nature18283","volume":"534","author":"MJ Vasek","year":"2016","unstructured":"Vasek MJ, Garber C, Dorsey D, Durrant DM, Bollman B, Soung A, et al. A complement-microglial axis drives synapse loss during virus-induced memory impairment. Nature. 2016;534(7608):538\u201343. https:\/\/doi.org\/10.1038\/nature18283.","journal-title":"Nature."},{"key":"2214_CR35","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1007\/978-1-4939-9454-0_12","volume":"1989","author":"TM Ashhurst","year":"2019","unstructured":"Ashhurst TM, Cox DA, Smith AL, King NJC. Analysis of the murine bone marrow hematopoietic system using mass and flow cytometry. Methods Mol Biol. 2019;1989:159\u201392.","journal-title":"Methods Mol Biol"},{"issue":"1","key":"2214_CR36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s42003-018-0216-2","volume":"1","author":"P Niewold","year":"2018","unstructured":"Niewold P, Cohen A, van Vreden C, Getts DR, Grau GE, King NJ. Experimental severe malaria is resolved by targeting newly-identified monocyte subsets using immune-modifying particles combined with artesunate. Commun Biol. 2018;1(1):1\u201313.","journal-title":"Commun Biol"},{"key":"2214_CR37","volume-title":"Cytometry analysis pipeline for large and compleX datasets. v2.5 ed: Github","author":"TM Ashhurst","year":"2018","unstructured":"Ashhurst TM. Cytometry analysis pipeline for large and compleX datasets. v2.5 ed: Github; 2018."},{"key":"2214_CR38","doi-asserted-by":"publisher","unstructured":"Ashhurst TM, Marsh-Wakefield F, Putri GH, et al. Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre [published online ahead of print, 2021 Apr 10].\u00a0Cytometry A. 2021;10.1002\/cyto.a.24350. https:\/\/doi.org\/10.1002\/cyto.a.24350.","DOI":"10.1002\/cyto.a.24350"},{"key":"2214_CR39","unstructured":"Kolde R.\u00a0pheatmap: pretty heatmaps. R package version 1.0.12;\u00a02019.\u00a0https:\/\/CRAN.R-project.org\/package=pheatmap."},{"issue":"12","key":"2214_CR40","doi-asserted-by":"publisher","first-page":"E1738","DOI":"10.1073\/pnas.1525528113","volume":"113","author":"ML Bennett","year":"2016","unstructured":"Bennett ML, Bennett FC, Liddelow SA, Ajami B, Zamanian JL, Fernhoff NB, et al. New tools for studying microglia in the mouse and human CNS. Proc Natl Acad Sci U S A. 2016;113(12):E1738\u201346. https:\/\/doi.org\/10.1073\/pnas.1525528113.","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"9","key":"2214_CR41","doi-asserted-by":"publisher","first-page":"1300","DOI":"10.1038\/nn.4610","volume":"20","author":"B Korin","year":"2017","unstructured":"Korin B, Ben-Shaanan TL, Schiller M, Dubovik T, Azulay-Debby H, Boshnak NT, et al. High-dimensional, single-cell characterization of the brain\u2019s immune compartment. Nat Neurosci. 2017;20(9):1300\u20139. https:\/\/doi.org\/10.1038\/nn.4610.","journal-title":"Nat Neurosci."},{"issue":"1-2","key":"2214_CR42","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.jneuroim.2014.09.014","volume":"277","author":"ND Lewis","year":"2014","unstructured":"Lewis ND, Hill JD, Juchem KW, Stefanopoulos DE, Modis LK. RNA sequencing of microglia and monocyte-derived macrophages from mice with experimental autoimmune encephalomyelitis illustrates a changing phenotype with disease course. J Neuroimmunol. 2014;277(1-2):26\u201338. https:\/\/doi.org\/10.1016\/j.jneuroim.2014.09.014.","journal-title":"J Neuroimmunol."},{"issue":"4","key":"2214_CR43","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1038\/s41593-018-0100-x","volume":"21","author":"B Ajami","year":"2018","unstructured":"Ajami B, Samusik N, Wieghofer P, Ho PP, Crotti A, Bjornson Z, et al. Single-cell mass cytometry reveals distinct populations of brain myeloid cells in mouse neuroinflammation and neurodegeneration models. Nat Neurosci. 2018;21(4):541\u201351. https:\/\/doi.org\/10.1038\/s41593-018-0100-x.","journal-title":"Nat Neurosci."},{"issue":"5","key":"2214_CR44","doi-asserted-by":"publisher","first-page":"844","DOI":"10.1002\/glia.23575","volume":"67","author":"AK Shukla","year":"2019","unstructured":"Shukla AK, McIntyre LL, Marsh SE, Schneider CA, Hoover EM, Walsh CM, et al. CD11a expression distinguishes infiltrating myeloid cells from plaque-associated microglia in Alzheimer\u2019s disease. Glia. 2019;67(5):844\u201356. https:\/\/doi.org\/10.1002\/glia.23575.","journal-title":"Glia"},{"key":"2214_CR45","first-page":"2579","volume":"9","author":"L van der Maaten","year":"2008","unstructured":"van der Maaten L, Hinton G. Visualizing data using t-SNE. J Machine Learn Res. 2008;9:2579\u2013605.","journal-title":"J Machine Learn Res"},{"issue":"9","key":"2214_CR46","doi-asserted-by":"publisher","first-page":"834","DOI":"10.1136\/bjo.79.9.834","volume":"79","author":"AD Dick","year":"1995","unstructured":"Dick AD, Ford AL, Forrester JV, Sedgwick JD. Flow cytometric identification of a minority population of MHC class II positive cells in the normal rat retina distinct from CD45lowCD11b\/c+CD4low parenchymal microglia. Br J Ophthalmol. 1995;79(9):834\u201340. https:\/\/doi.org\/10.1136\/bjo.79.9.834.","journal-title":"Br J Ophthalmol."},{"key":"2214_CR47","doi-asserted-by":"publisher","first-page":"249","DOI":"10.3389\/fimmu.2015.00249","volume":"6","author":"M Greter","year":"2015","unstructured":"Greter M, Lelios I, Croxford AL. Microglia versus myeloid cell nomenclature during brain inflammation. Front Immunol. 2015;6:249.","journal-title":"Front Immunol"},{"issue":"38","key":"2214_CR48","doi-asserted-by":"publisher","first-page":"E8929","DOI":"10.1073\/pnas.1806754115","volume":"115","author":"C K\u00e4ufer","year":"2018","unstructured":"K\u00e4ufer C, Chhatbar C, Br\u00f6er S, Waltl I, Ghita L, Gerhauser I, et al. Chemokine receptors CCR2 and CX3CR1 regulate viral encephalitis-induced hippocampal damage but not seizures. Proceedings of the National Academy of Sciences. 2018;115(38):E8929\u201338. https:\/\/doi.org\/10.1073\/pnas.1806754115.","journal-title":"Proceedings of the National Academy of Sciences."},{"issue":"1","key":"2214_CR49","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1159\/000365972","volume":"7","author":"RL Terry","year":"2015","unstructured":"Terry RL, Deffrasnes C, Getts DR, Minten C, Van Vreden C, Ashhurst TM, et al. Defective inflammatory monocyte development in IRF8-deficient mice abrogates migration to the West Nile virus-infected brain. J Innate Immun. 2015;7(1):102\u201312.","journal-title":"J Innate Immun"},{"key":"2214_CR50","doi-asserted-by":"crossref","unstructured":"Ransom JT, Elia J, Godfrey W, Wang J, Jiang N, Yang X, et al. Cyanine TruStain\u2122, an effective blocking buffer to eliminate non-specific cyanine-like dye-mediated monocyte binding. J Immunol. 2017;198(1 Supplement):81.25-81.25.","DOI":"10.4049\/jimmunol.198.Supp.81.25"},{"issue":"6425","key":"2214_CR51","doi-asserted-by":"publisher","first-page":"eaat7554","DOI":"10.1126\/science.aat7554","volume":"363","author":"MJC Jord\u00e3o","year":"2019","unstructured":"Jord\u00e3o MJC, Sankowski R, Brendecke SM, Sagar LG, Tai Y-H, et al. Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation. Science. 2019;363(6425):eaat7554.","journal-title":"Science"},{"issue":"7","key":"2214_CR52","doi-asserted-by":"publisher","first-page":"1276","DOI":"10.1016\/j.cell.2017.05.018","volume":"169","author":"H Keren-Shaul","year":"2017","unstructured":"Keren-Shaul H, Spinrad A, Weiner A, Matcovitch-Natan O, Dvir-Szternfeld R, Ulland TK, et al. A unique microglia type associated with restricting development of Alzheimer\u2019s disease. Cell. 2017;169(7):1276\u201390 e17. https:\/\/doi.org\/10.1016\/j.cell.2017.05.018.","journal-title":"Cell"},{"issue":"3","key":"2214_CR53","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1016\/j.immuni.2017.08.008","volume":"47","author":"S Krasemann","year":"2017","unstructured":"Krasemann S, Madore C, Cialic R, Baufeld C, Calcagno N, El Fatimy R, et al. The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases. Immunity. 2017;47(3):566\u201381 e9. https:\/\/doi.org\/10.1016\/j.immuni.2017.08.008.","journal-title":"Immunity"},{"issue":"2","key":"2214_CR54","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1128\/JVI.01167-06","volume":"81","author":"C Wacher","year":"2007","unstructured":"Wacher C, Muller M, Hofer MJ, Getts DR, Zabaras R, Ousman SS, et al. Coordinated regulation and widespread cellular expression of interferon-stimulated genes (ISG) ISG-49, ISG-54, and ISG-56 in the central nervous system after infection with distinct viruses. J Virol. 2007;81(2):860\u201371. https:\/\/doi.org\/10.1128\/JVI.01167-06.","journal-title":"J Virol"},{"issue":"3","key":"2214_CR55","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1111\/j.1471-4159.2007.04798.x","volume":"103","author":"DR Getts","year":"2007","unstructured":"Getts DR, Matsumoto I, M\u00fcller M, Getts MT, Radford J, Shrestha B, et al. Role of IFN-\u03b3 in an experimental murine model of West Nile virus-induced seizures. Journal of neurochemistry. 2007;103(3):1019\u201330. https:\/\/doi.org\/10.1111\/j.1471-4159.2007.04798.x.","journal-title":"Journal of neurochemistry."},{"issue":"8","key":"2214_CR56","doi-asserted-by":"publisher","first-page":"1533","DOI":"10.1084\/jem.20132477","volume":"211","author":"R Yamasaki","year":"2014","unstructured":"Yamasaki R, Lu H, Butovsky O, Ohno N, Rietsch AM, Cialic R, et al. Differential roles of microglia and monocytes in the inflamed central nervous system. J Exp Med. 2014;211(8):1533\u201349. https:\/\/doi.org\/10.1084\/jem.20132477.","journal-title":"J Exp Med."},{"key":"2214_CR57","doi-asserted-by":"publisher","unstructured":"Kalyuzhny A. Atlas of Immune Cell Populations of the Inflamed Mammalian CNS.\u00a0Cells. 2018;7(5):39. https:\/\/doi.org\/10.3390\/cells7050039.","DOI":"10.3390\/cells7050039"},{"issue":"7744","key":"2214_CR58","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1038\/s41586-019-0924-x","volume":"566","author":"T Masuda","year":"2019","unstructured":"Masuda T, Sankowski R, Staszewski O, Bottcher C, Amann L. Sagar, et al. Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution. Nature. 2019;566(7744):388\u201392. https:\/\/doi.org\/10.1038\/s41586-019-0924-x.","journal-title":"Nature"},{"issue":"7","key":"2214_CR59","doi-asserted-by":"publisher","first-page":"1900","DOI":"10.1093\/brain\/awx113","volume":"140","author":"T Zrzavy","year":"2017","unstructured":"Zrzavy T, Hametner S, Wimmer I, Butovsky O, Weiner HL, Lassmann H. Loss of \u2018homeostatic\u2019 microglia and patterns of their activation in active multiple sclerosis. Brain. 2017;140(7):1900\u201313. https:\/\/doi.org\/10.1093\/brain\/awx113.","journal-title":"Brain."},{"issue":"1","key":"2214_CR60","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1186\/s12974-019-1545-x","volume":"16","author":"AB DePaula-Silva","year":"2019","unstructured":"DePaula-Silva AB, Gorbea C, Doty DJ, Libbey JE, Sanchez JMS, Hanak TJ, et al. Differential transcriptional profiles identify microglial- and macrophage-specific gene markers expressed during virus-induced neuroinflammation. J Neuroinflamm. 2019;16(1):152. https:\/\/doi.org\/10.1186\/s12974-019-1545-x.","journal-title":"J Neuroinflamm"},{"issue":"5","key":"2214_CR61","doi-asserted-by":"publisher","first-page":"826","DOI":"10.1002\/glia.22966","volume":"64","author":"K Bisht","year":"2016","unstructured":"Bisht K, Sharma KP, Lecours C, Sanchez MG, El Hajj H, Milior G, et al. Dark microglia: a new phenotype predominantly associated with pathological states. Glia. 2016;64(5):826\u201339. https:\/\/doi.org\/10.1002\/glia.22966.","journal-title":"Glia"},{"issue":"10","key":"2214_CR62","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1038\/s41583-018-0057-5","volume":"19","author":"O Butovsky","year":"2018","unstructured":"Butovsky O, Weiner HL. Microglial signatures and their role in health and disease. Nat Rev Neurosci. 2018;19(10):622\u201335. https:\/\/doi.org\/10.1038\/s41583-018-0057-5.","journal-title":"Nat Rev Neurosci."},{"issue":"6","key":"2214_CR63","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1038\/s41593-019-0393-4","volume":"22","author":"H Van Hove","year":"2019","unstructured":"Van Hove H, Martens L, Scheyltjens I, De Vlaminck K, Pombo Antunes AR, De Prijck S, et al. A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment. Nat Neurosci. 2019;22(6):1021\u201335. https:\/\/doi.org\/10.1038\/s41593-019-0393-4.","journal-title":"Nat Neurosci"},{"issue":"35","key":"2214_CR64","doi-asserted-by":"publisher","first-page":"eabb2119","DOI":"10.1126\/sciadv.abb2119","volume":"6","author":"H-R Chen","year":"2020","unstructured":"Chen H-R, Sun Y-Y, Chen C-W, Kuo Y-M, Kuan IS, Tiger Li Z-R, et al. Fate mapping via CCR2-CreER mice reveals monocyte-to-microglia transition in development and neonatal stroke. Sci Adv. 2020;6(35):eabb2119.","journal-title":"Sci Adv"},{"issue":"3","key":"2214_CR65","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1038\/s41593-020-0585-y","volume":"23","author":"Y Werner","year":"2020","unstructured":"Werner Y, Mass E, Ashok Kumar P, Ulas T, Handler K, Horne A, et al. Cxcr4 distinguishes HSC-derived monocytes from microglia and reveals monocyte immune responses to experimental stroke. Nat Neurosci. 2020;23(3):351\u201362. https:\/\/doi.org\/10.1038\/s41593-020-0585-y.","journal-title":"Nat Neurosci"},{"key":"2214_CR66","first-page":"153","volume":"30","author":"M Miyake","year":"1964","unstructured":"Miyake M. The pathology of Japanese encephalitis. A review. Bull World Health Organ. 1964;30:153\u201360.","journal-title":"Bull World Health Organ"},{"issue":"4","key":"2214_CR67","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1093\/jnen\/nlw008","volume":"75","author":"JL Loewen","year":"2016","unstructured":"Loewen JL, Barker-Haliski ML, Dahle EJ, White HS, Wilcox KS. Neuronal injury, gliosis, and glial proliferation in two models of temporal lobe epilepsy. J Neuropathol Exp Neurol. 2016;75(4):366\u201378. https:\/\/doi.org\/10.1093\/jnen\/nlw008.","journal-title":"J Neuropathol Exp Neurol."},{"issue":"3","key":"2214_CR68","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1002\/jnr.20488","volume":"81","author":"ED Ponomarev","year":"2005","unstructured":"Ponomarev ED, Shriver LP, Maresz K, Dittel BN. Microglial cell activation and proliferation precedes the onset of CNS autoimmunity. J Neurosci Res. 2005;81(3):374\u201389. https:\/\/doi.org\/10.1002\/jnr.20488.","journal-title":"J Neurosci Res."},{"issue":"2","key":"2214_CR69","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1016\/j.immuni.2008.11.012","volume":"30","author":"T Town","year":"2009","unstructured":"Town T, Bai F, Wang T, Kaplan AT, Qian F, Montgomery RR, et al. Toll-like receptor 7 mitigates lethal West Nile encephalitis via interleukin 23-dependent immune cell infiltration and homing. Immunity. 2009;30(2):242\u201353. https:\/\/doi.org\/10.1016\/j.immuni.2008.11.012.","journal-title":"Immunity."},{"issue":"1-2","key":"2214_CR70","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/S0022-510X(03)00203-X","volume":"215","author":"J Li","year":"2003","unstructured":"Li J, Gran B, Zhang GX, Ventura ES, Siglienti I, Rostami A, et al. Differential expression and regulation of IL-23 and IL-12 subunits and receptors in adult mouse microglia. J Neurol Sci. 2003;215(1-2):95\u2013103. https:\/\/doi.org\/10.1016\/S0022-510X(03)00203-X.","journal-title":"J Neurol Sci."}],"container-title":["Journal of Neuroinflammation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12974-021-02214-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12974-021-02214-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12974-021-02214-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,5]],"date-time":"2023-01-05T09:00:51Z","timestamp":1672909251000},"score":1,"resource":{"primary":{"URL":"https:\/\/jneuroinflammation.biomedcentral.com\/articles\/10.1186\/s12974-021-02214-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,7,26]]},"references-count":70,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["2214"],"URL":"https:\/\/doi.org\/10.1186\/s12974-021-02214-y","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-388801\/v1","asserted-by":"object"}]},"ISSN":["1742-2094"],"issn-type":[{"value":"1742-2094","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,7,26]]},"assertion":[{"value":"2 April 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 July 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 July 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All experiments were completed with animal ethics approval number K20\/05-2016\/976 approved by the University of Sydney Animal Ethics Committee.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"N\/A","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"166"}}