{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T02:36:36Z","timestamp":1792722996690,"version":"4.5.0"},"reference-count":66,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T00:00:00Z","timestamp":1734566400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:p>Neurotropic alphaviruses such as Venezuelan equine encephalitis virus (VEEV) are critical human pathogens that continually expand to na\u00efve populations and for which there are no licensed vaccines or therapeutics. VEEV is highly infectious via the aerosol route and is a recognized weaponizable biothreat that causes neurological disease in humans. The neuropathology of VEEV has been attributed to an inflammatory immune response in the brain yet the underlying mechanisms and specific immune cell populations involved are not fully elucidated. This study uses single-cell RNA sequencing to produce a comprehensive transcriptional profile of immune cells isolated from the brain over a time course of infection in a mouse model of VEEV. Analyses reveal differentially activated subpopulations of microglia, including a distinct type I interferon-expressing subpopulation. This is followed by the sequential infiltration of myeloid cells and cytotoxic lymphocytes, also comprising subpopulations with unique transcriptional signatures. We identify a subpopulation of myeloid cells that form a distinct localization pattern in the hippocampal region whereas lymphocytes are widely distributed, indicating differential modes of recruitment, including that to specific regions of the brain. Altogether, this study provides a high-resolution analysis of the immune response to VEEV in the brain and highlights potential avenues of investigation for therapeutics that target neuroinflammation in the brain.<\/jats:p>","DOI":"10.3389\/fimmu.2024.1497839","type":"journal-article","created":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T06:24:15Z","timestamp":1734589455000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":7,"title":["Single-cell and spatiotemporal transcriptomic profiling of brain immune infiltration following Venezuelan equine encephalitis virus infection"],"prefix":"10.3389","volume":"15","author":[{"given":"Margarita V.","family":"Rangel","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aimy","family":"Sebastian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole F.","family":"Leon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashlee M.","family":"Phillips","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bria M.","family":"Gorman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas R.","family":"Hum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dina R.","family":"Weilhammer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,12,19]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.7759\/cureus.9674","article-title":"Molecular biology and epidemiology of neurotropic viruses","volume":"12","author":"Abdullahi","year":"2020","journal-title":"Cureus"},{"key":"B2","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.3390\/microorganisms8081167","article-title":"Epidemic alphaviruses: ecology, emergence and outbreaks","volume":"8","author":"Azar","year":"2020","journal-title":"Microorganisms"},{"key":"B3","doi-asserted-by":"crossref","first-page":"23","DOI":"10.3390\/v12010023","article-title":"Viral equine encephalitis, a growing threat to the horse population in Europe","volume":"12","author":"Lecollinet","year":"2019","journal-title":"Viruses"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1016\/j.jneuroim.2017.04.008","article-title":"Virus entry and replication in the brain precedes blood-brain barrier disruption during intranasal alphavirus infection","volume":"308","author":"Cain","year":"2017","journal-title":"J neuroimmunology"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1126\/science.158.3806.1283","article-title":"Arbovirus Infections of Laboratory Workers: Extent of problem emphasizes the need for more effective measures to reduce hazards","volume":"158","author":"Hanson","year":"1967","journal-title":"Science"},{"key":"B6","article-title":"An epiemiologfe'cal study of laboratory infections with Venezuelan equine encephalomyelitis","volume":"4","author":"Slepushkin","year":"1959","journal-title":"Problems Virology"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1016\/S0165-5728(00)00290-3","article-title":"Inflammation is a component of neurodegeneration in response to Venezuelan equine encephalitis virus infection in mice","volume":"109","author":"Schoneboom","year":"2000","journal-title":"J neuroimmunology"},{"key":"B8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1743-422X-8-197","article-title":"Role of adhesion molecules and inflammation in Venezuelan equine encephalitis virus infected mouse brain","volume":"8","author":"Sharma","year":"2011","journal-title":"Virol J"},{"key":"B9","doi-asserted-by":"publisher","first-page":"164","DOI":"10.3390\/v11020164","article-title":"Current understanding of the molecular basis of Venezuelan equine encephalitis virus pathogenesis and vaccine development","volume":"11","author":"Sharma","year":"2019","journal-title":"Viruses"},{"key":"B10","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.3390\/v15061307","article-title":"Tumour necrosis factor-\u03b1, chemokines, and leukocyte infiltrate are biomarkers for pathology in the brains of Venezuelan equine encephalitis (VEEV)-infected mice","volume":"15","author":"Phelps","year":"2023","journal-title":"Viruses"},{"key":"B11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-9-289","article-title":"Venezuelan equine encephalitis virus infection causes modulation of inflammatory and immune response genes in mouse brain","volume":"9","author":"Sharma","year":"2008","journal-title":"BMC Genomics"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.010280-0","article-title":"Oligonucleotide array analysis of Toll-like receptors and associated signalling genes in Venezuelan equine encephalitis virus-infected mouse brain","volume":"90","author":"Sharma","year":"2009","journal-title":"J Gen virology"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1089\/107999000312621","article-title":"Early expression of IFN-alpha\/beta and iNOS in the brains of Venezuelan equine encephalitis virus-infected mice","volume":"20","author":"Schoneboom","year":"2000","journal-title":"J Interferon Cytokine Res"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2007.05.041","article-title":"Alpha-beta T cells provide protection against lethal encephalitis in the murine model of VEEV infection","volume":"367","author":"Paessler","year":"2007","journal-title":"Virology"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2012.03.076","article-title":"Natural killer cell mediated pathogenesis determines outcome of central nervous system infection with Venezuelan equine encephalitis virus in C3H\/HeN mice","volume":"30","author":"Taylor","year":"2012","journal-title":"Vaccine"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1186\/1743-422X-3-63","article-title":"New low-viscosity overlay medium for viral plaque assays","volume":"3","author":"Matrosovich","year":"2006","journal-title":"Virol J"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3791\/55781","article-title":"Analysis of microglia and monocyte-derived macrophages from the central nervous system by flow cytometry","author":"Martin","year":"2017","journal-title":"J Vis Exp"},{"key":"B18","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp427","article-title":"ToppGene Suite for gene list enrichment analysis and candidate gene prioritization","volume":"37","author":"Chen","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4402","article-title":"Reversed graph embedding resolves complex single-cell trajectories","volume":"14","author":"Qiu","year":"2017","journal-title":"Nat Methods"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.938075","article-title":"Single-cell RNA-Seq reveals changes in immune landscape in post-traumatic osteoarthritis","volume":"13","author":"Sebastian","year":"2022","journal-title":"Front Immunol"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.00827-23","article-title":"Deep spatial profiling of Venezuelan equine encephalitis virus reveals increased genetic diversity amidst neuroinflammation and cell death during brain infection","volume":"97","author":"Williams","year":"2023","journal-title":"J Virol"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"B25","doi-asserted-by":"publisher","first-page":"R29","DOI":"10.1186\/gb-2014-15-2-r29","article-title":"voom: Precision weights unlock linear model analysis tools for RNA-seq read counts","volume":"15","author":"Law","year":"2014","journal-title":"Genome Biol"},{"key":"B26","article-title":"Pheatmap: pretty heatmaps","author":"Kolde","year":"2019"},{"key":"B27","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickam","year":"2016"},{"key":"B28","volume-title":"R: A Language and Environment for Statistical Computing","year":"2023"},{"key":"B29","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1006\/viro.2001.0878","article-title":"Immunopathogenesis and immune modulation of Venezuelan equine encephalitis virus-induced disease in the mouse","volume":"284","author":"Charles","year":"2001","journal-title":"Virology"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1016\/j.antiviral.2008.01.007","article-title":"C3H\/HeN mouse model for the evaluation of antiviral agents for the treatment of Venezuelan equine encephalitis virus infection","volume":"78","author":"Julander","year":"2008","journal-title":"Antiviral Res"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.02779","article-title":"Monocytes and monocyte-derived antigen-presenting cells have distinct gene signatures in experimental model of multiple sclerosis","volume":"10","author":"Monaghan","year":"2019","journal-title":"Front Immunol"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1007\/s00414-020-02384-z","article-title":"TMEM119 as a specific marker of microglia reaction in traumatic brain injury in postmortem examination","volume":"134","author":"Bohnert","year":"2020","journal-title":"Int J Legal Med"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.01295-20","article-title":"Single-cell RNA sequencing reveals the diversity of the immunological landscape following central nervous system infection by a murine coronavirus","volume":"94","author":"Syage","year":"2020","journal-title":"J Virology"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1016\/j.cyto.2006.08.006","article-title":"IL-18 acts synergistically with IL-15 in stimulating natural killer cell proliferation","volume":"35","author":"French","year":"2006","journal-title":"Cytokine"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1016\/S1074-7613(00)80543-9","article-title":"Defective NK cell activity and Th1 response in IL-18\u2013deficient mice","volume":"8","author":"Takeda","year":"1998","journal-title":"Immunity"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.162.9.5070","article-title":"IL-18 is a potent coinducer of IL-13 in NK and T cells: a new potential role for IL-18 in modulating the immune response","volume":"162","author":"Hoshino","year":"1999","journal-title":"J Immunol"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1093\/brain\/awp144","article-title":"CCR2+ Ly-6Chi monocytes are crucial for the effector phase of autoimmunity in the central nervous system","volume":"132","author":"Mildner","year":"2009","journal-title":"Brain"},{"key":"B38","doi-asserted-by":"publisher","first-page":"1052","DOI":"10.3390\/v11111052","article-title":"Characterization of brain inflammation, apoptosis, hypoxia, blood-brain barrier integrity and metabolism in Venezuelan equine encephalitis virus (VEEV TC-83) exposed mice by in vivo positron emission tomography imaging","volume":"11","author":"Bocan","year":"2019","journal-title":"Viruses"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1080\/21505594.2020.1870834","article-title":"Toll-like receptor 4 mediates blood-brain barrier permeability and disease in C3H mice during Venezuelan equine encephalitis virus infection: Venezuelan equine encephalitis virus and toll-like receptor 4","volume":"12","author":"Hollidge","year":"2021","journal-title":"Virulence"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1007\/s00702-017-1795-7","article-title":"Differential contribution of microglia and monocytes in neurodegenerative diseases","volume":"125","author":"Baufeld","year":"2018","journal-title":"J Neural transmission"},{"key":"B41","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00401-021-02384-2","article-title":"Microglia and monocytes in inflammatory CNS disease: integrating phenotype and function","volume":"143","author":"Spiteri","year":"2022","journal-title":"Acta neuropathologica"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1172\/JCI97229","article-title":"Microglia are required for protection against lethal coronavirus encephalitis in mice","volume":"128","author":"Wheeler","year":"2018","journal-title":"J Clin Invest"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1038\/nature18283","article-title":"A complement\u2013microglial axis drives synapse loss during virus-induced memory impairment","volume":"534","author":"Vasek","year":"2016","journal-title":"Nature"},{"key":"B44","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1016\/j.celrep.2018.09.003","article-title":"Type I interferon receptor signaling of neurons and astrocytes regulates microglia activation during viral encephalitis","volume":"25","author":"Chhatbar","year":"2018","journal-title":"Cell Rep"},{"key":"B45","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/s40478-023-01547-4","article-title":"Temporal tracking of microglial and monocyte single-cell transcriptomics in lethal flavivirus infection","volume":"11","author":"Spiteri","year":"2023","journal-title":"Acta Neuropathologica Commun"},{"key":"B46","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12974-019-1545-x","article-title":"Differential transcriptional profiles identify microglial-and macrophage-specific gene markers expressed during virus-induced neuroinflammation","volume":"16","author":"DePaula-Silva","year":"2019","journal-title":"J Neuroinflammation"},{"key":"B47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3233\/JAD-230109","article-title":"Senescent microglia represent a subset of disease-associated microglia in P301S mice","volume":"95","author":"Ng","year":"2023","journal-title":"J Alzheimer's Dis"},{"key":"B48","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1038\/s41598-023-27653-w","article-title":"Neuronal glutathione loss leads to neurodegeneration involving gasdermin activation","volume":"13","author":"Hashimoto","year":"2023","journal-title":"Sci Rep"},{"key":"B49","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1016\/j.immuni.2018.11.004","article-title":"Single-cell RNA sequencing of microglia throughout the mouse lifespan and in the injured brain reveals complex cell-state changes","volume":"50","author":"Hammond","year":"2019","journal-title":"Immunity"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000240","article-title":"MyD88 is required for protection from lethal infection with a mouse-adapted SARS-CoV","volume":"4","author":"Sheahan","year":"2008","journal-title":"PloS pathogens"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.167.8.4585","article-title":"Lack of CCR2 results in increased mortality and impaired leukocyte activation and trafficking following infection of the central nervous system with a neurotropic coronavirus","volume":"167","author":"Chen","year":"2001","journal-title":"J Immunol"},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1005201108","article-title":"Recruited inflammatory monocytes stimulate antiviral Th1 immunity in infected tissue","volume":"108","author":"Iijima","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.73.3.2563-2567.1999","article-title":"Resistance of interleukin-1\u03b2-deficient mice to fatal Sindbis virus encephalitis","volume":"73","author":"Liang","year":"1999","journal-title":"J virology"},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00458-11","article-title":"Interleukin-6, produced by resident cells of the central nervous system and infiltrating cells, contributes to the development of seizures following viral infection","volume":"85","author":"Libbey","year":"2011","journal-title":"J virology"},{"key":"B55","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20080421","article-title":"Ly6c+ \u201cinflammatory monocytes\u201d are microglial precursors recruited in a pathogenic manner in West Nile virus encephalitis","volume":"205","author":"Getts","year":"2008","journal-title":"J Exp Med"},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1016\/j.clim.2016.05.009","article-title":"Neutrophils and viral-induced neurologic disease","volume":"189","author":"Grist","year":"2018","journal-title":"Clin Immunol"},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20200213","article-title":"Brain transforms natural killer cells that exacerbate brain edema after intracerebral hemorrhage","volume":"217","author":"Li","year":"2020","journal-title":"J Exp Med"},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0111401","article-title":"Perforin competent CD8 T cells are sufficient to cause immune-mediated blood-brain barrier disruption","volume":"9","author":"Johnson","year":"2014","journal-title":"PloS One"},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.17.11457-11466.2005","article-title":"Neuronal CXCL10 directs CD8+ T-cell recruitment and control of West Nile virus encephalitis","volume":"79","author":"Klein","year":"2005","journal-title":"J virology"},{"key":"B60","doi-asserted-by":"publisher","DOI":"10.1038\/s41593-019-0427-y","article-title":"T cells promote microglia-mediated synaptic elimination and cognitive dysfunction during recovery from neuropathogenic flaviviruses","volume":"22","author":"Garber","year":"2019","journal-title":"Nat Neurosci"},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.805657","article-title":"How does the immune system enter the brain","volume":"13","author":"Mapunda","year":"2022","journal-title":"Front Immunol"},{"key":"B62","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbadis.2015.10.018","article-title":"Immune cell trafficking across the barriers of the central nervous system in multiple sclerosis and stroke","volume":"1862","author":"Pinheiro","year":"2016","journal-title":"Biochim Biophys Acta (BBA)-Molecular Basis Disease"},{"key":"B63","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2990.2000.00255.x","article-title":"Monocyte infiltration is highly associated with loss of the tight junction protein zonula occludens in HIV-1-associated dementia","volume":"26","author":"Boven","year":"2000","journal-title":"Neuropathology Appl neurobiology"},{"key":"B64","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2013.02.012","article-title":"Recruitment of beneficial M2 macrophages to injured spinal cord is orchestrated by remote brain choroid plexus","volume":"38","author":"Shechter","year":"2013","journal-title":"Immunity"},{"key":"B65","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1038\/srep00545","article-title":"Hippocampal protection in mice with an attenuated inflammatory monocyte response to acute CNS picornavirus infection","volume":"2","author":"Howe","year":"2012","journal-title":"Sci Rep"},{"key":"B66","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1177\/0300985810372508","article-title":"REVIEW PAPER : pathology of animal models of alphavirus encephalitis","volume":"47","author":"Steele","year":"2010","journal-title":"Veterinary Pathology"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2024.1497839\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T06:24:19Z","timestamp":1734589459000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2024.1497839\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,19]]},"references-count":66,"alternative-id":["10.3389\/fimmu.2024.1497839"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2024.1497839","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,19]]},"article-number":"1497839"}}