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Immunol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Macrophage function is determined by microenvironment and origin. Brain and retinal microglia are both derived from yolk sac progenitors, yet their microenvironments differ. Utilizing single-cell RNA sequencing (scRNA-seq) data from mice, we tested the hypothesis that retinal and brain microglia exhibit distinct transcriptional profiles due to their unique microenvironments.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Eyes and brains from 2-4 month wildtype mice were combined (20 eyes; 3 brains) to yield one biologically diverse sample per organ. Each tissue was digested into single cell suspensions, enriched for immune cells, and sorted for scRNA-seq. Analysis was performed in Seurat v3 including clustering, integration, and differential expression. Multi-parameter flow cytometry was used for validation of scRNA-seq results. Lymphocytic choriomeningitis virus (LCMV) Clone 13, which produces a systemic, chronic, and neurotropic infection, was used to validate scRNA-seq and flow cytometry results <jats:italic>in vivo<\/jats:italic>.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Cluster analysis of integrated gene expression data from eye and brain identified 6 <jats:italic>Tmem119<\/jats:italic><jats:sup>+<\/jats:sup><jats:italic>P2ry12<\/jats:italic><jats:sup>+<\/jats:sup> microglial clusters. Differential expression analysis revealed that eye microglia were enriched for more pro-inflammatory processes including antigen processing via MHC class I (14.0-fold, <jats:italic>H2-D1<\/jats:italic> and <jats:italic>H2-K1<\/jats:italic>) and positive regulation of T-cell immunity (8.4-fold) compared to brain microglia. Multi-parameter flow cytometry confirmed that retinal microglia expressed 3.2-fold greater H2-Db and 263.3-fold more H2-Kb than brain microglia. On Day 13 and 29 after LCMV infection, CD8<jats:sup>+<\/jats:sup> T-cell density was greater in the retina than the brain.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>Our data demonstrate that the microenvironment of retina and brain differs, resulting in microglia-specific gene expression changes. Specifically, retinal microglia express greater MHC class I by scRNA-seq and multi-parameter flow cytometry, resulting in a possibly enhanced capability to stimulate CD8<jats:sup>+<\/jats:sup> T-cell inflammation during LCMV infection. These results may explain tissue-specific differences between retina and brain during systemic viral infections and CD8<jats:sup>+<\/jats:sup> T-cell driven autoimmune disease.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fimmu.2024.1399989","type":"journal-article","created":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T04:31:15Z","timestamp":1715315475000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":18,"title":["Retinal microglia express more MHC class I and promote greater T-cell-driven inflammation than brain microglia"],"prefix":"10.3389","volume":"15","author":[{"given":"Christina 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