Journal: bioRxiv
Article Title: Cribriform Plate Microenvironment Assembles a Suppressive Myeloid Network during EAE-induced Neuroinflammation
doi: 10.64898/2026.01.07.698165
Figure Lengend Snippet: (A) Heatmap displaying scaled expression (z-score) of highly expressed representative genes involved in immune regulation, immune activation (e.g., Pdcd1 ) across four cell types: macrophages (MΦ), T cells, migratory dendritic cells (Mig DCs), and fibroblasts (e.g., Pdpn ). Color scale indicates expression levels. (B) Quantification and network map of predicted ligand-receptor interactions between fibroblasts and immune populations (macrophages, Mig DCs, and T cells) using integrated analysis from CellChat, CellPhoneDB, iCellNet, and the Ramilowsky dataset. The bar graph shows the number of unique ligand-receptor interactions per pairwise combination, with the most extensive communication observed between macrophages and fibroblasts. Analyzed with crossTALK IntEraction Network (TALKIEN) with microglia, neutrophils, and proliferating gene sets excluded. (C) Network plot illustrating specific ligand-receptor pairs involved in fibroblast-immune cell communication. Arrows point from ligand-expressing to receptor-expressing cell types. Notable interactions include Spp1-CD44 , Pdpn-Clec2d , and Thbs1-CD47 . (D) Immunofluorescence imaging of the cribriform plate region in EAE day 3.0 mice showing spatial organization of LYVE-1 + lymphatics (white), PDPN + lymphatics and ECM (red), and CSF1R-GFP + myeloid cells (green). DAPI (blue) marks nuclei. Scale bars: 30 µm. (E) Pathway enrichment analysis of ligand-receptor pairs among macrophages, Mig DCs, T cells, and fibroblasts. Enriched pathways include extracellular matrix organization, integrin-mediated interactions, interleukin 10 signaling. Gene ratio represents the proportion of identified genes contributing to each pathway; dot size reflects the number of genes, and color indicates adjusted p-value. (F) : UMAP projection shows major post contact cell types, including macrophages (purple), microglia (green), neutrophils (blue), T cells (orange), proliferating cells (light blue), migratory dendritic cells (yellow-orange), and fibroblasts (aqua). Feature plots highlight expression of Chil3 (CHI3L3), Arg1 , Spp1 , Ccr2 , Cxcr4 , Csf1r (G) : Volcano plot comparing post-contact vs no-contact cluster 2 macrophages (Highest Arg1 expressing cluster). Analysis reveals post contact macrophage have downregulated MHC-II processing and presentation genes ( H2-DMa , H2-Aa , H2-Ab1 , H2-DMb1 , H2-Eb1 , Cd74 , Ciita ) and elevated expression of Chil3 (CHI3L3), another alternatively activated macrophage marker and ECM binding protein. (H) : Gene ontology enrichment analysis (bottom) demonstrates post contact Macrophages are enriched for pathways in Fcγ receptor and complement receptor signaling, negative regulation of IL-12 production, homotypic cell-cell adhesion, and hemostasis.
Article Snippet: The following antibodies were used for immunohistochemistry: Podoplanin PE (eBioscience, Catalog #: 12-5381-80), CD31 Alexa647 (BD Biosciences, Catalog #: 563608), Lyve-1 eFluor660 (Thermo Fisher Scientific, Catalog #: 50-0443-80), MHC II eFluor450 (eBioscience, Catalog #: 48-5321-80), CD11c Alexa488 (Thermo Fisher Scientific, Catalog #: 53-0114-80), YM1 / CHI3L3 (R&D Systems Catalog #: AF2446), Arginase-1 (Invitrogen, Catalog #: PA5-29645), Cleaved Caspase-3 (Abcam, Catalog #: E83-77) .
Techniques: Expressing, Activation Assay, Immunofluorescence, Imaging, Marker, Binding Assay
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