scRNA-seq reveals dysregulation of antigen-presenting genes 4 days after MOG immunization in the dLNs. (A) Density plots overlaid on the UMAP of control (n = 4) and NIK^ΔCX3CR1 (n = 4) displaying clustering of myeloid cell type, excluding B, T, NK, and mast cells, pDCs, neutrophils, and granulocytes. (B) Heatmap displaying the top 10 highly expressed markers of each cluster in A with three of the top markers per cluster written out. (C) Proportions of each cell type within the UMAP of the control (n = 4) and NIK^ΔCX3CR1 (n = 4). (D) Antigen presentation cell signature score projected in each cluster, calculated with UCell. (E) 536 neighborhoods assigned by the Milo package overlaid on our UMAP of myeloid cell clusters. (F) Abundant neighborhoods across the different myeloid clusters. Red = more abundant in control, blue = more abundant in NIK^ΔCX3CR1, FDR = 10%. (G) Volcano plot of DEGs between NIK^ΔCX3CR1 and control in the migDC subset. Left is downregulated in NIK^ΔCX3CR1, and right is upregulated in NIK^ΔCX3CR1. (H) KEGG pathway enrichment analysis was performed on DEGs (adjusted P < 0.05 and |log₂ fold change| >0.1 and <0.1) from the migDC clusters. (I and J) Volcano plot of DEGs between NIK^ΔCX3CR1 and control in the Mac subset and (J) MoMac subset. Left is downregulated in NIK^ΔCX3CR1, and right is upregulated in NIK^ΔCX3CR1. (K) KEGG pathway enrichment analysis was performed on DEGs (adjusted P < 0.05 and |log₂ fold change| >0.1 and <0.1) from the Mac clusters (Macs/MoMacs).The dot plot shows enriched pathways ranked by significance. Circle size = count of DEGs found within each pathway; color = adjusted P value. Data in C are shown as mean percentage and analyzed using two-way ANOVA with Šídák’s multiple comparisons test. *P < 0.05, ***P < 0.001.