Fig. 2

Inflammatory and activation characteristics of microglial subtypes. A Three-dimensional UMAP plot of microglia and macrophages. The different colors correspond to different cell types. B Boxplot showing the marker genes of microglia and macrophages. According to their different gene expression profiles, the microglia were categorized into three groups: Egr2⁺ M1 microglia (C1qa⁺, Ccr5⁺, Egr2⁺), Egr2⁻ M1 microglia (C1qa⁺, Ccr5⁺, Egr2⁻) and M2 microglia (C1qa⁺, Ccr5⁻, Egr2⁻). Macrophages highly expressed Cxcr4. C Immunofluorescence labeling for C1qa (red) and Ccr5 (green) and DAPI nuclear staining (blue) in the rat retina. M1 microglia are indicated by arrows, and M2 microglia are indicated by arrowheads (above, 63 ×). Immunofluorescence labeling for Ccr5 (red) and Egr2 (green) and DAPI nuclear staining (blue) in the rat retina. Egr2⁺ M1 microglia are indicated by arrows, and Egr2⁻ M1 microglia are indicated by arrowheads (below, 63 ×). Scale bar 20 µm. D Immunofluorescence labeling for C1qa (red) and Ccr5 (green) and DAPI nuclear staining (blue). M2 microglia are indicated by arrows (left, 20 ×). Immunofluorescence labeling for Ccr5 (red) and Egr2 (green) and DAPI nuclear staining (blue). Egr2⁺ M1 microglia are indicated by arrowheads, and Egr2⁻ M1 microglia are indicated by asterisks (right, 20 ×). Scale bar 50 µm. E Plot showing the pathways enriched in M2 microglia in GSEA. The threshold limits were a p value < 0.1 and a FDR q-value < 0.25. F Heatmap showing the average expression of inflammatory mediators in microglia and macrophages. The plot is ordered by the three gene categories (labels on left). High expression is in red, and low expression is in blue. G Bubble plots showing the expression of inflammatory cytokines in microglia subpopulations from different data sets. The size of each circle is proportional to the percentage of gene expression. High expression is shown in blue, and low expression is shown in gray. Mouse_2, Mouse_3 and Mouse_brain were obtained from normal mouse samples. H Bubble plot showing the expression of inflammatory mediators in Egr2⁺ M1 microglia and Egr2⁻ M1 microglia in different stages of DR. The size of each circle is proportional to the percentage of gene expression. High expression is shown in red/yellow, and low expression is shown in gray