Fig. 7: Microglia depletion impairs SCI-induced transcriptional changes in astrocytes.

a Astrocytes were computationally isolated for analysis between experimental conditions. b Astrocytes were divided into three clusters based on dominant gene expression, and were characterized as: Transporter (green), Metabolism (blue), and Inflammation (orange). c Dot Plot showing the top DEGs in each cluster. d, e UMAP plots showing astrocytes in the vehicle (d) and PLX5622 (e) conditions. The Inflammation astrocyte subset increases proportion over time post-SCI only when microglia are present. Numbers in pie charts show each subset as a percent of total astrocytes in each group. f To determine how microglia depletion affected long-term SCI-induced changes in astrocytes, we compared 28 dpi astrocytes to sham vehicle astrocytes. Select genes are labeled. g Of all the genes increased in astrocytes at 28 dpi, 55% failed to increase if microglia are absent. h Of all the genes decreased in astrocytes at 28 dpi, 5% failed to decrease if microglia are absent. i: Heatmap showing SCI-dependent and microglia-dependent astrocyte genes. j–l Violin plots showing the first 3 genes in h. The percentages under each violin indicate the percent of cells in the group that express the gene^a. p_adj < 0.0001 compared to other groups, Wilcox rank-sum test, n = 107–310 astrocytes per group pooled from 3–4 mice per group. m–o Astrocyte genes increased by SCI and reversed by microglia depletion were entered into gene ontology (GO) term analysis using WebGestalt. Astrocyte biological processes (l), molecular functions (m), and cellular components (n) related to translation, cell proliferation, metabolism, and inflammation were impaired by microglia depletion. Source data are provided as a Source Data file.