Fig. 4

Microglia VISTA KO does not affect EAE progression and induces distinct microglia transcriptional profiles in spinal cord compared to brain. a EAE disease progression of VISTA WT and KO mice. Mice were terminated at score 1 (E1: early disease), score 4 (E4: peak disease), and chronic EAE (Ech) and microglia were isolated from spinal cord for mRNA sequencing analysis. b Number of differentially expressed genes (DEGs; logFC > 1; adjusted p-value < 0.05) comparing VISTA KO vs WT microglia from spinal cord at different EAE stages and in unimmunized mice. c Venn diagrams illustrating overlap in enriched (top) and depleted (bottom) genes in VISTA KO compared to WT microglia from PBS-treated mice in LPS experiment (brain; red) and EAE experiment (spinal cord; green). d Gene ontology biological processes (red bars), molecular signatures database hallmark (blue bars), and ENCODE/CHEA transcription factors (green bars) associated with genes enriched (left) and depleted (right) in VISTA KO spinal cord microglia compared to WT in unimmunized mice. e Four-way plot illustrating logFC of DEGs at different EAE stages compared to unimmunized control in VISTA WT and KO mice. Color of dots indicates whether genes are differentially expressed (adjusted p-value < 0.05) in WT (blue), KO (orange), or both (grey). f–g Average expression of genes uniquely upregulated (left) or downregulated (right) in VISTA KO (f) or WT G microglia at all stages of EAE across all samples