Fig. 3: BEC and astrocyte endfoot molecular changes during peripherally induced neuroinflammation.

a Schematic of brain endothelial cell (BEC) RNA-seq workflow. b Functional classification of altered pathways after LPS administration from Ingenuity Pathway Analysis with curated categories. c Example IPA pathways within each category and their predicted activation (orange) or inhibition (blue) IPA z-scores. d (Left) Classification of CellTalkDB ligands upregulated after LPS (total = 83 ligands). (Right) Dot plots for cytokine/chemokine ligands and other immune-related ligands upregulated after LPS. For dot plots, the color intensity of the dot corresponds to the abundance of the gene in LPS samples (Log₁₀FPKM), while the size of the dot corresponds to the log₂(LPS/PBS) of each gene. Proteins are referred to by their gene names. e Venn diagram comparing proteins found in the endfoot proteome of PBS-injected control mice (Endfoot-TurboID PBS, gray circle) and LPS-injected mice (Endfoot-TurboID LPS, teal circle). Unique proteins from each condition are indicated. f Volcano plot demonstrating the differential expression of shared proteins between Endfoot-TurboID LPS and Endfoot-TurboID PBS samples. 15 proteins were downregulated after LPS, and 25 proteins were upregulated. Differential expression was performed using Limma. g Functional classification of proteins altered by LPS (unique and enriched proteins, both up and down after LPS). Protein function was derived from Uniprot and curated into the categories listed. h IPA pathways significantly altered by LPS and their predicted activation (orange) or inhibition (blue) IPA z-scores. Source data are provided in Supplementary Data 4 and 5.