Fig 2: Extended characterization and validation of microglial populations.A UMAP embedding of microglial scRNA-Seq data colored by cluster (top left), experimental group (bottom left) and expression of selected markers (right). B Heatmap of average expression per microglial cluster measured by MERFISH (left) or by scRNA-Seq (right). C Pathway and Gene Ontology enrichment analysis of foamy microglia signature genes. One-sided Fisher exact test, nominal p-values. D Violin plots showing single-cell activity scores of homeostatic microglia, interferon-stimulated microglia, disease-associated microglia, and lipid-associated macrophages expression signatures collected from literature. E Boxplot of BODIPY fluorescence values of single microglia cells index-sorted from LPC-injected mice. Nominal p-values of post-hoc pairwise comparisons (two-tailed) following ANOVA, n = 560 cells obtained from 5 animals. Boxplots display the median (central line), interquartile range (IQR; box), and 1.5 * IQR (whiskers). Points beyond the whiskers represent outliers. F Rank plot of Pearson correlation coefficients between gene expression and BODIPY values in metacells. G Scatter plots of metacell gene expression vs BODIPY values for selected genes. Trendline represents generalized additive model fit, error band displays 95% confidence interval. H Network of pathways and Gene Ontology terms enriched in genes positively correlating with BODIPY. Gene Set Enrichment Analysis test, nominal p-values are shown. I Stainings of GPNMB, Galectin3 (Foamy microglia signature genes), IBA1 (microglia) and PLIN2 (lipid droplets) in LPC-injected white matter. Scale bar 10 µm. J Quantification of Galectin3 positivity in PLIN2-positive and PLIN2-negative microglia. Paired T-test (two-tailed, p-val = 4.021e−6), n = 5 animals. Data are presented as mean values +/- SEM. K Quantifications of Galectin3 and PLIN2 single and double positive Iba1+ microglia. N = 5 animals. Boxplots display the median (central line), interquartile range (IQR; box), and 1.5 * IQR (whiskers). Source data are provided as a Source Data file.

Fig 3: Attenuating effects of intracerebroventricular 2-hydroxypropyl-ß-cyclodextrin (HP-ß-CD) treatment on liver manifestations in Npc1-/- mice. Glycoprotein nonmetastatic melanoma protein B (GPNMB) levels in liver homogenate (A), GPNMB immunohistochemistry in liver (B), serum alanine aminotransferase (ALT) levels (C), and hematoxylin-and-eosin (H&E)-stained hepatic histology (D) are shown. Scale bar: 100 µm for GPNMB and H&E staining. Each bar represents the mean ± S.E.M. (n = 8–11). *** p < 0.001 compared with the wild-type group. # p < 0.05, ### p < 0.001 compared with the saline group.