Fig. 4
Phenotypic and transcriptomic changes in human microglia upon ASO mediated APOE and TREM2 knockdown. A,B APOE (A) and TREM2 (B) expression in human microglia isolated from 6-month-old AppNL−G−F mice treated with 45ug APOE ASO-1 (A) or 90ug TREM2 ASO-171 (B) for 1 or 4 weeks. C ASO concentration in human microglia isolated from 6-month-old AppNL−G−F mice treated with APOE ASO-1 or TREM2 ASO-171 for 1 or 4 weeks. CNRQ = Calibrated Normalized Relative Quantities. Dots or bars represent mean ± SEM, n = 4/group. Statistical differences based on Two-way ANOVA test: *p < 0.05, **p < 0.01. D Representative images showing activated human microglia targeting X-34 positive amyloid-β fibrils 4 weeks post APOE and TREM2 knockdown. Arrow indicates an instance of activated human microglia around plaques. Scale bars = 100 µm (E) Quantification of mean fluorescence intensity for hP2RY12 and hCD9 at varying distances from the plaque assessed 4 weeks following ASOs treatment. F Quantification of hCD9 intensity at the plaque site (10 µm) normalized against signal intensity at the distal site from the plaque (74 – 81 µm) 4 weeks post ASOs treatment. Analysis was restricted to plaques surrounded by engrafted human microglia, determined by hP2RY12 signal (see Suppl Fig. 11A). Data represented as mean ± SD, n = 3/group. Statistical significance was evaluated with One-way ANOVA test (*p < 0.05, ns, not significant). G Gene set enrichment analysis (GSEA): Pre-ranked results of the microglial subtype gene sets (top 50 most significantly up-regulated genes of each microglial subtype [22]). The color represents the Normalized Enrichment Score (NES) of each gene set against the full list of genes ranked by the log-fold change when comparing the treatment group against the vehicle group. The asterisk indicates gene sets that are significantly enriched with FDR *p < 0.05. All analysis were performed on xenotransplanted microglia isolated from 6–7-month-old AppNL−G−F mice treated with APOE ASO-1 or TREM2 ASO-171 for 1 or 4 weeks