Fig. 5: Single-cell RNA sequencing identifies MHC-I genes as main targets of SCDi in 3xTg hippocampal microglia. | Nature Communications

Fig. 5: Single-cell RNA sequencing identifies MHC-I genes as main targets of SCDi in 3xTg hippocampal microglia.

From: Stearoyl-CoA Desaturase inhibition reverses immune, synaptic and cognitive impairments in an Alzheimer’s disease mouse model

Fig. 5

a, b Immunohistochemistry of PSD95 and Iba-1 in the hippocampus (CA1). a Quantification of PSD95+ puncta on Iba1+ microglial cells, WT-D (46 microglia/5 animals), 3xTg-D (40 microglia/4 animals), WT-S (42 microglia/5 animals), 3xTg-S (43 microglia/5 animals) (2-way ANOVA, Dunnett’s post-hoc test: WT-D/3xTg-D, p = 0.012; WT-D/3xTg-S, p = 0.963). Inset: box plot (minimum, 1st quartile, median, 3rd quartile and maximum), WT-D (8–14 microglia/animal), 3xTg-D (6–10 microglia/animal), WT-S (5–12 microglia/animal), 3xTg-S (7–11 microglia/animal). 2-way ANOVA, Dunnett’s post-hoc test. b Collapsed z-stack. Scale bar in b, 5 µm. c–i Single-cell RNA sequencing on WT and 3xTg mice treated with vehicle or SCDi (4 mice per group, pooled). c UMAP of all cells. d Microglia as percentage of CD45+ tagged cells. e Heatmap of WT-D/3xTg-D microglia DEGs (p-adjusted ≤ 0.05). f Venn diagram of WT-D/3xTg-D and WT-D/3xTg-S microglial DEG lists. g, h Heatmap of Restored (g) and New (h) genes. i Dot plot of average expression (z-score) of the top microglia DEGs between 3xTg-D and 3xTg-S: H2-D1, -K1, -T23, -Q6, -M3 genes (p-adjusted ≤ 0.05) and Trem2 (p-adjusted = 0.06). j Venn diagram overlapping the WT-D/3xTg-D microglial DEGs with public datasets from other Alzheimer’s disease mouse models. k–n qPCR analysis of TNFα (k), IL1β (l), H2-D1 (m), and H2-K1 (n) expression in WT (n = 8 mice) and SCD1-KO (n = 3 mice) microglia treated with Vehicle, LPS, or LPS + SCDi (L + S). TNFα (WT-Vehicle/WT-LPS p = 0.0001, SCD1-KO-Vehicle/SCD1-KO-LPS p = 0.0092) (k), IL1β (WT-Vehicle/WT-LPS p = 0.0001, SCD1-KO-Vehicle/SCD1-KO-LPS p = 0.277) (l), H2-D1 (WT-Vehicle/WT-LPS p = 0.047, SCD1-KO-Vehicle/SCD1-KO-LPS p = 0.901) (m), and H2-K1 (WT-Vehicle/WT-LPS p = 0.0001, SCD1-KO-Vehicle/SCD1-KO-LPS p = 0.059) (n). WT-LPS and SCD1-KO-LPS comparison showed a decrease in TNFα (p = 0.019) and a trend for IL1β (p = 0.075), 2-way ANOVA, Tukey’s post-hoc test. WT-LPS to WT-L + S showed a decrease in TNFα (p = 0.007), IL1β (p = 0.024) and H2-K1(p = 0.039) but not H2-D1 (p = 0.215) following SCDi treatment. WT-Vehicle to WT-L + S showed an increase in TNFα (p = 0.0001) and H2-K1 (p = 0.038) but not IL1β (p = 0.073) and H2-K1 (p = 0.626), 1-way ANOVA, Tukey’s post-hoc test. Note no significant differences were found between WT-L + S and SCD1-KO-LPS, 2 tailed t-test (comparison with Scd1-KO LPS). *p ≤ 0.05 **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001. Error bars represent mean ± SEM. SCDi: Stearoyl-CoA desaturase inhibitor. Source data are provided as a Source Data file.

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