Reduced plaque-associated microglia in the APPPS1 mouse model of AD with CX3CR1 deficiency. Brain sections (30 μm) from APPPS1;Cx3cr1+/+ (A–C), APPPS1;Cx3cr1+/− (D–F), and APPPS1;Cx3cr1−/− (G–I) mice at 4 months of age were immunostained with monoclonal Aβ antibody 4G8 (red; A, D, and G), with an antibody against the pan-microglial marker Iba1 (green; B, E, and H), and counterstained with the nuclear TO-PRO-3 dye (blue, C, F, and I). Confocal microscopy was used to obtain maximum projections reconstructed from Z-stacks spanning 20–30 μm in depth. As expected, APPPS1;Cx3cr1+/+ controls exhibit extensive accumulation of Iba1-positive microglia around senile plaques (A–C). However, age-matched APPPS1;Cx3cr1+/− (D–F) and APPPS1;Cx3cr1−/− animals (G–I) exhibit gene dose-dependent reduction in the number of Iba1-positive microglia surrounding the senile plaques. The number of Iba1-positive microglia associated with senile plaques in the three genotypes was quantified in three nonadjacent sections from each of the four animals per genotype. APPPS1 mice with either one or two copies of Cx3cr1 loss-of-function alleles exhibited a statistically significant reduction in microglia surrounding both large (>1000 μm2; J), medium (>500 μm2, <1000 μm2; K), and small (<500 μm2; L) Aβ deposits when compared to age-matched APPPS1;Cx3cr1+/+ controls (*P < 0.05; **P < 0.001, respectively). The APPPS1;Cx3cr1+/− and APPPS1;Cx3cr1−/− genotypes exhibited a statistically significant difference in microglial accumulation around medium Aβ deposits (P < 0.05), suggesting a gene dose-dependent effect. n = 35 for all analyses. Scale bar = 25 μm.