Atg7 deficiency in microglia modifies the conformation of Aβ plaques, enhancing axonal damage. (A) Representative confocal images of the cortex from 5- and 12-mo-old Atg7^fl/fl-5xFAD and Atg7^ΔMG-5xFAD mice showing distinct forms of Aβ plaques. These included 6E10^−/low (red) Methoxy-X04⁺ (green) inert plaques, 6E10⁺ Methoxy-X04⁺ mixed plaques, and 6E10⁺ Methoxy-X04^−/low filamentous plaques. The zoom in views of representative plaques show Methoxy-X04 staining (top), 6E10 staining (middle), and merged staining (bottom). Scale bars represent 30 μm in the four panels on the left and 10 μm in the zoomed in views on the right. (B) Quantification of the percentages of inert, mixed, and filamentous plaques in each genotype of 5- or 12-mo-old mice. A total of 1,449 plaques from 5-mo-old and 1,402 plaques from 12-mo-old were analyzed, respectively. Each point represents data from one mouse with two technical repeats. *, P < 0.05 by two-way ANOVA with Sidak’s multiple comparisons test. Data are presented as mean ± SEM. (C) Representative confocal images showing Methoxy-X04–labeled Aβ plaques (blue) and surrounding LAMP1⁺ dystrophic neurites (green). Scale bar = 30 μm. (D) Quantification of the average volume of dystrophic neurites (LAMP1⁺) surrounding plaques (presented as volume/plaque). Each point represents data from one mouse with two technical repeats. **, P < 0.01 by two-way ANOVA with Sidak’s multiple comparisons test. Data are presented as mean ± SEM. (E) Schematic diagram for in vivo phagocytosis assay. (F) Representative FACS plots showing the percentage of Methoxy-X04⁺ microglia in the Atg7^fl/fl-5xFAD and Atg7^ΔMG-5xFAD mice. Atg7^fl/fl mice not on a 5xFAD background were used as negative controls to set up the Methoxy-X04⁺ gate. (G) Quantification of the frequency of Methoxy-X04⁺ microglia from Atg7^fl/fl-5xFAD and Atg7^ΔMG-5xFAD mice (n = 4 for each genotype). Each point represents data from one mouse. **, P < 0.01 by two-tailed unpaired t test. Data are presented as mean ± SEM. (H) Representative confocal images showing microglia (IBA1, red), CD68 (green), and Methoxy-X04 (blue) from 5-mo-old Atg7^fl/fl-5xFAD and Atg7^ΔMG-5xFAD mice. Scale bar = 100 μm. (I) Quantification of the percentages of CD68⁺ areas within cortex regions of 5-mo-old mice. Each point represents data from one mouse with two technical repeats. ***, P < 0.001 by two-tailed unpaired t test. Data are presented as mean ± SEM. (J) Quantification of the ratio of CD68⁺IBA1⁺ voxels to IBA1⁺ voxels in the cortical regions of 5-mo-old mice. Each point represents data from one mouse with two technical repeats. Data are presented as mean ± SEM.