Extended Data Fig. 5: MEF2C KO microglia exhibit phagocytic, lysosomal, and aging-related defects.

a. Quantification of Staphylococcus aureus bioparticle phagocytosis over five hours (left) with Area Under the Curve (AUC) calculation demonstrating phagocytic deficit in KO compared to Control (Ctl) and MHS iMGs (n = 3 Ctl, 3 MHS and 3 KO iMG biological samples derived from independent iPSC lines). b. Representative images of Lysotracker (n = 5 Ctl, 6 MHS, and 6 KO iMG biological samples derived from independent iPSC lines from separate differentiation batches). c. Representative images and quantification of lysosomal marker, LAMP2 (n = 3 Ctl, 4 MHS, and 4 KO iMG biological samples derived from independent iPSC lines from separate differentiation batches). d. One representative pSTAT1 immunoblot analysis with vehicle and IFNβ-treated iMGs (n = 3 Ctl and 3 KO iMG biological samples derived from independent iPSC lines treated with vehicle or IFNβ). e. Representative images and quantification of Beta-galactosidase (β-gal, n = 3 Ctl, 3 MHS, and 3 KO iMG biological samples derived from independent iPSC lines). f. Representative images and quantification of neurodegenerative marker, APOE (n = 3 Ctl, 4 MHS, and 4 KO iMG biological samples derived from independent iPSC lines from separate differentiation batches). g. Representative images and quantification of neurodegenerative marker, TREM2 (n = 3 Ctl, 4 MHS, and 4 KO iMG biological samples derived from independent iPSC lines from separate differentiation batches). h. Principal component analysis of lipidomic profiles (n = 9 Ctl, 9 MHS, and 9 KO iMG biological samples derived from independent iPSC lines from separate differentiation batches). i. Quantification of baseline cell migration demonstrates reduced migration in KO compared to Ctl and MHS iMGs. (n = 3 Ctl, 3 MHS and 3 KO iMG biological samples derived from independent iPSC lines). Scale bar = 10 μm in b, c, e, f, and g. Data in c, e, f, and g are presented as mean values ± SEM. Each data point represents the mean measurement for all technical replicates from one independent line in a differentiation batch. Statistical analyses in c, e, f, and g were performed using one-way ANOVA tests with P values adjusted for multiple comparisons by Tukey’s method. P values in a and i were determined using one-way ANOVA tests on the area under the curve computed from the related time course measurements with adjustments by Tukey’s method.