Figure 5.

Microglia prune synapses in microglia-containing brain organoids

(A) Representative images showing IBA1⁺ microglia interact with MAP2⁺ neuronal processes in day 55 brain organoids. Scale bars, 50 or 20 μm as indicated.

(B) Representative images showing PSD95⁺ and SYNAPSIN 1⁺ synaptic puncta, and the juxtaposition of pre- and post-synaptic puncta complexes along MAP2⁺ processes in day 55 brain organoids. Arrows and arrowheads indicate the juxtaposition of pre- and post-synaptic puncta, respectively. Scale bars, 5 μm.

(C) Quantification of pooled data from two hiPSC lines and one hESC line showing the density of SYNAPSIN 1⁺, PSD95⁺, and colocalized PSD95⁺ per 10 μm² MAP2 in day 55 organoids. Pooled data from two hiPSC lines and one hESC line. Three independent experiments (n = 3) were performed, and for each experiment, four to six organoids from each hPSC line were used. Data are presented as mean ± SEM.

(D) Representative images showing co-localization of IBA1⁺, CD68⁺, and PSD95⁺ staining in day 55 organoids. Left, a raw fluorescent super-resolution image. Right, a 3D surface rendered image from the same raw image. Scale bars, 3 μm.

(E) Representative 3D reconstruction of super-resolution images showing CD68⁺ microglial engulfment of SYNAPSIN 1 and PSD95 in day 55 organoids. Scale bars, 3 or 1 μm as indicated.

(F) Quantification of the number of SYNAPSIN 1⁺, PSD95⁺, and colocalized PSD95⁺ per 100 μm³ CD68⁺ microglial phagolysosomes in day 55 organoids. Pooled data from two hiPSC lines and one hESC line. Three independent experiments (n = 3) were performed, and, for each experiment, four to six organoids from each hPSC line were used. Data are presented as mean ± SEM.

See also Figure S3.