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. Author manuscript; available in PMC: 2026 Jul 8.
Published in final edited form as: Cell. 2026 Mar 11;189(6):1656–1679.e42. doi: 10.1016/j.cell.2026.02.008

Figure 3. Sildenafil treatment in LS brain organoids affects progenitor populations.

Figure 3.

(A) Representative images of cortical brain organoids from controls (CTRL_2) and LS (ATP6_4, ATP6_7) at day 35 stained with neural progenitor marker PAX6 and neuronal marker TUJ1. Scale bar: 200 μm. (B) Differentiation ratio based on gene expression of CTIP2 over SOX2 in day 70 brain organoids from controls (CTRL_1 and CTRL_2) and LS (ATP6_4, ATP6_7). 2-3 brain organoids per line per experiment, n=3 independent experiments. ***p<0.001; unpaired two-tailed t-test. (C) Experimental setup in brain organoids to assess the acute sildenafil signature with bulk transcriptomics from controls (CTRL_1, CTRL_2) and LS (ATP6_4, ATP6_7) and the chronic sildenafil signature with single-nucleus RNA sequencing (snRNAseq) from controls (CTRL_1) and LS (ATP6_7). (D) Differentiation ratio in day 70 brain organoids from LS (ATP6_4). 10 brain organoids per line per experiment, n=3 independent experiments. ****p<0.0001; unpaired two-tailed t-test. (E) qPCR analysis in LS brain organoids (ATP6_4), 10 brain organoids per line n=3 independent experiments. *p<0.05; unpaired two-tailed t-test. (F) Dot plot highlighting top ten enriched GO biological processes by acute sildenafil (10 μM for 24 h) in day 70 LS brain organoids (ATP6_4, ATP6_7) based on transcriptomics. 5 brain organoids per line per experiment, n=3 independent experiments. (G-H) Uniform manifold approximation and projection (UMAP) plot and bar plot showing distribution of day 70 brain organoids from controls (CTRL_1) and LS (ATP6_7) treated with chronic sildenafil (10 μM for 45 days) or only DMSO. 15 brain organoids per line per experiment, n=3 independent experiments. (I) Volcano plot of pseudo-bulk analysis of snRNAseq dataset depicting the disease signature in the progenitor population. (J) Pseudo-bulk analysis of snRNAseq dataset showing the expression pattern of PRKG1, RGS6, and STMN2 across distinct populations of day 70 brain organoids.