Fig. 3

Profiling of HPS1 patient-specific alveolar organoids (AOs). A Overview of the generation of AOs from iPSCs. B Immunofluorescent imaging of AOs. Gray, SPC; Red, NaPi2B; Blue, nuclei (Hoechst). (Scale bars: 20 μm) C Total number of EpCAM⁺ cells in a well. The manually counted total number of dissociated cells was multiplied by the ratio of EpCAM⁺ cells obtained from flow cytometric analysis. Data are presented as mean ± SEM (n = 9 from 9 independent experiments). Two-way ANOVA with Sidak’s multiple comparisons test: **P < 0.01. n.s.: not significance. D Quantification of organoid size. Data are presented as mean ± SEM (n = 120 organoids from 6 independent experiments). Mann–Whitney U test. E Gating on flow cytometry for transcriptomic analysis of NaPi2B^high cells. Representative flow cytometry plots of HPS1 patient-specific AOs and their gene-corrected counterparts are shown. AOs after 3 passages using NaPi2B-based sorting were used for analysis. F Volcano plot of differentially expressed genes (DEGs) of NaPi2B^high cells in HPS1 patient-specific AOs compared with the gene-corrected counterparts. The volcano plot shows log₂ (fold change) and −log₁₀ (padj value) calculated by DESeq2. Significantly upregulated 302 genes with padj value < 0.05 and log₂ (fold change) > 0 are plotted in red. G Gene ontology enrichment analysis of biological process using the upregulated 302 genes in NaPi2B^high cells of HPS1 patient-specific AOs over the gene-corrected counterparts