Fig 2: SOX2 enables JAK–STAT activation in a positive feedback fashion.a–d, SOX2 ChIP–qPCR of JAK1 (a,c) and STAT1 (b,d) genomic loci in LNCaP/AR cells transduced with annotated CRISPR guide RNAs or overexpressing constructs. e, Relative cell numbers of LNCaP/AR cells transduced with annotated constructs and treated with Enz or vehicle, normalized to the vehicle group; Enz, 10 μM Enz; vehicle, DMSO treatment with equal volume as Enz. Cells were treated for 6 d, and cell numbers were measured by cell proliferation assay. f, Relative cell number fold change of LNCaP/AR cells transduced with annotated constructs. Data are normalized to the SOX2-OE + sgNT group; Enz, 10 μM Enz treatment for 8 d. Cell numbers were measured by a CellTiter-Glo assay. P values were calculated by one-way ANOVA with a Bonferroni multiple-comparison test. g, Relative expression of canonical lineage marker genes in LNCaP/AR SOX2-OE cells transduced with annotated constructs. h, Relative expression of canonical lineage marker genes in LNCaP/AR cells transduced with JAK1 or STAT1 cDNA constructs. SOX2 expression is highlighted in red. i, Relative expression of SOX2 in LNCaP/AR cells transduced with annotated guide RNAs. j, Relative expression of SOX2 in LNCaP/AR cells treated with 5 µM Filg or 5 µM ruxolitinib (Rux) or DMSO for 8 d. P values in i and j were calculated by one-way ANOVA with a Bonferroni multiple-comparison test. k, Relative gene expression levels of canonical JAK–STAT signaling and lineage marker genes in the inducible shTP53/RB1 LNCaP/AR cells treated with Dox for various lengths of time. Data are normalized to 0 h. Unless otherwise noted, n = 3 independent treated cell cultures, and data represent mean ± s.e.m. P values were calculated by two-way ANOVA with a Bonferroni multiple-comparison test.Source data

Fig 3: Free energy of binding decomposition per amino acid residue in the N-terminus of full-length SOX2. The free energies were calculated with both the PBSA and GBSA methods. Numbering is based on full-length SOX2.

Fig 4: Cell type specification occurs in Rptor-deficient saccules despite loss of cell types in the conducting airways.a Immunostaining of lung sections collected from Rptorf/f; ShhCre/+ mice and control littermates at 17.5 days post coitus (dpc). NKX2.1 labeled all epithelial cells, while SOX2 labeled the conducting airways. Scale bar = 25 μm. b Immunostaining of lung sections collected from Rptorf/f; ShhCre/+ mice and control littermates at 17.5 dpc. E-Cadherin (E-Cad) labeled all epithelial cells including the epithelium of the airways and saccules; pRPS6 is a marker of mTORC1 activity. pRPS6 signal was sharply reduced in the lung epithelium of Rptorf/f; ShhCre/+ mice at 17.5 dpc. Scale bar = 10 μm. c Immunostaining of lung sections collected from Rptorf/f; ShhCre/+ mice and control littermates at 17.5 dpc. SPC labeled alveolar epithelial type II (AT2) cells, while T1α (PDPN) or HOPX marked alveolar epithelial type I (AT1) cells. Scale bar = 25 μm. d Immunostaining of lung sections collected from Rptorf/f; ShhCre/+ mice and control littermates at 17.5 dpc. CC10 marked club (Clara) cells and Ac-tub marked ciliated cells in the airways. Scale bar = 10 μm. e Quantification of the percentage of SOX2+ cells in the conducting airways (n = 3 for each group), shown in (a). f Quantification of the percentage of Ac-tub+ and CC10+ cells in the conducting airways (n = 3 for each group), shown in (d). g Quantification of the percentage of HOPX+ (AT1) cells and SPC+ (AT2) cells in the saccules (n = 3 for each group), shown in (c). h Quantification of the percentage of T1α+ cells in the non-saccular epithelium (excluding the trachea and main stem bronchi) (n = 3 for each group), shown in (c). i Quantification of the relative pRPS6 signal in the lung epithelium (n = 3 for each group), shown in (b). Five views per lung (a total of 15 views) were used for counting in (e–i). All values are mean ± SEM. (**) p < 0.01; (***) p < 0.001; ns not significant (two-tailed, unpaired Student’s t-test). Source data are provided as a Source Data file.

Fig 5: Acquisition of glutamatergic neuronal precursor cells by induced differentiation of iPSCs in vitro. (A) The four factors (cmy‐c/oct‐4/klf‐4/sox‐2) were transplanted into human fibroblast cells, bar = 50 μm. (B) (Left) iPSCs in good growth conditions and (Right) the formation of the neuroepithelial layer. (C) Typical neural rosette structure. (D) Immunofluorescence staining to confirm the cortical identity of induced neural tissue (Pax6, OTX‐2, Ki67, Tbr2, sox2, and nestin) is shown. (E) Confirmation of the glutamatergic identity of neurons by immunostaining for vesicular glutamate transporter 1 (vGlut 1, green) and neuron‐specific tubulin (Tuj1, red). (F) Glutamatergic neuronal precursor cells began to appear approximately 30 days after induction and began to decrease after Day 50. (G) The vast majority of cells obtained by induction were neurons (Tuj1+), and the proportion of these glutamatergic neurons (vGlut1+/Tuj1+) peaked at approximately Day 40 after induction. (H, I) Confirmation of mature glutamatergic neurons by immunofluorescent staining for neuronal markers (Tuj1, Glut1, PSD95, and map2). (J) Confirmation of glutamatergic neuronal precursor cells by immunofluorescent staining for specific markers (Tbr1 and tuj1). Nuclei are stained with DAPI. Scale bar, 50 μm.