Extended Data Fig. 5: ASCL1 loss promotes POU2F3+ tuft-like SCLC. Related to Fig. 2 and Supplementary Table 3.
From: Basal cell of origin resolves neuroendocrine–tuft lineage plasticity in cancer
a, Recombination PCR for RPMA basal organoids for indicated alleles pre- (None) and post-treatment with TAT-Cre recombinase or Ad-CMV-Cre at two concentrations (2.5e7 or 5e7 pfu). *Organoids subject to spinoculation with CMV-Cre virus. Red font indicates condition used for subsequent allografting. For gel source data, see Supplementary Fig. 1. b, Quantification of tumour volume (mm^3) over time (weeks) in RPM (purple) vs RPMA (orange) basal allografts. Number of tumours quantified are indicated in legend. No suffix=Passage 1 (solid line), p2/p3= Passage 2 or 3 (dashed line). Red “X” indicates censored animals due to early tumour ulceration. c, Bar charts indicating fraction of Ascl1, Neurod1, or Pou2f3-high cells (count expression >0.01) in RPM vs RPMA basal-organoid-derived allografts from scRNA-seq data in Fig. 2e. Red=Positive = “High”; Blue=Negative = “Low”. d, Representative IHC images from RPM and RPMA basal-organoid-derived tumours for indicated markers (left). H-score quantification for indicated proteins (right) in RPM (SCLC only) and RPMA (SCLC- and NSCLC-dominant tumours, >50% of tumour region). Each dot represents one tumour. Only first-passage tumours included. For each marker, n = 11 RPM and 12 RPMA (n = 7 SCLC, n = 5 NSCLC) tumours quantified per genotype from n = 7 RPM and n = 9 RPMA mice. One-way ANOVA with post-hoc Fisher’s LSD pairwise comparisons (exact p-values in figure). Error bars = mean ± s.d. Scale bar, 50 μm. e, Expression of indicated genes in UMAP in RPM and RPMA basal allograft tumours (scRNA-seq data from Fig. 2e) (top), and corresponding violin plots by Leiden cluster (assigned in Fig. 2f) (bottom). Kruskal-Wallis (KW) test (p-value indicated in figure). f, Expression of indicated Neuroendocrine, Neuronal, Mesenchymal/Stem, Basal, SCLC-A2 archetype, Tuft, Ionocyte, Tuft-Ionocyte-Progenitor (TIP), Hillock basal, and SCLC-Atoh1 markers in UMAP of RPM and RPMA basal-derived allograft tumours (from scRNA-seq in Fig. 2e).
