Extended Data Fig. 4: Basal-derived GEMM organoids give rise to neuroendocrine, neuronal, and tuft-like SCLC in vivo. Related to Fig. 1 and Supplementary Tables 1 and 2.
From: Basal cell of origin resolves neuroendocrine–tuft lineage plasticity in cancer
a, UMAP of scRNA-seq data from wildtype (orange, n = 1 sample) and transformed RPM basal organoids (purple, n = 2 independent samples) (left) and by Leiden cluster (right) (Supplementary Table 1), as in Fig. 1i. Number of cells analyzed in figure. b, Dot plot expression of indicated marker genes in wildtype (WT) versus transformed RPM organoids, grouped by Leiden cluster as in (a). c, UMAP of RPM organoids pre- (wildtype = “WT”) and post-CMV-Cre (“RPM”) by cell cycle phase. Proportion of cells in each phase (“frequency”), represented as % of cells per sample (right). d, UMAP as in Fig. 1i of RPM organoids pre- (“WT”) and post-CMV-Cre (“RPM”) and RPM basal allograft tumour (“Allo”) by cell cycle phase (left). Proportion of cells in each phase (“frequency”), represented as % of cells per sample (right). e, Dot plot of indicated marker genes in RPM basal allograft tumours by Leiden cluster (from Fig. 1j) (Supplementary Table 1). f, Violin plot with expression of SCLC archetype signatures where A = ASCL1, A2 = ASCL1-A2, N = NEUROD1, and P = POU2F3 (Supplementary Table 2) in RPM allograft tumour cells by Leiden cluster (from Fig. 1j). Kruskal-Wallis (KW) test (p-value in figure). g, Recombination PCR for RPR2 basal organoids for indicated alleles pre- (“None”) and post-treatment with TAT-Cre or Ad-CMV-Cre at two concentrations (2.5e7 or 5e7 pfu). *Organoids subject to spinoculation with CMV-Cre virus. Red font = condition for subsequent allografting. For gel source data, see Supplementary Fig. 1. h, Representative H&E and IHC of RPR2 basal-derived allograft tumours for indicated SCLC subtype markers (left) with H-score quantification compared to RPM basal allograft tumours (right). N = 6 RPR2 tumours per stain and n = 11 (ASCL1, POU2F3) and 8 (NEUROD1) RPM tumours quantified. Median (black line) and quartiles (dotted black lines) indicated. Scale bar, 50 μm. Welch’s two-tailed t-test. Exact p-values in figure. i, UMAP of scRNA-seq from basal-organoid-derived RPM (turquoise, n = 2) and RPR2 (maroon, n = 1 independent samples) allografts; number of cells analyzed per genotype indicated (left). UMAP and corresponding violin plots with expression of indicated SCLC subtype markers and Myc family oncogenes (right). Yellow diamond=mean expression. j, UMAP in (i) by Leiden cluster (Supplementary Table 1) (left). Proportion of cells from RPM vs RPR2 allograft tumours per Leiden cluster, as % of all cells per sample (right). k, UMAP of scRNA-seq data in (i) by NE score (left). Violin plot of NE score in RPM vs RPR2 basal allograft tumour cells, compared to Cluster 8 in (j) (right) with median and quartiles indicated. KW test with post-hoc Dunn’s (Bonferroni correction) (p-values in figure). l, UMAP of SCLC fate in RPM allograft tumours (from Fig. 1k) compared to location of RPR2 tumour cells (maroon) as in (i). m, Violin plots of SCLC archetype signatures or (n) ChIP target genes signatures (Supplementary Table 2) in RPM vs RPR2 basal allograft samples from scRNA-seq in (i). Unless otherwise noted, statistics are two-sided Wilcoxon rank-sum tests; **** p < 2.2e-16 and other exact p-values in figure.
