Extended Data Fig. 4: Clonality analyses of single LNCaP+FOXA2 cells support a mixed model of clonal transformation and expansion during NET.
a, Heatmap showing two clones delineated by single-cell CNV profiles inferred from scRNA-seq data by CopyKAT in FOXA2-driven NET model. Columns are gene windows ordered by genomic positions, while rows are individual cells that have been clustered using hierarchical clustering. Red color in the heatmap indicates amplification, and blue color indicates deletion. Color bar indicates log copy number ratios of each segment. b, scRNA-seq UMAP visualization of D0, D14 and D21 LNCaP+FOXA2 cells indicating clone 1 and clone 2 D0, D14 and D21 LNCaP+FOXA2 cells. c, Violin plots showing AR and NE signature scores of clone 1 and clone 2 in D0, D14 and D21 LNCaP+FOXA2 scRNA-seq samples. d, Heatmap showing two clones separated by SNVs (n = 1,093) inferred from scNanoRNA-seq data of D0 and D28 LNCaP+FOXA2 cells, clustered by k-means. Each row is one SNV, and each column is a cell. Variant allele frequency (VAF) is calculated as alternate allele read counts divided by all read counts for that nucleotide such as red represents mutant and blue for WT. e, UMAP visualization of scNanoRNA-seq data of D0 and D28 LNCaP+FOXA2 cells and their clonality. f, UMAP visualization of scNanoRNA-seq data of D0 and D28 LNCaP+FOXA2 cells and their expression of AR and NE signature genes. g, Violin plots showing AR and NE signature scores of clone 1 and clone 2 in D0 and D28 LNCaP+FOXA2 cells based on scNanoRNA-seq data. h, Heatmap showing germline mutations in D0 and/or D28 LNCaP+FOXA2 cells based on scNanoRNA-seq data. Each row represents one germline mutation, and each column is a cell. WT represents SNVs with supporting reads for the wildtype allele only, MUT are those that have at least 1 supporting read for the alternative allele and NA are those with 0 read coverage. Germline mutations were separately identified for each time point, with their mutation status plotted across the other time point without pre-filtering, wherein they might have 0 (showing as NA) or insufficient read coverage to capture the mutant allele (appearing as WT). Violin plots in c and g show median values (black line), interquartile range (IQR, black box) and the range of all data points within 1.5× IQR (whiskers).
