Extended Data Fig. 7: Single cell-derived BPDCN signature enables malignant cell classification.

a, UMAPs show all cells classified as pDCs across the entire scRNA-seq dataset (n = 14,430 cells), coloured according to patient/sample (left), samples with and without known BPDCN involvement (middle), and BPDCN signature score (right). b, Volcano plot shows differentially expressed between healthy pDCs and malignant BPDCN cells. We used 45 genes with log2 fold change > 1 and adjusted P-value < 1E-30 (green symbols), including BCL2 and TCL1A, to calculate the BPDCN signature score in downstream analyses. All 45 genes are provided in Supplementary Table 3c. P-values were calculated using a two-sided Wilcoxon Rank Sum test and adjusted using Bonferroni correction as implemented in the Seurat function FindMarkers. c, Scatterplot shows signature scores in all cells that were classified as pDC (n = 14,430). We calculated scores using a previously published BPDCN module²⁷ (x-axis) and using the 45 signature genes we defined in panel a (y-axis). d, Sinaplot shows BPDCN signature scores in all single cells (n = 87,011) that we profiled in this study, split by donor type. The colour indicates cell type classification by the RandomForest algorithm. e, Scatterplots show single cells from all patient samples (n = 66,600) according to their random forest pDC prediction score (x-axis) and BPDCN signature score (y-axis). Red dots indicate detection of mutant transcripts (n = 16 founder mutations, left; n = 15 progression mutations, right), grey dots indicate detection of wild-type transcripts. f, Sinaplot shows BPDCN signature scores in all single cells (n = 87,011), split by cell type and coloured by final classification. g, Violin plots show expression of canonical marker genes in cells that were originally classified as proB cells and plasma cells. Cells with a BPDCN signature score exceeding 0.5 were reclassified as malignant cells. The absence of CD19 in reclassified proB cells and the absence of CD138 in reclassified plasma cells supports our reclassification. h, Flow chart illustrates classification of healthy pDCs, premalignant pDCs, and malignant BPDCN cells for single cells across the dataset. Related to Fig. 2.