Fig. 2: Single-cell profiling resolves premalignant pDCs and BPDCN.

a, Uniform manifold approximation and projection (UMAP) representation of the scRNA-seq analysis of marrow (n = 20,411 cells) from six healthy donors. Clusters show expected cell types, including progenitor, myeloid, erythroid and lymphocyte-lineage cells and pDCs (box). HSPC, hematopoietic stem and progenitor cell; ery, erythroid; GMP, granulocyte macrophage progenitor; ProMono, promonocyte; Mono, monocyte; ncMono, non-classical monocyte; cDC, conventional dendritic cell; pDC, plasmacytoid dendritic cell; Pro-B, pro-B cell; Pre-B, pre-B cell; CD8 term exh, CD8 terminally exhausted; NKT, natural killer T cell; NK, natural killer cell. b, UMAP representation of the density of cells from marrow samples of patients with BPDCN (n = 11) projected by transcriptional similarity to the cell types defined in a and coloured by two-dimensional kernel density estimation. The samples include those without known involvement by BPDCN cells (top; n = 5 patients, n = 36,018 cells) and those with involvement (bottom; n = 6 patients, n = 30,582 cells). BM, bone marrow. c, The XV-seq procedure. Mutations identified by DNA sequencing were selected for enrichment on the basis of their detection in matched scRNA-seq data. d, UMAP representation of the XV-seq results for enrichment of 16 founder mutations from 5 patients with BPDCN without known marrow involvement. Cells are projected onto the clusters defined in a and coloured according to whether mutant (red; n = 1,204 cells) or wild-type (grey; n = 10,245 cells) transcripts were detected. Cells without mutant or wild-type calls are not shown. e, The expression of BPDCN signature genes (rows; n = 45) in cells classified as pDCs from six healthy donors (left; n = 203 cells) and six marrow samples from patients with BPDCN involvement (right, n = 14,209) (top). Malignant cells are downsampled to 30 cells per sample with genotyping information. The annotation bars (top) indicate the sample identifiers and BPDCN signature scores. Bottom, founder and progression mutations detected by XV-seq. f, Expression of BPDCN signature genes (top) and XV-seq mutations (bottom) in cells classified as pDCs from patients without known marrow involvement, as in e. Premalignant pDCs (left; n = 91 cells with genotyping information) show low signature scores and founder mutations exclusively. Occult BPDCN cells (right; n = 23) show high signature scores and a mix of founder and progression mutations. Pt, patient; Dx, diagnosis; Rem, remission; Rel, relapse; WT, wild-type. The diagram in c was created using BioRender.