Fig. 8: Interplay of clonal evolution and cellular plasticity in HB.

a Clonality of somatic mutations identified by whole genome sequencing in patient #2959. Each point represents a mutation, with its cancer cell fraction (CCF) in #2959 T on the x-axis, and in #2960 T on the y-axis. Trunk mutations (CCF ~ 1 in both samples) are highlighted, together with subclone 1 and 2 mutations, specific to sample #2960 T and #2959 T, respectively. b Projection of trunk (left), subclone 1 (midle) and subclone 2 (right) mutations on the snRNA-seq UMAP of patient #2959. The two main clusters in the snRNA-seq UMAP correspond to cells coming from each sample, as indicated with the dashed line. c Virtual copy-number profiles reveal 2 subclones matching mutation subclones. d Tumor progression tree reconstructed for patient #2959 by integrating WGS and single-nucleus data. Copy-number alterations and driver mutations are indicated on each branch, as well as the number of cells belonging to each subclone. Below, snRNA-seq UMAPs are annotated by genetic subclone (left) and PC2 contribution (right) indicating the level of scLP/scH differentiation. e, f, Same as (d) for patients #3131 and #3660. The tumor progression trees of the 2 remaining cases are shown in Supplementary Fig. 15, together with the projection of genetic subclones on snATAC-seq UMAPs. g Phenotypic characterization of genetic subclones (grouped by patient). From top to bottom: Distribution of PC2 contributions indicating the level of scLP/scH differentiation; Proportion of cycling cells based on the expression of G2/M and S phase marker genes; Proportion of potential cancer stem cells (CSC) based on the expression of PROM1 and EPCAM markers; Mean expression of 141 DNA repair genes (‘Hallmark_DNA_repair’ gene set from MSigDB⁵⁶). Box-and-whisker plots: middle bar, median; box, interquartile range; bars extend to 1.5 times the interquartile range. Barplot error bars represent the 95% confidence intervals. P values were obtained using Wilcoxon rank sum tests (for PC2 and expression of DNA repair genes) or Fisher’s exact test (for the proportion of cycling cells and CSC). All tests were two-sided. Source data are provided in the Source Data file.