Fig. 5

Pseudotemporal analysis reveals early-stage drivers acting on therapeutic resistance. A UMAP visualization illustrates inferred trajectories. Starting and end points are labeled with gray circles. Branch points are shown in black circles. Each dot represents one cell and is colored according to clinical outcome. B UMAP visualization colored by inferred pseudotime. (C) Left: UMAP visualization of cells used for comparison of BTKi-R/Dual-R (1/2/4) and BTKi-Slow (6/7/8) trajectories. Right: Scatter plot with fitted smooth curves shows the expression of top hit HNRNPH3 across pseudotime in the BTKi-R/Dual-R (1/2/4, purple) and BTKi-Slow (6/7/8, yellow) trajectories. A vertical dashed blue line marks the pseudotime at the branch point. D Heatmap shows the expression pattern of differentially expressed genes (rows) at the bifurcation point between the BTKi-R/Dual-R (1/2/4) and BTKi-Slow (6/7/8) trajectories (columns). Columns are ordered by trajectory with increasing pseudotime. Blue and yellow colors represent low and high expression, respectively. Bars on top illustrate clinical outcome, pseudotime, and inferred trajectories. E Gene set enrichment analysis summarizes the top enriched pathways. x-axis: normalized enrichment score. (F–H) Similar visualization as in C–E, focusing on the comparison of the Dual-R (1/2) and BTKi-R (4) trajectories