Fig. 3

Biopsy- and CSF-derived cells but not blood cells share hyperexpanded B cell clones. A Geneset feature plot of G2/M and S phase with the UMAP embeddings of C. Color encodes gene expression. B Feature plots of two lineages of pseudotime analysis. Pseudotime is color-coded and the UMAP embeddings refer to C. C RNA velocity analysis of mBc1-4 clusters (Fig. 2A). Streamlines represent vector velocity fields, which show the developmental pathways. D UMAP plot of all B cell clusters (45,890 cells) from 5 samples (patient 1: biopsy, blood, CSF; patient 2: biopsy, blood) with color-coded frequency of B cell clones. Cells colored in transparent grey represent cells with missing BCR information. E, F Proportions of B cells with BCR information split by sample (E) or cluster (F) and colored by frequency. Frequency was defined by the number of B cells expressing a unique clone (paired BCR heavy and light chains). G Alluvial plot shows the origin tissue and cluster of the hyperexpanded clones. H, J Volcano plots of the differentially expressed (DE) genes of the hyperexpanded clones versus all remaining clones (H) and DE genes of the hyperexpanded clone of patient 1 after treatment at relapse (CSF-derived) versus before treatment (biopsy-derived) (I). The threshold for the log₂ fold change was set to 1 and the threshold for the negative log₁₀p-value to 30. I Significantly enriched terms of DE genes based on the NCI-Nature Pathway Interaction Database corresponding to H. Size encodes the significance and color encodes whether the term was enriched in genes with elevated or reduced gene expression. K Correlation coefficients between gene expression of mBc1-4 clusters (row) and different lymphomas (column) from Roider et al. [15] including four follicular lymphoma (FL1-4), four GC-derived DLBCLs, of which two were transformed from FLs (DLBCL1, DLBCL2, tFL1, and tFL2) and one non-GC-derived DLBCL (DLBCL3), visualized in a heatmap. High correlation coefficients, colored in yellow, indicate a high transcriptional overlap. Abbreviations: mBc - malignant B cells; nmBc - non-malignant B cells; p1 - patient 1; p2 - patient 2; Bc - B cells; CSF - cerebrospinal fluid; NS - not significant; FC - fold change; p val - p-value; DLBCL - diffuse large B cell lymphoma; FL - follicular lymphoma (FL); tFL - transformed FL