Intratumor heterogeneity and identification of PBL signature lymphoma cells. (A) UMAP plot of B cells colored according to the samples. The black arrow shows the separated cell subpopulation (PBL subcluster). (B) Venn diagram shows the overlap between the DEGs and differential expression proteins (DEPs) of the distinct PBL subcluster compared with other B-cell subclusters. DEPs are displayed. The UMAP plot shows the gene and protein expression levels of CD38, CD39 (ENTPD1), and CD319 (SLAMF7). (C) The UMAP plot shows nonnegative matrix factorization clustering (NMF) based on the GC signature score, and the dot plot shows the representative genes of each GC signature. (D) Dot plot showing the pathway upregulated in GC signature subclusters using WikiPathways. (E) Upper bar chart shows the proportion of the GC signature subcluster in each patient. Lower bar chart shows cell cycle stages in each GC signature subcluster. (F) Dot plot shows the enriched pathways in tumor PBL cells, commonly upregulated pathways in tumor PBL and normal PBL cells, and differentially upregulated pathways in normal PBL cells using WikiPathways. (G) UMAP plot of NMF clustering based on the GC signature score in our data and publicly available single-cell PCNSL data after integration assay (Heming et al⁸ and Liu et al⁹). (H) The pie chart shows the fraction of the PBLa/PBLb cluster originating from each data set. PBL, plasmablast; DEGs, differential expression genes; PreM, precursor memory B-cell; INT, intermediate zone; LZ, light zone; dark zone; UMAP, Uniform Manifold Approximation and Projection.