Fig. 2

Single-cell transcriptomic reveals heterogeneous malignant B cell phenotypes in PCNSL. A UMAP plot of 73,896 total single-cell transcriptomes aggregated from five samples (patient 1: biopsy, blood, CSF; patient2: biopsy, blood). B Gene and protein (C) cell markers of the clusters identified by single-cell RNA sequencing (scRNA-seq) and CITE-seq (biopsy and blood from patient 1). Color encodes average gene/protein expression, and dot size represents the percentage of cells expressing the gene. The threshold of percentage of cells expressing the gene/protein was set to 15% in B and 90% in C. D UMAP plot of 45,890 reclustered B cells (mBc and nmBc cluster from A). E Analysis of copy number variations of downsampled B cell clusters. The nmBc1-2 clusters were used as reference cells and mBc1-4 as observations. The amplification of chromosomal regions is colored in red and the deletion of chromosomal regions in blue. F Feature plots of chromosomal gains and losses with the UMAP embeddings of D. Color encodes the proportion of chromosomal aberration. G Top ten differentially expressed genes of each B cell cluster shown in a heatmap. Selected genes are highlighted. Gene expression values were scaled gene-wise. H Proportions of B cells split by sample and colored by cluster name. I–J Gene expression heatmap of known PCNSL- associated genes (I) and of chemokines and their receptors (J) in B cell clusters, scaled gene-wise. Gene name - alias: MS4A1 - CD20; SDC1 - CD138; SELL - CD62L; IRF4 - MUM1. Abbreviations: mBc - malignant B cells; nmBc - non-malignant B cells; mDC1 - myeloid dendritic cells type 1; oligo - oligodendrocytes; Tc - T cells; PLT -platelets; p1 - patient 1; p2 - patient 2; CSF - cerebrospinal fluid