Fig. 4

Increased expression of regulatory and T cell exhaustion molecules in the PCNSL microenvironment. A UMAP plot of all T cell subclusters, including 17,175 single-cell transcriptomes from 5 samples (patient 1: biopsy, blood, CSF; patient 2: biopsy, blood). B Dot plot of T cell markers in T cell subclusters. Color encodes average gene expression and dot size shows the percentage of cells expressing the gene with the threshold of percentage of cells expressing the gene set to 10%. C Proportion of T cells split by sample and colorized by cluster name. D Comparison of T cell subcluster abundances between biopsy and blood by plotting the log₂ fold change. E,F Gene expression heatmaps of canonical immune checkpoints (D), exhaustion profiles from Singer et al. [50], Tirosh et al. [51], Chihara et al. [52] (F), and regulatory T cell markers (G) in T subclusters. Values were scaled row-wise and color encodes gene expression. Exhaustion signatures are listed in Additional file 14: Table S12. H Gene expression heatmap of immune checkpoint ligands in B cell clusters, scaled gene-wise, color encodes gene expression. I,J Biopsy-derived T cells (I) and blood-derived T cells (J) were projected on the latent space of a reference T cell dataset [24]. Gene name - alias: HAVCR2 - TIM3; PDCD1 - PD1; IRF4 - MUM1; PDCD1LG2 - PD-L2; LGALS9 - Galectin9. Abbreviations: NK - natural killer cells; memCD4/CD8 - memory-like CD4⁺/CD8⁺ T cells; naiveCD4/CD8 - naive-like CD4⁺/CD8⁺ T cells; actTc - activated T cells; exhTc - exhausted T cells; TregCD4 - regulatory CD4+ T cells; p1 - patient1; p2 - patient2; CSF - cerebrospinal fluid; mBc - malignant B cells; nmBc - non-malignant B cells; Tex -terminally-exhausted; Tpex - precursor-exhausted; Tfh - CD4+ follicular-helper cells