biostudies-literatureHeming MWestfälische Wilhelms-Universität MünsterDeutsche ForschungsgemeinschaftInterdisciplinary Center for Clinical Research of the medical faculty of Münster109https://www.ebi.ac.uk/biostudies/studies/S-EPMC9509601biostudies-literatureUnknown14(1)<h4>Background</h4>Primary central nervous system lymphoma (PCNSL) is a rare lymphoma of the central nervous system, usually of diffuse large B cell phenotype. Stereotactic biopsy followed by histopathology is the diagnostic standard. However, limited material is available from CNS biopsies, thus impeding an in-depth characterization of PCNSL.<h4>Methods</h4>We performed flow cytometry, single-cell RNA sequencing, and B cell receptor sequencing of PCNSL cells released from biopsy material, blood, and cerebrospinal fluid (CSF), and spatial transcriptomics of biopsy samples.<h4>Results</h4>PCNSL-released cells were predominantly activated CD19⁺CD20⁺CD38⁺CD27⁺ B cells. In single-cell RNA sequencing, PCNSL cells were transcriptionally heterogeneous, forming multiple malignant B cell clusters. Hyperexpanded B cell clones were shared between biopsy- and CSF- but not blood-derived cells. T cells in the tumor microenvironment upregulated immune checkpoint molecules, thereby recognizing immune evasion signals from PCNSL cells. Spatial transcriptomics revealed heterogeneous spatial organization of malignant B cell clusters, mirroring their transcriptional heterogeneity across patients, and pronounced expression of T cell exhaustion markers, co-localizing with a highly malignant B cell cluster.<h4>Conclusions</h4>Malignant B cells in PCNSL show transcriptional and spatial intratumor heterogeneity. T cell exhaustion is frequent in the PCNSL microenvironment, co-localizes with malignant cells, and highlights the potential of personalized treatments.Genome medicineIntratumor heterogeneity and T cell exhaustion in primary CNS lymphoma.PMC9509601FF-2016-10ME4050/8-1ME4050/13-1ME4050/4-1SEED/016/21ME4050/12-1)MzH3/020/20Wiendl HHolling MThomas CWolbert JBrokinkel BHailfinger SSchulte-Mecklenbeck ALi Xde Faria FGrauer OMHaessner SLu INMuther MStummer WHeming MStoeckius MMeyer Zu Horste GLenz GKerl KfalseIntratumor heterogeneity and T cell exhaustion in primary CNS lymphoma.<h4>Background</h4>Primary central nervous system lymphoma (PCNSL) is a rare lymphoma of the central nervous system, usually of diffuse large B cell phenotype. Stereotactic biopsy followed by histopathology is the diagnostic standard. However, limited material is available from CNS biopsies, thus impeding an in-depth characterization of PCNSL.<h4>Methods</h4>We performed flow cytometry, single-cell RNA sequencing, and B cell receptor sequencing of PCNSL cells released from biopsy material, blood, and cerebrospinal fluid (CSF), and spatial transcriptomics of biopsy samples.<h4>Results</h4>PCNSL-released cells were predominantly activated CD19⁺CD20⁺CD38⁺CD27⁺ B cells. In single-cell RNA sequencing, PCNSL cells were transcriptionally heterogeneous, forming multiple malignant B cell clusters. Hyperexpanded B cell clones were shared between biopsy- and CSF- but not blood-derived cells. T cells in the tumor microenvironment upregulated immune checkpoint molecules, thereby recognizing immune evasion signals from PCNSL cells. Spatial transcriptomics revealed heterogeneous spatial organization of malignant B cell clusters, mirroring their transcriptional heterogeneity across patients, and pronounced expression of T cell exhaustion markers, co-localizing with a highly malignant B cell cluster.<h4>Conclusions</h4>Malignant B cells in PCNSL show transcriptional and spatial intratumor heterogeneity. T cell exhaustion is frequent in the PCNSL microenvironment, co-localizes with malignant cells, and highlights the potential of personalized treatments.2022-01-01T00:00:00Z2022 Sep2026-06-01T02:26:17.877Z2025-04-05T13:31:04.354ZS-EPMC95096013615359310.1186/s13073-022-01110-1