Intratumor heterogeneity and T cell exhaustion in primary CNS lymphoma

Abstract

Background 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. Methods 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. Results 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. Conclusions 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.

Comparison of methods of positioning ROI and whole-tumor histogram analysis of ADC maps for differentiating hyperperfused primary central nervous system lymphoma from atypical glioblastoma

“…Ahn et al suggested that the mean ADC calculated from the whole tumor was the highest performing predictor for distinguishing PCNSL from GBM. Heterogeneity [25][26][27] is mainly possible reason for the inconsistent results of different parameters. And because the cases in this study were atypical GBMs with homogeneous enhancement, the heterogeneity was less pronounced than that of typical GBM, which led to a small difference in the mean ADC obtained from single-section and whole-volume approaches between aGBM and hPCNSL, and the differential diagnostic values were limited; instead, the minimum ADC based on the three-ROIs approach was more meaningful.…”

Single-cell omics: A new direction for functional genetic research in human diseases and animal models

“…By using single-cell RNA sequencing, B-cell receptor sequencing of rare PCNSL cells, and spatial transcriptomics of biopsy samples, results found that malignant B-cell in PCNSL exhibit transcriptional and spatial intratumor heterogeneity. T-cell exhaustion is common in the PCNSL microenvironment, where it co-localizes with malignant cells, highlighting the potential for personalized treatments ( Heming et al, 2022 ). For molecular driver evolution, researchers decipher the intra-tumor and inter-lesion diversity of CTCL patients and propose a multi-step tumor evolution model using single-cell RNA analysis and bulk whole-exome sequencing on 19 skin lesions from 15 CTCL patients.…”

New hopes in relapsed refractory primary central nervous system lymphoma

“…A possible explanation of these contradictory findings lies in the fact that the frequency of genetic alterations encompassing PD-1 ligands in PCNSL appears to be much lower than the one initially reported [38 && ,68,69]. In addition, recurrent deletion of HLA genes [38 && ,68,69] and presence of multiple inhibitory receptors on T cells infiltrating PCNSL [70] might represent additional reasons why T cells unleashed upon PD-1 blockade did yield the expected benefit.…”