Dissecting the Interplay between Primary Central Nervous System Lymphoma Cells and the Microenvironment Using Single-Cell Transcriptomic Analysis

Primary central nervous system lymphoma (PCNSL) is a rare subtype of diffuse large B-cell lymphoma (DLBCL) confined to the central nervous system (CNS), primarily affecting brain parenchyma. Genetic alterations and the local microenvironment collectively contribute to the pathophysiology of PCNSL. Recurrent mutations in genes such as MYD88, CD79B, and CDKN2A are frequently observed in PCNSL. PCNSLs also exhibit frequent focal deletions of 6p21-22, encompassing the human leukocyte antigen (HLA) locus, as a potential mechanism of immune evasion. Regarding the microenvironment, reduced cerebrospinal fluid (CSF) glucose levels have been reported in PCNSL patients. Compared to systemic DLBCL, PCNSL is characterized by pronounced T cell exhaustion. However, the impact of low CSF glucose levels on tumor cells, as well as the interplay between tumor cells and infiltrating T cells in PCNSL, remains elusive.

Here, we performed single-cell RNA-seq (scRNA-seq) on PCNSL tumor specimens (n=7) and three control sample groups obtained from peripheral blood (PB) (n=3), adjacent normal tissues (n=3), and surgical resections from individuals with brain injuries (n=2). After filtering out low-quality cells, we obtained 140844 single cells in total. Cell types in PCNSL tumor and control samples were identified and annotated based on the expression of canonical gene markers.

We first compared tumor B cells from PCNSL with B cells from tumor-adjacent tissues. Copy number alterations (CNAs) inferred by InferCNV analysis showed that B cells from tumor-adjacent tissues exhibit altered CNVs. We further calculated the light chain ratio (κ/λ) of B cells from PCNSL tumor and tumor-adjacent tissues. The light chain restriction in B cells from tumor-adjacent tissues further indicates their malignancy. The presence of malignant B cells in PCNSL tumor-adjacent tissues underscores the importance of administering chemotherapy and/or radiotherapy following surgical resection in the treatment of PCNSL. To determine the gene programs associated with aberrant PCNSL activities, we next compared tumor B cells in PCNSL with normal B cells from PB. The fructose transporter gene SLC2A5 (encoding GLUT5) and the fructose metabolism pathway were significantly upregulated. Comparison of PCNSL with two public DLBCL scRNA-seq datasets (Steen et al. and Roider et al. ) also demonstrated the significant upregulation of fructose metabolism pathway in PCNSL tumor B cells, indicating that low glucose conditions in the CSF may drive PCNSL to utilize fructose metabolism as a crucial alternative pathway. Genetic and pharmacologic inhibition of fructose uptake through SLC2A5 knockdown or the employment of 2,5-anhydro-D-mannitol (2,5-AM), a fructose analog with high affinity for GLUT5, in DLBCL Activated B cell-like (ABC) cell lines suggested that inhibiting fructose utilization impairs B-cell lymphoma cells under low glucose conditions. Additionally, we investigated the microenvironment of PCNSL. In a PCNSL patient who showed significantly lower expression of B2M in tumor cells, a substantial infiltration of γδ T cells in the microenvironment was detected. This is consistent with previous findings from de Vries et al., which demonstrated a positive association between HLA class I gene defects of cancer cells and the infiltration of γδ T cells. Molecular signatures of infiltrating γδ T cells suggest that they retain anti-tumor effector functions.

Together, our studies dissected the interplay between PCNSL cells and their microenvironment using scRNA-seq, revealing the metabolic pathways that PCNSL cells utilize as crucial alternatives under low CSF glucose conditions. Additionally, we identified a substantial infiltration of γδ T cells with anti-tumor immunity signature in a PCNSL patient with potential HLA class I defects. These findings provide potential metabolic targets for PCNSL and highlight the exploration of γδ T cells in cancer immunotherapy for PCNSL.