The Effect of Ibrutinib on the Myeloid Cell Compartment in Central Nervous System Lymphoma Slice Cultures
Authors: Kuehn Julia C. , Neidert Nicolas N. , Zhang Junyi , Mutter Jurik A , Alig Stefan K. , Klingler Christian , Hummel Fabian , Bleul Sabine , Ranganathan Lavanya , Beck Jürgen , Prinz Marco , Diehn Maximilian , Alizadeh Ash A. , Duyster Justus , Sankowski Roman , Heiland Dieter Henrik , Scherer Florian 
Published: December 2024

Introduction:
The Bruton's tyrosine kinase inhibitor (BTKi) ibrutinib has shown clinical efficacy as monotherapy and in combination with immunochemotherapy in patients with central nervous system lymphoma (CNSL). In addition to its direct impact on lymphoma cells, there is growing evidence that ibrutinib regulates the tumor microenvironment (TME) and T-cell immunity in systemic B-cell lymphomas such as chronic lymphocytic leukemia. However, the effect of ibrutinib on the unique TME of the brain in CNSL patients has not been explored yet. Here, we used human slice cultures from a CNSL patient undergoing complete brain tumor resection due to a radiologically suspected glioblastoma to investigate the influence of ibrutinib treatment on the myeloid compartment of the brain TME.
Methods:
Slices of human CNSL tissue were cultured and treated over five consecutive days either with ibrutinib in physiological concentrations observed in the cerebrospinal fluid (CSF) of lymphoma patients (ibrutinib-treated) or with DMSO (DMSO-treated). Untreated slice cultures served as additional controls. Single nuclei suspensions from the slice cultures of all three conditions were analyzed using 10x single nucleus RNA sequencing (snRNA-Seq), with the primary focus of investigating the cellular composition and transcriptional profiles of tumor cells and the TME. In addition, we performed shallow whole genome sequencing and targeted capture NGS (CAPP-Seq) of the bulk tumor as well as the slice cultures to characterize their genetic profiles. To validate our results, we performed snRNA-Seq of cells isolated from CSF of an additional patient undergoing ibrutinib therapy for progressive CNSL.
Results:
Genetic profiling of the slice cultures revealed the presence of characteristic mutations in MYD88, CD79B, PIM1, and TBL1XR1 genes as well as copy number alterations that are associated with immune evasion, including losses of 6p21 (HLA-D) and 1p13 (CD58). These genetic alterations were identical to those identified in the tumor bulk and their allelic representation mirrored the fraction of B-cells in the slice cultures, confirming the presence of the same malignant B-cell clone. Next, we successfully delineated nine cellular components of the brain from slice cultures by snRNA-Seq, including B-cells, T-cells, myeloid cells, endothelial cells, stromal cells, oligodendrocytes, astrocytes, and neurons. By integrating the myeloid cell compartment from all three conditions, we identified five distinct subclusters based on their transcriptional signatures. In ibrutinib-treated slices, the proportion of myeloid cells with an antigen-presenting expression pattern, defined by high expression of CIITA, CD74, and other HLAs, increased compared to those in DMSO-treated or untreated slice cultures. Conversely, the cluster of SPP1-expressing myeloid cells substantially decreased after ibrutinib treatment compared to the controls. Pseudotime analysis indicated that these two expression patterns are the result of two distinct polarization states of myeloid cells within the TME of CNSL. Finally, snRNA-Seq of CSF cells from an additional CNSL patient receiving ibrutinib identified the same upregulated antigen-presenting expression pattern in the myeloid cell compartment, validating these findings.
Conclusion:
Based on a unique human slice culture model from primary CNSL tissue, our data suggest a modulating effect of ibrutinib on the myeloid compartment in human CNSL by shifting myeloid cells from an immunosuppressive phenotype expressing SPP1 to an antigen-presenting phenotype. Despite being inherently limited by this single-case analysis, these results indicate an unknown immune-activating effect of ibrutinib on the brain TME in CNSL patients.