Cerebrospinal Fluid Reflects Disease-Specific Immune Profiles

In advanced cancers, including breast, lung, and melanoma, leptomeningeal disease (LMD), a condition associated with rapid neurological deterioration, can develop. Treatment options remain limited, but researchers believe immune cells within the central nervous system are key to understanding the disease’s biology and informing therapeutic strategies.

To address this gap, a team of scientists from the National Center for Genomic Analysis (CNAG) and Goethe University Frankfurt focused on analyzing cerebrospinal fluid (CSF). This clear, colorless fluid surrounds and supports the central nervous system (CNS) and can contain valuable biological signals, including indicators of immune cell activity.

In their recent study, published in Cell Reports Medicine, the researchers performed single-cell RNA sequencing of CSF liquid biopsies from patients with different CNS tumors.¹ They found disease-specific immune responses, suggesting that CSF could serve as a valuable tool for monitoring immune and treatment responses in CNS tumors and LMD.

First, the researchers assessed CSF liquid biopsies from patients with CNS lymphoma (CNSL), brain metastases (BrM), and glioblastomas (GB). Using single-cell RNA sequencing, the team mapped distinct immune profiles among these patient groups alongside patients with neuroinflammatory disorders and healthy participants.

Their analysis revealed two broad immune patterns. CSF from patients with CNSL, neuroinflammatory disorders, and healthy individuals was predominantly composed of lymphoid cells, whereas samples from patients with BrM and GB showed a myeloid-dominated immune profile.

A closer look at specific immune cell populations uncovered distinct disease-associated immune landscapes. CNSL showed increased T cell activation and T-cell receptor expansion. In particular, the BrM and GB groups showed a marked reduction in CD4⁺ and CD8⁺ T cells compared with healthy controls. Then, CSF from patients with neuroinflammatory disorders displayed an increased abundance of pro-inflammatory macrophages.

The researchers also applied transcriptomic analysis to characterize gene expression across CSF cell types. For instance, they observed elevated expression of lactate-associated genetic programs in the BrM and GB groups, which correlated with increased CSF lactate levels. This change in metabolism could serve as a disease biomarker.

To complement these findings, the team also used spatial transcriptomics and found that the CSF cells mirrored features of the immune microenvironment seen in brain tissue samples of the CNS tumor groups.

“Thanks to this innovative approach, we’ve learned that each tumor type creates its own microenvironment in the cerebrospinal fluid, reflecting what may be occurring at the disease’s epicenter,” explained coauthor and CNAG immunologist Juan Nieto in a press release. “This helps us better understand tumor behavior and immune response, providing very useful information for developing new tools to monitor tumor dynamics.”