Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease

Leptomeningeal disease (LMD) is a devastating manifestation of advanced cancer, marked by rapid neurological decline and limited treatment options. Immune profiling in central nervous system (CNS) neoplasms, including LMD, is critical for understanding disease biology and guiding therapy. Here, we use single-cell RNA and T cell receptor (TCR) sequencing of cerebrospinal fluid (CSF) from patients with CNS lymphoma (CNSL), brain metastases (BrMs), and glioblastoma (GB), alongside deep TCR sequencing of blood and spatial transcriptomics of brain lesions. We uncover distinct, disease-specific CSF immune landscapes: CNSL-associated LMD shows clonal T cell expansion, while BrMs and GB are enriched in blood-derived and resident-like myeloid cells. Spatial analysis confirms transcriptional similarities between CSF and tumor microenvironments. Longitudinal sampling reveals dynamic immune changes and emerging resistant clones. These findings establish the CSF as an immune-active compartment reflecting disease-specific features and highlight the value of CSF liquid biopsy for immune monitoring and therapeutic stratification in LMD.