Single-cell profiling of blood and cerebrospinal fluid in tuberculous meningitis

Tuberculous meningitis (TBM) is the most severe form of tuberculosis, with a fatality rate of 20% to 50% in treated individuals. Although corticosteroid therapy can increase survival in HIV-negative people with TBM, better antimicrobial and host-directed therapies are required to improve outcome. There is, therefore, a need to better understand local immunopathologic pathways. Despite its power in identifying disease-specific cellular profiles, single-cell RNA sequencing (scRNA-seq) has been underutilized in cerebral samples in brain infection. We employed scRNA-seq to analyze fresh pretreatment cerebrospinal fluid (CSF) from 4 TBM patients, along with paired PBMCs. While 29 cell subtypes were present in both tissues, their relative abundance varied significantly. In particular, CSF was enriched with highly inflammatory microglia-like macrophages, GZMK+CD8+ effector-memory T (TEM) cells, and CD56bright NK cells. The latter 2 subsets exhibited reduced cytotoxicity compared with their blood-enriched counterparts, namely cytotoxic GNLY+CD8+ TEM and CD56dim NK cells, respectively. Across multiple cell types, inflammatory signaling pathways were increased and oxidative phosphorylation was decreased in CSF compared to PBMCs. This study highlights the value of scRNA-seq for exploring CSF immunopathogenesis in TBM patients and offers a resource for future studies investigating the pathophysiology of TBM and other brain infections, including potentially targetable cell populations linked with immune-mediated pathology.