Dynamic single-cell mapping of cerebrospinal fluid unveils immune suppressive states during cryptococcal meningitis

Background Cryptococcal meningitis (CM), caused by Cryptococcus spp ., ranks as the most severe fungal infection, accounting for approximately 200,000 deaths globally each year. However, the intricate interplay between disease severity and the host immune response remains incompletely understood, especially the nuanced immune dynamics driving CM progression. Methods We conducted single-cell RNA sequencing paired with assembled T cell receptor sequencing on human cerebrospinal fluid (CSF) samples, including those from five untreated (UCM) and six matched treated (TCM) patients, alongside eight controls from patients with non-CNS inflammatory diseases (NCID). Results We unexpectedly observed an expansion of highly metabolically activated Macrophages_MRC1 in the CSF of UCM patients, characterized by enriched apoptosis and M2-polarization signatures, as well as an expansion of exhausted CD4 ⁺ Temra_KLRB1 cells. As expected, this phenomenon was alleviated in the CSF of the TCM group. Moreover, repertoire analysis revealed a broader clonal T cell expansion in the UCM group compared with the NCID and TCM groups. Notably, C-C motif chemokine receptor 5 (CCR5) and its ligands CCL3 and CCL4 were upregulated in CD4 ⁺ Temra_KLRB1 cells in the CSF of CM patients. Importantly, CCL3 and CCL4 levels showed a positive correlation with CSF leukocyte counts, suggesting that CCL3/4-CCR5 signaling may represent a key mechanism underlying the Cryptococcus -specific immune response. Conclusions Taken together, our findings describe the CSF immune compartment in CM patients and indicate that the antifungal response is compromised in this context.