Single cell mRNA profiles of CSF from children with BM

Purpose: Characterizing the cell heterogeneity of CSF during the BM development in children. Method: CSF samples were obtained via lumbar puncture from numbers of BM patients in different stages of disease progression. CSF cells were separated by direct centrifugation. A mimic assay based on QUARTZ-SEQ2 was adopted here for library preparations for scRNA-seq. Single CSF cells were sorted into two pre-prepared 384-well plates with cell lysis buffer by flow cytometry, in which each well contained a unique cell barcoding primer. An independent scRNA-seq library was constructed for 768 cells of each CSF sample, and was sequenced using a HiSeq X Ten sequencing system (Illumina). The generation of a cell-count matrix were processed in the combined workflow of UMI-tools and STAR. Secondary analysis were handled by Seurat package. Results: The heterogeneities of CSF cells in BM progression were deciphered. Multiple immune cell clusters in CSF were identified, including two neutrophils, two monocytes, one macrophage, four myeloid dendritic cells, five T cells, one natural killer cell, one B cell, one plasmacytoid dendritic cell, and one plasma cell subtype. Their population profiles and dynamics in the initial onset, remission, and recovery stages during BM progression were also characterized. Conclusions: This study conducted an in-depth exploration of the heterogeneities of CSF cells in BM progression, which provided novel insights into immune cell engagement in acute CNS infection. Single cell mRNA profiles of CSF from children with BM. *** For consistency with the publication (PMID 36119025), new data have been added (GSM8118500-GSM8118537, February 2024). The original data (GSM4974392-GSM4974410, December 2020) are not discussed in the above publication and have been removed. ***