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. Overall design: 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. ***