Single-cell profiling of immune cells in Multiple Sclerosis using CITE-seq and FLASH-seq
This project characterizes the immune landscape of multiple sclerosis (MS) at single-cell resolution across peripheral blood and central nervous system compartments. It comprises two complementary single-cell sequencing datasets from MS patients and healthy controls: (1) a droplet-based multiomic CITE-seq dataset of peripheral blood mononuclear cells (PBMCs) that jointly profiles gene expression and cell-surface proteins in 16 donors (4 healthy controls and 12 MS patients representing relapsing and primary progressive disease subtypes); and (2) a plate-based full-length single-cell RNA-seq (FLASH-seq) dataset of FACS-sorted T and B cells from paired cerebrospinal fluid (CSF) and peripheral blood samples from 3 MS patients representing clinically isolated syndrome, relapsing MS, and primary progressive MS. All libraries were sequenced on an Illumina NovaSeq 6000 platform. CITE-seq data were processed using Cell Ranger with the GRCh38 reference genome to generate gene expression and antibody-derived tag count matrices, while FLASH-seq data were quantified into gene-level count matrices for individual cells. The objective of this project is to identify disease-associated immune cell states and to improve understanding of the immune mechanisms underlying MS, a chronic inflammatory demyelinating disease of the central nervous system in which adaptive immune cells play a key pathogenic role. By providing multimodal single-cell data from blood and CSF across multiple disease subtypes, this resource supports the discovery of disease-associated cell populations, candidate biomarkers, and potential therapeutic targets, and serves as a reference for future studies of MS immunopathology. All donors are identified only by non-identifiable study codes.