Multiple Sclerosis (MS) is an immune mediated disease of the central nervous system (CNS). To better understand the role and mechanism of the immune system in MS, we performed single cell RNA-seq (scRNA-seq) on cerebrospinal fluid (CSF) cells of 14 untreated MS patients under the 10x Genomics Chromium Single Cell Immune Profiling system.
To immunoprofile MS CSF cells and to identify specific cell types that may be relevant to MS pathogenesis or disease subtype.
Fourteen untreated MS CSF samples were obtained via lumbar puncture; 7 relapsing remitting MS (RRMS), 5 primary progressive MS (PPMS), and 2 secondary progressive MS (SPMS). Cells were isolated and processed according to 10x Genomics’ protocol. For each sample, 2 libraries were made; a 5’ gene expression library and a VDJ enriched library which targets the αβ chains of the T cell receptor (TCR). The combination of these libraries allows for the identification and analysis of clonally expanded T cells. 10x Genomics’ Cellranger pipeline was used for sequence analysis.
Analyzing the top 15 expanded T cell clones for each sample, 11 of the 14 samples had more expanded CD8 T cell clones than expanded CD4 T cell clones. Of these 11 samples that have more CD8 expanded clones, 9 of the 11 samples actually have more total CD4 T cells than CD8 T cells in the CSF. In examining only highly expanded clones (10 cells or more), 9 of the 14 samples retained this CD8 T cell expansion bias. Our data suggests that expanded T cell clones in MS CSF are more likely to be of the CD8 subtype despite a total T cell ratio that favors CD4 T cells.
Immune clonal expansion suggests a targeted response that may be an integral part of the pathogenesis of MS. A bias of the T cell expansion toward CD8 cells may indicate a more cytotoxic environment in the MS CNS. More samples will be needed to determine if this CD8 bias correlates with a particular subtype of MS or if this is a general MS phenomenon.