Profiling CIS progression and stability using RNA-seq single-cell analysis in peripheral blood mononuclear cells

Abstract Objective: To use single-cell mRNA analyses to identify immune cell profiles in CIS patients associated with a higher risk of developing an MS relapse or new central nervous system (CNS) disease activity on brain MRI. Methods: Cryopreserved peripheral blood mononuclear cells were collected at study entry and six months from six CIS participants in the ITN020AI STAyCIS trial of atorvastatin. Three participants met the primary endpoint defined as ≥ 3 new T2 lesions on MRI or an MS relapse within 12 months, while the other three did not. RNA from about 10,000 PBMC per sample were identified at the single-cell level using the 10X Genomics Chromium platform and analyzed using Cell Ranger software. Seurat R software package was used for downstream analysis. Results: 31 clusters of differentially expressed genes were assigned as specific cell types; baseline frequencies of clusters enriched >2-fold for macrophage, NK, NKT, CD4+ T cell, and B cell markers were associated with disparate outcomes at six months. Several clusters of B cells, CD4+ and CD8+ T cells were expanded from baseline at six months in participants with CNS disease activity at that time point, while no notable changes were observed in those with stable disease. Conclusion: Our results show varied frequencies of innate and adaptive leukocyte populations in participants with disparate clinical outcomes, suggesting a predictive biomarker for aggressive early intervention. Expanded clusters of CD4+ and CD8+ T cells and B cells in blood at the time of disease activity may identify biomarkers leading to acute demyelination. Follow-up studies are underway to increase sample size and incorporate protein data to better define cell subtypes associated with disparate outcomes in the STAyCIS trial.