Biomarkers and Bioinformatics Poster Presentation

P0090 - Immune cell profiles associated with CIS progression and stability using RNA-seq single-cell analysis (ID 577)

  • J. Giarraputo
  • J. Giarraputo
  • V. Jain
  • S. Arvai
  • D. Smilek
  • K. Harris
  • S. Gregory
Presentation Number
Presentation Topic
Biomarkers and Bioinformatics



Clinically Isolated Syndrome (CIS) can be an initial multiple sclerosis (MS) presentation, but the risk for developing future demyelinating episodes is often uncertain. The singular clinical episode of demyelination is thought to be driven by acute inflammation brought about by proinflammatory macrophages, autoreactive CD8+ and CD4+ T cells, and B cells crossing the blood-brain-barrier.


To use single-cell transcriptome 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.


Cryopreserved peripheral blood mononuclear cells (PBMC) were collected at study entry and six months from six CIS participants from 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 sequenced 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, with cell type annotated both computationally (SingleR) and by matching differentially expressed genes with canonical markers using online genomics databases.


Approximately 30 clusters of differentially expressed transcripts were assigned as specific cell types; baseline frequencies of seven clusters enriched >2-fold for macrophage, NK, NKT, CD4+ T cell, and B cell transcripts were associated with disparate outcomes at six months. Several clusters assigned as 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.


An understanding of the immunological changes associated with future disease activity in CIS may be useful for making early treatment decisions. Our preliminary data suggest that participants with disparate clinical outcomes exhibited different frequencies of innate and adaptive leukocyte populations in PBMC, which may represent a predictive biomarker for aggressive early intervention. Also, expanded clusters of CD4+ and CD8+ T cells and B cells in blood at the time of disease activity may identify biomarkers that contribute to acute demyelination. Follow-up studies are underway to increase sample size and incorporate protein expression data to better define cell subtypes and clonality of T and B cells associated with disparate outcomes in the STAyCIS trial.