We performed single-cell RNA sequencing (scRNA-seq) of monocytes in rigorously defined clinical MS subtypes to identify unique features of monocyte in secondary progressive MS (SPMS). 

Progressive Multiple Sclerosis (MS) involves abnormalities of the innate immune system and one of the major cells of innate immune system are monocytes. We hypothesized that there are unique changes in peripheral blood monocytes associated with progressive forms of the disease. 

We classified SPMS patients in our unique CLIMB longitudinal cohort as “progressors” (n=5) or “non-progressors” (n=4). Progressors worsened clinically in the two years after blood drawing whereas non-progressors were stable.  For controls, we analyzed age and sex matched healthy controls (n=6) and subjects with relapsing MS (RRMS) (n=6). All patients were untreated.  Computational analyses consisted of dimensionality reduction of these data, conducting differential gene expression of monocyte subsets grouped by disease state, and investigating differential splicing rates of monocyte subsets to determine cell-state variability between disease states.

Classical monocytes from patients characterized as “progressors” had downregulation of estrogen and thyroid hormone signaling pathways, associated with chromatin modifying enzymes. The FoxO signaling pathway was significantly downregulated in “progressors” and upregulated in “non-progressors”. Classical and non-classical monocytes from “non-progressors” showed upregulation of MAP kinase signal transduction, especially mediated by BRAF, which regulates processes including cell division. 

We identified the immune basis for two new sub-categories of SPMS, “progressors” vs. “non-progressors”. These new subcategories correlated with the FoxO signaling pathway, specifically the FOXO1 transcription factor. Our findings provide the foundation for modeling SPMS which will enable identification of biologic processes associated with progression and new therapeutic targets. These subtypes may respond differently to disease modifying therapy. Finally, it will enable development of blood biomarkers to predict which patients with RRMS will develop SPMS MS and the type of SPMS they will develop.