Intrathecal mesenchymal stem cell therapy in progressive multiple sclerosis: integrated blood and CSF profiling in the SMART-MS randomized trial

Abstract Therapeutic options for progressive multiple sclerosis (MS) remain limited, and the mechanisms engaged by intrathecal mesenchymal stem cell (MSC) therapy are incompletely understood. MSCs are proposed to exert immunomodulatory and trophic effects, yet most studies rely on targeted biomarkers and lack systems-level analysis across immune compartments. Here, we applied an integrated blood–cerebrospinal fluid (CSF) multi-omics framework to characterize responses after intrathecal MSC exposure in patients with progressive MS enrolled in the SMART-MS trial, a randomized, placebo-controlled crossover study of a single intrathecal MSC injection. Although the trial did not demonstrate a neuro-regenerative signal for the primary endpoint, exploratory MRI findings and adverse events, including fever and back pain, suggested localized responses after intrathecal administration. Within the 18-participant SMART-MS cohort, peripheral blood mass cytometry was analysed longitudinally across baseline, six months, and 12 months, whereas matched CSF proteomics was analysed using paired baseline and six-month samples from the first treatment period. Immune phenotypes and marker-derived functional program scores were quantified using mixed-effects modelling. To summarize CSF proteomic changes, we generated exploratory composite scores reflecting extracellular matrix/interface-associated, innate/vascular inflammatory, metabolic/cytoskeletal, and reactivity-associated proteins. These scores enabled exploratory integration with circulating immune programs. MSC exposure was not associated with broad remodelling of peripheral immune-cell composition or marker-derived functional programs across circulating lymphocyte, monocyte, B-cell, and NK-cell populations. Instead, the most consistent treatment-associated changes were observed within the CSF proteome, where MSC exposure was associated with coordinated extracellular-matrix-associated protein changes, including fibrillar collagens and matrix-regulatory proteins, together with changes in innate, vascular, metabolic, and cytoskeletal pathways. Inflammatory, metabolic, and reactivity-associated CSF protein signatures tended to show greater changes in exploratory analyses of patients with adverse events or spinal MRI reactivity, consistent with heterogeneous local responsiveness rather than a uniform response. Cross-compartment analyses showed weak and heterogeneous coupling between circulating immune programs and CSF proteomic changes. Together, these findings suggest that intrathecal MSC exposure in progressive MS is associated with compartmentalized CSF proteomic changes rather than broad systemic immune alterations. This study demonstrates the value of integrated blood–CSF profiling for dissecting treatment-associated biology in CNS-targeted interventional trials.