Proteomic Biomarker Discovery in Cerebrospinal Fluid Identifies CD74 and CD14 for Differentiating Multiple Sclerosis from Neuromyelitis Optica

Multiple sclerosis (MS) and neuromyelitis optica (NMO) are distinct autoimmune demyelinating diseases of the central nervous system with overlapping clinical features, complicating early diagnosis. Accurate differentiation is essential to avoid inappropriate treatment and improve outcomes. We conducted a comprehensive proteomic analysis of cerebrospinal fluid (CSF) from MS and NMO patients using both conventional proteomics and a nanoparticle-based low-abundance protein enrichment strategy (LAPE). Deep CSF proteome coverage yielded 3,816 proteins. Proteomic profiling revealed shared and distinct molecular features of MS and NMO. The common downregulation of neuronal adhesion pathways and the activation of immune responses highlight convergent mechanisms of neurodegeneration and inflammation, whereas MS-specific alterations in glycosylation suggest divergent molecular processes. Differential proteomic analysis delineated disease-specific signatures, with MS characterized by enhanced macrophage signaling, chemokine production, and complement activation, while NMO was distinguished by hemostasis-related pathways, Toll-like receptor 4 signaling, and neuroinflammatory responses. LAPE uncovered MS-associated changes in focal adhesion, cognition, and learning, and NMO-associated enrichment of lysosomal and phagocytic processes. Validation in an independent cohort using enzyme-linked immunosorbent assay (ELISA) confirmed CD74 as an MS-specific and CD14 as an NMO-specific biomarker with ROC analyses (AUC 0.75 for CD74; 0.72 for CD14) supporting their robust utility as discriminating biomarkers in clinical practice.