Proteomic Profiling of Cerebrospinal Fluid Identifies Immune and Synapto-Axonal ALS Subtypes

Amyotrophic lateral sclerosis (ALS) is the most common adult-onset motor neuron disease, yet therapeutic progress remains slow due to pronounced biological heterogeneity. Here, we present a high-resolution proteomic map of cerebrospinal fluid (CSF) in a clinically well-characterized cohort of 93 individuals with ALS and 101 controls, defining molecular differences. Building on this landscape, unsupervised analysis revealed two reproducible ALS subtypes: an immune-enriched alpha subtype and a synapto-axonal beta subtype, further validated in an independent cohort (n=43 ALS). The alpha subtype was associated with higher neurofilament concentrations, whereas the beta subtype showed slower disease progression, indicating distinct pathological trajectories. We further derived a five-protein classifier (PARK7, PTPRS, ATRN, CNTN1, PCSK1N) that robustly discriminated subtypes across cohorts (AUC 0.951 ± 0.007). Together, this work defines the CSF proteomic landscape of ALS and establishes a foundation for molecular stratification in precision therapy and clinical trial design.