Proteomic profiling of CSF reveals stage-specific changes in Amyotrophic lateral sclerosis patients

Amyotrophic lateral sclerosis (ALS) is a rapidly progressing neurodegenerative disease with a heterogeneous clinical presentation, complicating early diagnosis and therapeutic monitoring. To identify disease-specific biomarkers, we performed an unbiased cerebrospinal fluid (CSF) proteomic analysis in 87 ALS patients, 89 healthy controls, and 61 neurological controls using data-independent mass spectrometry. Across all quantified proteins, 399 were significantly dysregulated in ALS, including established neurodegeneration (NEFL, NEFM, UCHL1) and neuroinflammatory (CHIT1, CHI3L1, CHI3L2) markers. Correlation and pathway analyses uncovered dysregulation of immune, synaptic, and metabolic processes, with aberrant complement activation emerging as a hallmark. Complement proteins increased progressively with declining ALS Functional Rating Scale-Revised and longer disease duration, whereas early-stage markers (CLSTN3, CHAD, RELN) indicated pre-symptomatic neuronal and synaptic disruptions. Machine learning identified a minimal five-protein CSF panel (MB, ITLN1, YWHAG, FCGR3A, PGAM1) that accurately distinguished ALS patients from healthy controls, capturing disease-specific pathophysiology beyond general neurodegeneration. Our findings define a robust ALS-specific CSF proteomic signature, reveal prognostic protein candidates across disease stages, and provide a framework for diagnostic biomarker development, enabling earlier intervention and monitoring.