CSF Proteomics and Machine Learning Reveal Distinct Stages Across the Alzheimer’s Disease Continuum

Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by heterogeneous pathophysiological changes that begin years before symptoms emerge. Existing biomarkers like Aβ and pTau capture only fragments of this complexity, limiting diagnosis and therapeutic development. Leveraging high-resolution cerebrospinal fluid (CSF) proteomics, quantifying 2,492 proteins using tandem-mass-tag mass spectrometry (TMT-MS), in 1,104 ADNI participants, we identified pathways reflecting AD pathogenesis and stage-specific molecular events in-vivo . In biomarker-positive MCI (due-to-AD) and AD Dementia, beyond well-established metabolic and mitochondrial dysfunction, we observed upregulated neuropeptide signaling, G-protein-coupled receptors activity, and synaptic remodeling, highlighting underrecognized synaptic and signaling alterations. Asymptomatic AD showed significant alterations in mitoschondrial metabolism, RNA processing, and extracellular matrix pathways. Across the continuum from asymptomatic AD to MCI (due-to-AD) and AD Dementia, 92 proteins were differentially abundant, revealing a stage-specific progression, with early disruptions in neurodevelopmental and extracellular vesicle-related pathways in asymptomatic and MCI (due-to-AD) participants, transitioning to impairments in intracellular signaling, synaptic architecture, and cytoskeletal integrity in AD Dementia. This progressive dysregulation supports a continuum model where early compensatory mechanisms gradually give way to widespread neuronal degeneration. Using machine learning, we derived CSF proteomic panels capable of accurately distinguishing disease stages (asymptomatic AD vs. MCI (due-to-AD): AUC=0.92; MCI (due-to-AD) vs. AD Dementia: AUC=0.87). In parallel, we developed machine learning models to estimate pathological burden (Aβ-PET, tau-PET), which substantially outperformed conventional biomarkers. These findings uncover protein signatures that reflect underlying AD biology and provide a foundation for stage-specific biomarkers and therapeutic targeting, with important implications for patient stratification and personalized intervention strategies.