Cerebrospinal fluid proteomics for predictive assessment of Alzheimer’s Disease risk

Alzheimer’s disease (AD) involves early molecular changes beyond amyloid-β (Aβ) and tau, that create heterogeneous disease biology, giving rise to variable disease initiation and highly variable longitudinal trajectories. Accurately predicting trajectories is vital for design of clinical trials and for clinical care, yet current CSF and PET biomarkers provide limited predictive capabilities despite their excellent diagnostic value. We performed CSF proteomics using tandem-mass-tag mass spectrometry in 1,104 ADNI participants with extensive longitudinal assessments. Machine learning–derived protein panels accurately predicted two classes of outcomes. First, they identified several key inflection points along the disease trajectory, including onset of 1) amyloid plaque pathology (Aβ- to Aβ+; AUC=0.88), 2) symptoms (asymptomatic to symptomatic; AUC=0.89), and 3) functional decline (MCI [due-to-AD] to AD Dementia; AUC=0.88). Second, protein panels forecast longitudinal trajectories of decline, spanning both clinical domains (cognition and function) and pathological process, including tau accumulation measured by tau-PET neocortical standardized uptake value ratio (SUVR) and neurodegeneration indexed by hippocampal volume and FDG-PET SUVR. Proteomics panels outperformed conventional CSF- and PET-based Aβ and tau markers. Importantly, these predictions were driven by novel mechanisms, spanning synaptic signaling, proteostasis, metabolic stress, vascular remodeling, and immune dysregulation, that anchor distinct inflection points and shape long-term trajectories. Together, these findings position CSF proteomics as a powerful approach for anticipating disease onset and progression, with direct implications for patient stratification and personalized intervention.