Circulating Cell-Free DNA Methylation Profiles Enable Disease-Specific Detection of Alzheimer’s, Parkinson’s, and ALS from Blood

Noninvasive biomarkers for neurodegenerative diseases are urgently needed for earlier detection, monitoring, and intervention. To address this, we developed a blood-based cfDNA methylation platform. A whole-genome nanopore methylation atlas of six primary human neural cell types—cortical, dopaminergic, and spinal motor neurons, astrocytes, Schwann cells, microglia—was used to train classifiers that assign cfDNA to its neuronal or glial origin. Classifiers were validated in silico and applied to 219 plasma samples from patients with Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and controls. Cortical cfDNA was elevated in AD, dopaminergic cfDNA in PD, and spinal motor neuron cfDNA in ALS, with predictive modeling achieving AUCs >0.98. In mild cognitive impairment, cortical cfDNA elevations identified individuals who later progressed to AD, supporting predictive utility. A multivariate model integrating multiple neurons improved accuracy, suggesting cfDNA methylation profiling as a scalable framework for noninvasive neurodegeneration detection and monitoring.