Objective:

To develop a sensitive and scalable blood test for early detection and monitoring of neurodegeneration in Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis.

Background:

In AD, PD, and ALS, significant neuron loss occurs before symptom onset, making early detection challenging. Existing protein biomarkers, such as amyloid and tau in AD, are limited in their sensitivity, narrow scope, and inter-individual variability, making them unsuitable for early screening. We propose neuron-derived cfDNA as a promising alternative. We can detect cfDNA from cortical, dopaminergic, and motor neurons as biomarkers of neurodegeneration in AD, PD, and ALS via cell-of-origin methylation analysis. Our previous work showed that elevated cortical neuron-derived cfDNA in the blood correlates with AD diagnosis. Here we improve this method and expand it to PD and ALS.

Design/Methods:

We developed a proprietary nanopore-based whole-genome methylation sequencing protocol that detects native DNA methylation without bisulfite conversion or PCR amplification bias. Methylation signatures for cortical, dopaminergic, and motor neurons were identified, and machine learning models were developed to predict neuron-of-origin from blood cfDNA. Assays were tested on blood from patients with mild cognitive impairment (MCI), AD, PD, and ALS.

Results:

Cortical cfDNA was significantly elevated in MCI (n = 25) and AD (n = 61) patients compared to controls (p = 2.2e-16, n = 80). Dopaminergic cfDNA was elevated in PD (p = 1.014e-9, n = 64), and motor neuron-derived cfDNA was elevated in sporadic (n = 34) and familial (n = 36) ALS (p = 2.056e-14). We are refining methods to optimize neuron-type signal separation and validating findings with longitudinal samples from the University of Kansas ADRC.

Conclusions:

Our cfDNA assay demonstrates promise for early detection and monitoring of neurodegenerative diseases, offering improved sensitivity and specificity over current biomarkers with the potential to advance diagnostic and therapeutic strategies for AD, PD, ALS, and other neurodegenerative conditions.