Abstract

Neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS) are characterized by the progressive loss of distinct neuronal subtypes, yet current diagnostic tools are either invasive, limited in resolution, or poorly suited for early detection and longitudinal monitoring. This dissertation began with a proof-of- concept study using bisulfite-PCR at a neuron-enriched locus to detect cortical neuron-derived cell-free DNA (cfDNA) in AD plasma samples, establishing the potential of cfDNA as a marker of neuronal injury. Building on these preliminary findings, a novel framework was developed utilizing Oxford Nanopore Technologies (ONT) to profile genome-wide native DNA methylation in purified primary cortical neurons, dopaminergic neurons, spinal motor neurons, and glial cell types. Differentially methylated regions (DMRs) were defined for each cell type and used to train classifiers capable of deconvoluting cfDNA mixtures. Classifier performance was assessed using a synthetic spike-in dilution series and validated across 254 clinical plasma samples spanning AD, PD, ALS, MCI, and healthy control groups. Results demonstrated that cfDNA methylation signals from cortical and dopaminergic neurons could reliably distinguish AD and PD from age-matched controls with 100% sensitivity and specificity, and differentiate these diseases from each other with 96% accuracy. Importantly, the combined use of multiple classifiers enabled a multidimensional view of disease state from a single blood draw. In contrast, protein-based biomarkers such as amyloid-β and tau, while included for comparison, failed to achieve comparable classification performance. Models derived from iPSC-based neurons performed poorly, underscoring the necessity of using primary tissue for accurate cfDNA source attribution. Together, these findings establish a scalable, disease-agnostic framework for cfDNA-based neurodegenerative disease detection, with potential applications in early diagnosis, differential classification, and therapeutic response monitoring.

Degree

PhD

College and Department

Life Sciences; Physiology and Developmental Biology

Rights

https://lib.byu.edu/about/copyright/

Date Submitted

2025-07-18

Document Type

Dissertation

Keywords

cell-free DNA, cfDNA, methylation, Oxford Nanopore, neurodegeneration, Alzheimer's disease, Parkinson's disease, ALS, cortical neuron, dopaminergic neuron, liquid biopsy, diagnostic biomarkers, epigenetics, cell-of-origin, single blood draw

Language

english

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