Epigenetic Changes Associated with the Progression of Prion Disease in Syrian Hamsters (Mesocricetus auratus)

Prion diseases are fatal neurodegenerative disorders that affect mammals, including Creutzfeldt-Jakob disease in humans, chronic wasting disease in cervids, and bovine spongiform encephalopathy in cattle. During the disease, abnormally folded prion proteins induce misfolding of normal prion proteins, leading to neurotoxic fibrils and plaques. Epigenetic mechanisms, particularly DNA methylation, are increasingly implicated in prion-like diseases (e.g., Alzheimer’s disease), but their role in prion pathogenesis remains unclear. To investigate, we used nanopore sequencing and RNAseq to measure genome-wide methylation and gene expression in the brains of Syrian hamsters (Mesocricetus auratus) experimentally infected with a hamster-adapted murine synthetic prion strain (n = 9) and age-matched mock-infected controls (n = 9) at 80, 120, and 160 days post-infection (dpi). We identified 1,586, 1,692, and 2,429 differentially methylated regions (DMRs) at 80, 120, and 160 dpi, respectively. Early and mid-stage prion disease (80 and 120 dpi) were skewed toward hypermethylation, whereas late-stage prion disease (160 dpi) was skewed toward hypomethylation. Gene ontology (GO) of nearest genes to DMRs at 160 dpi included terms related to neuron regulation and signaling, neurodevelopment, and cellular stress pathways. We identified 178 differentially expressed genes (DEGs) at 80 dpi, 90 at 120 dpi, and 616 at 160 dpi. The majority of DEGs were downregulated at 80 dpi, and at 120 and 160 dpi, most DEGs were upregulated. Overlap in DEGs across timepoints was limited, and GO terms were related to upregulation of disease/injury response and cell death pathways in later timepoints. Overall, we found stage-specific responses to infection with a transcriptional shift from suppression of immune pathways to widespread immune and inflammation pathway activation. These findings indicate dynamic epigenetic and transcriptional changes marked by progressive and heterogeneous disruption of neuronal structure, function, and communication.