Objective: To investigate differential methylation patterns of cell-free DNA (cfDNA) between Parkinson’s Disease (PD), REM Sleep Behavior Disorder (RBD), and Healthy Control (HC) groups.

Background: Several genes have been implicated in the risk of developing PD [1,2,3], but epigenomic contributions to risk profiles are largely unknown. One observation has been a difference in the pattern of DNA methylation between HC and PD [4]. CfDNA has also been found at elevated levels in the serum of PD patients [5] and implicated in immune system regulation in plasma [6].

Method: CfDNA from plasma obtained from PD (n = 43), RBD (n = 10), and HC (n = 27) was analyzed. Methylated cytosine sites were enriched using Twist Epigenetic Methylation Sequencing. Differentially Methylated Positions (DMP) were classified as hyper- or hypomethylated sites and mapped to their corresponding genes. Genes that showed to be hyper- or hypomethylated following the spectrum HC, RBD, PD were found. The functional gene pathways of the overlapping genes were enriched using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Enrichment.

Results: PD cfDNA was found to have 893 DMP compared to HC, and 5324 DMP compared to RBD. RBD had 6862 DMP compared to HC. Of the 3462 unique hypomethylated genes implicated in these tests, 49 were found in all 3 tests (Figure 1A). Of the 3312 unique hypermethylated genes implicated in these tests, 51 were found in all 3 tests (Figure 1B). KEGG Enrichment revealed the functional pathways of the top 10 hypermethylated genes (Figure 2). Pathways that have been previously implicated in neurodegenerative disease pathogenesis were implicated, including aldosterone synthesis, part of the Renin-Angiotensin System, O-Glycan Biosynthesis, and calcium signaling [7,8,9]. No significant gene pathway enrichments were found in the 49 shared hypomethylated genes.

Conclusion: The repeated observation of aldosterone synthesis, O-glycan synthesis, and calcium signaling abnormalities in PD warrants further exploration. Simultaneous profiling across the genomic-post-translational spectrum may elucidate the role of these pathways in PD pathogenesis, providing new insights for disease modifying therapies.

Table 1. Participant Demographics

Figure 1. Venn Diagram of Gene Counts

Figure 2. KEGG-Enriched Pathways

References: 1. Erkkinen, M. G., Kim, M., & Geschwind, M. D. (2017). Clinical neurology and epidemiology of the major neurodegenerative diseases. Cold Spring Harbor Perspectives in Biology, 10(4), a033118. https://doi.org/10.1101/cshperspect.a033118
2. Ye, H., Robak, L. A., Yu, M., Cykowski, M., & Shulman, J. M. (2022). Genetics and pathogenesis of Parkinson’s Syndrome. Annual Review of Pathology Mechanisms of Disease, 18(1), 95–121. https://doi.org/10.1146/annurev-pathmechdis-031521-034145
3. Blauwendraat, C., Nalls, M. A., & Singleton, A. B. (2019). The genetic architecture of Parkinson’s disease. The Lancet Neurology, 19(2), 170–178. https://doi.org/10.1016/s1474-4422(19)30287-x
4. Chuang, Y., Paul, K. C., Bronstein, J. M., Bordelon, Y., Horvath, S., & Ritz, B. (2017). Parkinson’s disease is associated with DNA methylation levels in human blood and saliva. Genome Medicine, 9(1). https://doi.org/10.1186/s13073-017-0466-5
5. Wojtkowska, M., Karczewska, N., Pacewicz, K., Pacak, A., Kopeć, P., Florczak-Wyspiańska, J., Popławska-Domaszewicz, K., Małkiewicz, T., & Sokół, B. (2024). Quantification of circulating Cell-Free DNA in idiopathic Parkinson’s Disease patients. International Journal of Molecular Sciences, 25(5), 2818. https://doi.org/10.3390/ijms25052818
6. Korabecna, M., Zinkova, A., Brynychova, I., Chylikova, B., Prikryl, P., Sedova, L., Neuzil, P., & Seda, O. (2020). Cell-free DNA in plasma as an essential immune system regulator. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-74288-2
7. Barbeau, A., Gillo-Joffroy, L., Boucher, R., Nowaczynski, W., & Genest, J. (1969). Renin-Aldosterone system in Parkinson’s disease. Science, 165(3890), 291–292. https://doi.org/10.1126/science.165.3890.291
8. Wilkinson, H., Thomsson, K. A., Rebelo, A. L., Hilliard, M., Pandit, A., Rudd, P. M., Karlsson, N. G., & Saldova, R. (2021). The O-Glycome of human nigrostriatal tissue and its alteration in Parkinson’s disease. Journal of Proteome Research, 20(8), 3913–3924. https://doi.org/10.1021/acs.jproteome.1c00219
9. Sukumaran, P., Da Conceicao, V. N., Sun, Y., Ahamad, N., Saraiva, L. R., Selvaraj, S., & Singh, B. B. (2021). Calcium signaling regulates autophagy and apoptosis. Cells, 10(8), 2125. https://doi.org/10.3390/cells10082125

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MDS Abstracts - https://www.mdsabstracts.org/abstract/identifying-differential-dna-methylation-pathways-in-parkinsons-disease-and-rem-sleep-behavior-disorder/