Alpha-synuclein induces epigenomic dysregulation of glutamate signaling and locomotor pathways

Schaffner, S. L.; Wassouf, Z.; Lazaro, D.; Xylaki, M.; Gladish, N.; Lin, D. T. S.; MacIsaac, J.; Ramadori, K.; Schulze-Hentrich, J. M.; Outeiro, T. F.; Kobor, M. S.

doi:10.1101/2021.06.12.448150

bioRxiv · 10.1101/2021.06.12.448150

Alpha-synuclein induces epigenomic dysregulation of glutamate signaling and locomotor pathways

Schaffner, S. L.·Wassouf, Z.·Lazaro, D.·Xylaki, M.·Gladish, N.·Lin, D. T. S.·MacIsaac, J.·Ramadori, K.·Schulze-Hentrich, J. M.·Outeiro, T. F.·Kobor, M. S.

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Abstract

BackgroundMutations and multiplications in the gene encoding for alpha-synuclein are associated with Parkinsons disease (PD). However, not all individuals with alpha-synuclein variants develop PD, suggesting that additional factors are involved. We hypothesized that increased alpha-synuclein might alter epigenetic regulation of PD pathways. ObjectivesTo identify genome-wide DNA methylation and hydroxymethylation changes induced by overexpression of two alpha-synuclein variants in human dopaminergic neurons, and to relate these to the corresponding transcriptome. MethodsWe assessed DNA methylation and hydroxymethylation at >850,000 CpGs using the EPIC BeadChip in LUHMES cells differentiated to dopaminergic neurons. Control LUHMES neurons, LUHMES neurons overexpressing wild type alpha-synuclein, and LUHMES neurons overexpressing A30P alpha-synuclein were compared. We used SMITE network analysis to identify functionally related genes with altered DNA methylation, DNA hydroxymethylation, and/or gene expression, incorporating LUHMES H3K4me1 ChIP-seq to delineate enhancers in addition to the default promoter and gene body regions. ResultsUsing stringent statistical thresholds, we found that increased expression of wild type or A30P mutant alpha-synuclein induced DNA methylation changes at thousands of CpGs and DNA hydroxymethylation changes at hundreds of CpGs. Differentially methylated sites in both genotypes were enriched for several processes including movement-associated pathways and glutamate signaling. For glutamate and other signaling pathways (i.e. PDGF, insulin), this differential DNA methylation was also associated with transcriptional changes. ConclusionsOur results indicated that alpha-synuclein altered the DNA methylome of dopaminergic neurons, influencing regulation of pathways involved in development, signaling, and metabolism. This supports a role for alpha-synuclein in the epigenetic etiology of PD.

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Schaffner, S. L., Wassouf, Z., Lazaro, D., Xylaki, M., Gladish, N., Lin, D. T. S., MacIsaac, J., Ramadori, K., Schulze-Hentrich, J. M., Outeiro, T. F., Kobor, M. S.. 2021-06-12. Alpha-synuclein induces epigenomic dysregulation of glutamate signaling and locomotor pathways. https://doi.org/10.1101/2021.06.12.448150

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