The link between gut and brain health is becoming apparent in a growing number of disease states. In some cases of Parkinson’s disease (PD) that appear without an identifiable cause, it has been suggested that the pathology may be initiated in the gut, specifically the appendix, with pathological alpha-syn protein aggregates accumulating in this location long before the pathology reaches the brain. However, the appearance of these aggregates in the appendix of both healthy individuals and PD patients suggest that additional mechanism may be at play. In a recent study by Gordevicius and colleagues, researchers study how changes in the expression of genes belonging to a specific degradation pathway, the autophagy-lysosome pathway (ALP), may be affecting how and where pathological protein aggregates accumulate in individuals with PD. They specifically looked at DNA methylation in the genes of the ALP pathway, as this modification can affect the level of gene expression in a cell. The authors mapped DNA methylation sites in the ALP pathway to identify the genes that may be affected, and then confirmed associated changes in the transcription of those same genes using RNA sequencing. As a final step, they confirmed that the altered gene expression had a significant impact on global protein abundance in both the appendix and brain of PD patients and healthy controls using a label-free quantitative proteomics strategy, which, among the thousands of proteins quantified, identified 34 ALP proteins with altered abundance and elevated alpha-syn. The proteomics findings were validated in a replication cohort, with the addition of sub-cellular fractionation, isotopic labeling, and chromatographic separation of peptides to the LC-MS/MS methods. This study is an excellent example of the power of combining multiple molecular techniques to study disease processes from epigenetic changes in DNA molecules, through altered transcription, to the final outcome of modified protein abundance.

How was PEAKS used?

PEAKS was used to analyze the data from the replication cohort study. This data set was generated using isotopic labelling in the form of tandem mass tags (TMT, 10-plex), and chromatographic fractionation of the labelled peptides. Importantly, data loading and analysis parameter settings in PEAKS can accommodate multiple fractions and isotopic tags. The latter is included as a specific fixed modification, which can include, as it did in this study, purity correction factors for isotopic distribution of reporter ions. The authors used the de novo sequencing, database search, PTM search, and quantification work flows in PEAKS to quantify over 2000 proteins from the appendix of patients with PD and healthy controls.

Gordevicius, Juozas, et al. “Epigenetic Inactivation of the Autophagy–Lysosomal System in Appendix in Parkinson’s Disease.” Nature Communications, no. 1, Springer Science and Business Media LLC, Aug. 2021. Crossref, doi:10.1038/s41467-021-25474-x.

Abstract

The gastrointestinal tract may be a site of origin for α-synuclein pathology in idiopathic Parkinson’s disease (PD). Disruption of the autophagy-lysosome pathway (ALP) may contribute to α-synuclein aggregation. Here we examined epigenetic alterations in the ALP in the appendix by deep sequencing DNA methylation at 521 ALP genes. We identified aberrant methylation at 928 cytosines affecting 326 ALP genes in the appendix of individuals with PD and widespread hypermethylation that is also seen in the brain of individuals with PD. In mice, we find that DNA methylation changes at ALP genes induced by chronic gut inflammation are greatly exacerbated by α-synuclein pathology. DNA methylation changes at ALP genes induced by synucleinopathy are associated with the ALP abnormalities observed in the appendix of individuals with PD specifically involving lysosomal genes. Our work identifies epigenetic dysregulation of the ALP which may suggest a potential mechanism for accumulation of α-synuclein pathology in idiopathic PD.