Cross-Comparative Study of DNA Methylation Patterns in the Frontal Lobe White Matter of Multiple System Atrophy, Parkinson’s Disease, and Progressive Supranuclear Palsy

Academic Background

Multiple System Atrophy (MSA) is a rare neurodegenerative disease characterized by neuronal loss and gliosis, accompanied by glial cytoplasmic inclusions (GCIs) rich in α-synuclein within oligodendrocytes. MSA’s clinical manifestations overlap significantly with other parkinsonian syndromes, such as Parkinson’s Disease (PD), Dementia with Lewy Bodies (DLB), and Progressive Supranuclear Palsy (PSP), posing challenges for early diagnosis. Although these diseases exhibit some common neuropathological features in advanced stages, each has unique pathological markers. For instance, both MSA and PD are synucleinopathies, but MSA is characterized by cytoplasmic inclusions in oligodendrocytes containing α-synuclein, whereas PD primarily shows α-synuclein aggregation in neurons, known as Lewy bodies. PSP, on the other hand, is a 4R tauopathy characterized by gliosis, Tau protein aggregates forming tangles, and coiled bodies. Traditionally, research has focused on changes in grey matter, but pathological studies of white matter have also provided new evidence.

DNA methylation is a well-known mechanism in epigenetic regulation, and researchers have found changes in DNA methylation in several neurodegenerative diseases. However, research on DNA methylation patterns in the white matter of multiple parkinsonian diseases, such as MSA, PD, and PSP, is unprecedented. This study aims to identify common and specific DNA methylation changes in these diseases through genome-wide DNA methylation analysis of the frontal lobe white matter in MSA, PD, and PSP patients.

Article Source

This research paper, titled “DNA methylation patterns in the frontal lobe white matter of multiple system atrophy, Parkinson’s disease, and progressive supranuclear palsy: a cross-comparative investigation,” was collaboratively conducted by Megha Murthy, Katherine Fodder, Yasuo Miki, and others from various research institutions, including UCL Queen Square Institute of Neurology (UK), Hirosaki University Graduate School of Medicine (Japan), Oslo University Hospital (Norway), and University of Exeter (UK). The paper was published in the 2024 edition of Acta Neuropathologica and was accepted on July 4, 2024.

Research Process

1. Subjects and Sample Source: The study included patients diagnosed with MSA, PD, and PSP, along with healthy controls, totaling 66 cases. Samples were sourced from the UCL Queen Square Institute of Neurology Queen Square Brain Bank, with all brain tissue samples ethically approved.

   • MSA patients: 17 cases
   • PD patients: 17 cases
   • PSP patients: 16 cases
   • Healthy controls: 15 cases

2. DNA Extraction and Methylation Analysis: Approximately 100 micrograms of white matter tissue was extracted from the fresh frozen frontal lobe (Brodmann area 9) using the phenol-chloroform-isoamyl alcohol method to extract genomic DNA. The EZ DNA Methylation Kit (Zymo Research) was used for bisulfite conversion, and genome-wide DNA methylation was analyzed using the Infinium HumanMethylationEPIC BeadChip (Illumina).

3. Data Processing and Quality Control: Raw intensity files were imported into R software, and detailed and stringent preprocessing and quality control were performed using Bioconductor packages (e.g., Minfi, CHAMP, and Watermelon).

4. Cell Type Decomposition: The cell type decomposition algorithm in the Minfi package was used to estimate the relative proportions of neurons (NeuN+), oligodendrocytes (SOX10+), and other glial cell types (Double-) in different samples.

5. Differential DNA Methylation Analysis: Linear regression models (Limma package) were used to detect differentially methylated sites in MSA, PD, and PSP compared to healthy controls and between the diseases.

6. Weighted Gene Co-Methylation Network Analysis (WGCNA): WGCNA was used to construct co-methylation networks to identify modules (clusters of highly correlated methylation sites) associated with the diseases.

Main Findings and Discussion

Methylation Analysis and Shared DNA Methylation Patterns

The study found significant commonalities in DNA methylation in the frontal lobe white matter of MSA, PD, and PSP, especially showing similar directional effects among subgroups of DNA methylation sites. Specifically, several genes associated with glial cells and demyelination, such as EtNK1, Fam8A1, and DFNA5, were identified with common differential methylation. This suggests these genes may play a role in the shared pathological processes of these parkinsonian diseases.

Specific DNA Methylation Changes and Unique Modules

Despite the significant commonalities overall, the study also identified disease-specific DNA methylation changes. For example, the promoter region of Bcl7b showed hypomethylation in MSA patients, UBE2f showed hypermethylation in PD patients, and D2HGDH showed hypermethylation in PSP patients. In cell type enrichment analysis, some modules were found to be primarily related to oligodendrocytes and showed functional enrichment in RNA interference, signal transduction, endoplasmic reticulum stress, and mitochondrial processes, all associated with neurodegeneration.

Co-Methylation Network Analysis and Module Preservation

Using the WGCNA method, 32 co-methylation modules were identified, 15 of which were significantly associated with at least one disease state. Further functional enrichment analysis revealed these modules were rich in molecular mechanisms related to neurodegenerative diseases. Analysis of other brain regions and tissue types also showed that many disease-related modules exhibited medium to high preservation in other datasets, further validating their importance in neurodegenerative diseases.

Association with Clinical and Pathological Features

The study also explored the association between key differentially methylated sites and disease characteristics such as the number of GCIs in MSA, age at onset, and disease duration. For example, hypomethylated site cg15274294 was negatively correlated with the number of GCIs in the frontal lobe of MSA patients, suggesting that the methylation status of this site may be related to pathological changes in different disease processes.

Significance and Value of the Study

This study is the first to systematically compare DNA methylation patterns in the frontal lobe white matter of MSA, PD, and PSP, providing important insights. The study reveals that these three parkinsonian diseases share many common DNA methylation features in the frontal lobe white matter, suggesting similar pathological mechanisms and molecular pathways. Additionally, the identified disease-specific methylation changes can serve as new targets for early diagnosis and therapeutic interventions. These findings not only help us better understand the molecular mechanisms of neurodegenerative diseases but also provide a crucial foundation for future multi-omics comprehensive research and clinical applications.