A Single-Nuclei Paired Multiomic Analysis of the Human Midbrain Reveals Age- and Parkinson’s Disease–Associated Glial Changes

Single-nucleus Multi-omics Analysis Reveals Age-related and Parkinson’s Disease-related Changes in Neuroglia in the Human Midbrain

Research Background

Age is a major risk factor for Parkinson’s Disease (PD). Although the significant role of age in PD onset is known, details about how age alters the gene expression and regulatory landscape of the brain remain unclear. Most existing studies focus on transcriptomics analyses or genetic factors, lacking detailed data on the gene expression and chromatin accessibility changes in different cell types of the human midbrain during aging and the PD course. Therefore, this study employs multi-omics approaches using single-nucleus analysis techniques to reveal the gene expression and chromatin accessibility changes in the midbrains of young, elderly, and PD patients, to understand the role of aging in PD onset.

Source of the Paper

This research paper was published in the journal Nature Aging under the title “Paired Single-Nucleus Multi-Omics Analysis of the Human Midbrain Reveals Age- and Parkinson’s Disease-related Gliosis”. The authors include Levi Adams, Min Kyung Song, Samantha Yuen, Yoshiaki Tanaka, and Yoon-Seong Kim, from institutions such as Rutgers-Robert Wood Johnson Medical School, Bates College, Kyung Hee University, Maisonneuve-Rosemont Hospital Research Center, and University of Montreal. The article was published online in March 2024.

Detailed Research Process

Sample Collection and Single-nucleus Isolation

The research team isolated nuclei from postmortem midbrain samples of young (average 24 years), elderly (average 75 years), and PD patients (average 81 years), detailed in Supplementary Table 1. They selected the substantia nigra for analysis and used single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq) technologies through the 10x Genomics single cell multiome ATAC + gene expression kit. After initial filtering, 39,289 high-quality nuclei from 31 individuals (including 9 young donors, 8 elderly donors, and 14 PD patients) were retained.

Data Processing and Analysis

Data were batch processed, normalized using Seurat and Harmony packages, followed by variable gene and principal component analysis (PCA), and uniform manifold approximation and projection (UMAP) dimensional reduction. A total of 23 nuclei clusters were identified and classified into seven major cell types using marker genes of known cell types: neurons (NS), oligodendrocytes (ODCs), astrocytes (ASs), microglia (MG), oligodendrocyte precursors (OPCs), endothelial cells (ECs), and peripheral immune cells/T cells (Ts).

Major Experimental Results

Comprehensive analysis showed that the majority of midbrain cells were oligodendrocytes (ODCs), followed by microglia (MG), oligodendrocyte precursors (OPCs), astrocytes (ASs), and neurons (NS). Clustering based on ATAC data showed unique chromatin accessibility at key sites of these cells. Further analysis revealed significant differences between young and elderly, and between elderly and PD groups in oligodendrocytes and microglia (P < 0.01 and P < 0.05).

Cell type-specific gene expression patterns exhibited differentially expressed genes between groups. Some genes, such as neat1, fkbp5, and slc38a2, were differentially expressed in various cell types. These results hint at possible changes in neural functions and metabolic pathways.

Multi-omics Peak-gene Association Analysis

Although there were significant differences in chromatin accessibility distribution between different cell types, differences within the same cell type across groups were minimal. Gene expression and chromatin accessibility were not always closely correlated, indicating possible dependence on more complex interactions among distal DNA regulatory elements. The study utilized a peak-gene association analysis framework matched with single-nucleus data to generate peak-gene association maps, revealing significant changes between groups, such as neat1 and rasgrf1.

Analysis of PD-related Single Nucleotide Polymorphisms (SNPs)

Comparing the study data with previously published PD GWAS databases, the researchers identified PD-related SNPs in each cell type. Most PD-related SNPs were detected in different cell types, related to finely accessible peaks in the brain but less associated with genome-wide differential expression regions. Comparing these SNPs with known high-trimethylated histone H3K27ac HiChIP data, significant overlaps were found in ODC peak-gene associations (P<1.0×10−334).

By integrating these data, specific chromatin accessibility peaks in substantia nigra cell types and their potential regulatory roles were confirmed, as well as identifying PD-related SNPs.

Research Conclusion

This study reveals dynamic changes in neuroglia in the human midbrain during aging and the PD course through single-nucleus multi-omics analysis, highlighting a potentially important role of oligodendrocytes in PD onset. The research provides significant insights