Mass spectrometry‐based proteomics analysis of human globus pallidus from progressive supranuclear palsy patients discovers multiple disease pathways

Abstract

Background Progressive supranuclear palsy (PSP) is a neurodegenerative disorder clinically characterized by progressive postural instability, supranuclear gaze palsy, parkinsonism, and cognitive decline caused by degeneration in specific areas of the brain including globus pallidus (GP), substantia nigra, and subthalamic nucleus. However, the pathogenetic mechanism of PSP remains unclear to date.Unbiased global proteome analysis of patients' brain samples is an important step toward understanding PSP pathogenesis, as proteins serve as workhorses and building blocks of the cell. Methods In this study, we conducted unbiased mass spectrometry‐based global proteome analysis of GP samples from 15 PSP patients, 15 Parkinson disease (PD) patients, and 15 healthy control (HC) individuals. To analyze 45 samples, we conducted 5 batches of 11‐plex isobaric tandem mass tag (TMT)‐based multiplexing experiments. The identified proteins were subjected to statistical analysis, such as a permutation‐based statistical analysis in the significance analysis of microarray (SAM) method and bootstrap receiver operating characteristic curve (ROC)‐based statistical analysis. Subsequently, we conducted bioinformatics analyses using gene set enrichment analysis, Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) protein‐protein interaction (PPI) analysis, and weighted gene co‐expression network analysis (WGCNA). Results We have identified 10,231 proteins with ∼1,000 differentially expressed proteins. The gene set enrichment analysis results showed that the PD pathway was the most highly enriched, followed by pathways for oxidative phosphorylation, Alzheimer disease, Huntington disease, and non‐alcoholic fatty liver disease (NAFLD) when PSP was compared to HC or PD. Most of the proteins enriched in the gene set enrichment analysis were mitochondrial proteins such as cytochrome c oxidase, NADH dehydrogenase, acyl carrier protein, succinate dehydrogenase, ADP/ATP translocase, cytochrome b‐c1 complex, and/or ATP synthase. Strikingly, all of the enriched mitochondrial proteins in the PD pathway were downregulated in PSP compared to both HC and PD. The subsequent STRING PPI analysis and the WGCNA further supported that the mitochondrial proteins were the most highly enriched in PSP. Conclusion Our study showed that the mitochondrial respiratory electron transport chain complex was the key proteins that were dysregulated in GP of PSP, suggesting that the mitochondrial respiratory electron transport chain complex could potentially be involved in the pathogenesis of PSP. This is the first global proteome analysis of human GP from PSP patients, and this study paves the way to understanding the mechanistic pathogenesis of PSP.

Neuronal loss drives differentially expressed protein‐pathways in the PSP globus pallidus

“…Differential protein expression (DPE) without cell composition adjustment (model I) identified N = 54 significant (False discovery rate (FDR) < 0.05) proteins, which were enriched for mitochondrial‐related pathways, as reported 1 . DPE analysis with cell adjustment (model II) revealed no significant proteins after multiple testing correction.…”

“…Our results show that the pathways identified to be associated with PSP 1 are most likely driven by neuronal loss, rather than by disease‐specific regulatory changes. This is expected as neurons are enriched in mitochondria compared to other cell types in the brain.…”

“…recently reported differentially expressed protein profiles in bulk‐tissue samples from the globus pallidus (GP) of individuals with progressive supranuclear palsy (PSP). Employing mass spectrometry‐based proteomics, the authors showed that PSP is characterized by downregulation of mainly mitochondrial proteins and concluded that this is potentially linked to the pathogenesis of the disease 1 …”

“…Employing mass spectrometry-based proteomics, the authors showed that PSP is characterized by downregulation of mainly mitochondrial proteins and concluded that this is potentially linked to the pathogenesis of the disease. 1 Since the GP is characterized by severe neurodegeneration in PSP, 2 we wondered whether the reported findings may reflect altered cell composition in the samples, rather than regulatory disease-processes. We have previously shown that a similar reduction in mitochondrial transcripts is secondary to neurodegeneration in Parkinson's disease (PD).…”

“…Differential protein expression (DPE) without cell composition adjustment (model I) identified N = 54 significant (False discovery rate (FDR) < 0.05) proteins, which were enriched for mitochondrial-related pathways, as reported. 1 correction. To specifically explore the effect of cell composition on Mitochondrial respiratory chain (MRC) proteins, which constituted the strongest signal reported by Jang et al, we selected MRC proteins which were reported significant (q-value < 0.05) in the original work and assessed the effects of adjusting for cell-type composition on significance and effect size (Figure 2A).…”