Mitochondrial dysfunction, oxidative stress, and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson's disease

Abstract

The molecular mechanisms underlying the changes in the nigrostriatal pathway in Parkinson's disease (PD) are not completely understood. Here, we use mass spectrometry and microarrays to study the proteomic and transcriptomic changes in the striatum of two mouse models of PD, induced by the distinct neurotoxins 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and methamphetamine (METH). Proteomic analyses resulted in the identification and relative quantification of 912 proteins with two or more unique peptides and 86 proteins with significant abundance changes following neurotoxin treatment. Similarly, microarray analyses revealed 181 genes with significant changes in mRNA, following neurotoxin treatment. The combined protein and gene list provides a clearer picture of the potential mechanisms underlying neurodegeneration observed in PD. Functional analysis of this combined list revealed a number of significant categories, including mitochondrial dysfunction, oxidative stress response, and apoptosis. These results constitute one of the largest descriptive data sets integrating protein and transcript changes for these neurotoxin models with many similar end point phenotypes but distinct mechanisms.

Figure 1. Flowchart showing the experimental strategy

Mouse striata are prepared using a combination of global tryptic digestion, ¹⁶O/¹⁸O labeling, and CPE methodology, followed by LC–FTICR analysis of each fraction and peptide/protein identification using the AMT tag approach.

Figure 2. Reproducibility of proteomic analysis

(A) Correlation plots comparing protein expression ratios for the five MPTP and METH replicates relative to controls. This comparison demonstrates significantly similar inter- and intratoxin response at the protein level (R 0.91 and 0.89, respectively). (B) Heatmap of proteins identified as significantly differentially regulated (p < 0.05). The regulated proteins show consistency across samples. (C) Multiple peptides detected from individual proteins show good consistency in expression levels.

Figure 3. Proteins regulated by MPTP and METH

(A) Proteins that have significant upregulation (p < 0.05) in response to both MPTP and METH treatment in the striatum. These are the five top-ranked proteins selected from the combined MPTP and METH data. The graph shows separate data for the two neurotoxins. (B) Top five significantly downregulated proteins in response to both drug treatments. (C) Protein abundances in MPTP- and METH-treated striata compared to controls for all detected peptides passing initial quality control. The Spearman correlation coefficient (R 0.6563) is significant (p < 10⁻²⁰).

Figure 4. Microarray analysis reveals genes regulated in common in MPTP- and METH-treated striata

(A) Upregulated genes shared by both treatment groups (MPTP and METH). These are the five top-ranked genes selected from the combined MPTP and METH data. The graph shows separate data for the two neurotoxins. (B) Top five genes found to be significantly downregulated in response to both drug treatments. (C) Gene expression ratios (treatment over control) are compared across MPTP and METH treatments (R 0.718, p < 10⁻¹⁶). (D) Selected gene expression levels confirmed using quantitative real-time polymerase chain reaction (qRT-PCR) (p < 0.05, all tests). (E) mRNA levels compared to protein abundance. A scatter plot comparing protein to mRNA levels averaged across treated and control samples. LOWESS fitted curve (dark line) (R 0.289, p < 10⁻²¹). Efficiently transcribed genes lie > 2 standard deviations (SD) above the LOWESS curve (upper gray line indicates 2 SD cutoff), and inefficiently transcribed genes lie < 1.4 SD below the curve (lower gray line).