Sequential and concerted gene expression changes in a chronic in vitro model of parkinsonism

Abstract

Many mechanisms of neurodegeneration have been implicated in Parkinson's disease, but which ones are most important and potential interactions among them are unclear. To provide a broader perspective on the parkinsonian neurodegenerative process, we have performed a global analysis of gene expression changes caused by chronic, low-level exposure of neuroblastoma cells to the mitochondrial complex I inhibitor and parkinsonian neurotoxin rotenone. Undifferentiated SK-N-MC human neuroblastoma cells were grown in the presence of rotenone (5 nM), and RNA was extracted at three different time points (baseline, 1 week, and 4 weeks) for labeling and hybridization to Affymetrix Human U133 Plus 2.0 GeneChips. Our results show that rotenone induces concerted alterations in gene expression that change over time. Particularly, alterations in transcripts related to DNA damage, energy metabolism, and protein metabolism are prominent during chronic complex I inhibition. These data suggest that early augmentation of capacity for energy production in response to mitochondrial inhibition might be deleterious to cellular function and survival. These experiments provide the first transcriptional analysis of a rotenone model of Parkinson's disease and insight into which mechanisms of neurodegeneration may be targeted for therapeutic intervention.

Figure 1. Upregulation of oxidative phosphorylation genes in rotenone-treated cells

Each cell in the heatmap represents the expression level of a gene (row) in a single sample (column). N=6 for both control and rotenone-treated samples. Deep red reflects overexpression of the transcript, whereas deep blue represents underexpression.

Figure 2. Upregulation of a DNA repair pathway involving ATR and BRCA (ATRBRCAPATHWAY) in cells treated with rotenone for 4 weeks

Each cell in the heatmap represents the expression level of a gene (row) in a single rotenone-treated sample (column) normalized to the average expression of that transcript in vehicle-treated samples. N=3 for both 1 and 4 week rotenone-treated samples. Deep red reflects overexpression of the transcript, whereas deep blue represents underexpression.

Figure 3. Elevation of energy metabolism transcripts precedes elevation of DNA repair transcripts during rotenone intoxication

The mean percentage change (± SEM) is comprised of individual expression changes of transcripts in that category relative to control induced by rotenone treatment. The energy generation category contained 48 genes and the DNA repair category 26.

Figure 4. Time-dependent effects of rotenone on gene expression

Each cell in the heat map represents the expression level of a gene (row) in a single sample (column) normalized to the average of that transcript in vehicle-treated samples. Note that samples cluster together based on gene expression profile. The right side of the figure denotes GO biological process classifications that are overrepresented in the adjacent cluster as compared to the whole. The number of genes in that cluster fitting a particular classification are compared with the total number of differentially expressed genes in that classification using Fisher’s exact test (eGOn).