Expression analysis of dopaminergic neurons in Parkinson’s disease and aging links transcriptional dysregulation of energy metabolism to cell death

Abstract

Dopaminergic (DA) neuron degeneration is a feature of brain aging but is markedly increased in patients with Parkinson's disease (PD). Recent data indicate elevated metabolic stress as a possible explanation for DA neuron vulnerability. Using laser capture microdissection, we isolated DA neurons from the substantia nigra pars compacta of PD patients, age-matched and young controls to determine transcriptional changes by expression profiling and pathway analysis. We verified our findings by comparison to a published dataset. Parallel processing of isolated neurons and bulk tissue allowed the discrimination of neuronal and glial transcription signals. Our data show that genes known to be involved in neural plasticity, axon and synaptic function, as well as cell fate are differentially regulated in aging DA neurons. The transcription patterns in aging suggest a largely maintained expression of genes in energy-related pathways in surviving neurons, possibly supported by the mediation of PPAR/RAR and CREB signaling. In contrast, a profound down-regulation of genes coding for mitochondrial and ubiquitin--proteasome system proteins was seen in PD when compared to the age-matched controls. This is in accordance with the established mitochondrial dysfunction in PD and provides evidence for mitochondrial impairment at the transcriptional level. In addition, the PD neurons had disrupted pathways that comprise a network involved in the control of energy metabolism and cell survival in response to growth factors, oxidative stress, and nutrient deprivation (PI3K/Akt, mTOR, eIF4/p70S6K and Hif-1α). PI3K/Akt and mTOR signaling are central hubs of this network which is of relevance to longevity and--together with induction of mitochondrial biogenesis--may constitute potential targets for therapeutic intervention.

The Role of Oxidative Stress in Parkinson's Disease

“…Several groups have reported decreased Complex I activity and ubiquinone in the SN of PD patients, abnormalities that may lead to neuronal degeneration [140–142]. In addition, gene expression profiling in dopaminergic neurons from PD patients showed down-regulation of genes encoding mitochondrial proteins, among others, providing further evidence for mitochondrial dysfunction in PD [143]. Unexpectedly, complex I deficiency has also been observed in the platelets and skeletal muscle of PD patients [144–146], although not all reports agree about the latter likely due to methodological differences [147, 148].…”

Age-related gene expression changes in substantia nigra dopamine neurons of the rat

“…Importantly, we used a relatively pure population of rat SNpc DA neurons, obtained through laser microdissection (Brown et al, 2013;Brown and Smith, 2009). Analyses of such samples, with known cellular composition, increase the likelihood of detecting cell-specific and subtle changes, especially changes in low abundance transcripts (Elstner et al, 2011;Grimm et al, 2004;Grundemann et al, 2008;Simunovic et al, 2009). Furthermore, we quantified gene expression using qPCR, thereby obviating the need for amplification, which is necessary for microarray analysis.…”

Laser Capture Microdissection of Enriched Populations of Neurons or Single Neurons for Gene Expression Analysis After Traumatic Brain Injury

“…LCM would be a valuable tool in similar studies of other brain regions that are known to be implicated in diverse neurological and neuropsychiatric disorders. For example, studies using LCM have shed light into the pathogenesis of Parkinson's disease in dopamine neurons of the substantia nigra, 14 and aided genome-wide profiling studies of the nucleus accumbens, which is involved in reward circuits implicated in substance abuse disorders. 15 Neuronal heterogeneity is reflected at the genome level 16 and may contribute to the lack of success of experimental treatments for TBI in clinical trials.…”