Molecular-level Analyses Reveal Possible Mechanisms Underlying Parkinson's Disease
Selected proteins showing consistent abundance changes for both neurotoxin treatments. Each row on the heat map corresponds to a unique peptide (short polymer) with each column representing one sample from an individual mouse. Two proteins marked with * were previously reported to be correlated with dopamine neuron damage. Enlarge Image
Proteomics—the large-scale study of proteins, particularly their structure and function—combined with transcriptomics—the examination of the expression level of messenger ribonucleic acids (mRNAs) in a given cell population-played a significant role in the recent derivation of a combined protein and gene list that constitutes one of the largest descriptive data sets of its kind. Derived by researchers at the Pacific Northwest National Laboratory and their colleagues at the University of California-Los Angeles, the data set integrates drug-induced change in the abundance of proteins and the expression of genes in two mouse models of brain disease. Comparing molecular-level changes in parallel provided two different sets of regulated genes for a combined list that provides a clearer picture of the mechanisms underlying the progressive neurodegeneration observed in Parkinson's disease.
Regulation of gene expression (or gene regulation) refers to the cellular control of the amount and timing of changes to the appearance of the functional product of a gene, which may be an RNA or a protein. Gene regulation gives the cell control over its structure and function, and is the basis for cellular differentiation, spatial distribution, and the versatility and adaptability of any organism. Up-regulation occurs when a cell is deficient in some kind of receptor so that more receptor protein is synthesized and transported to the membrane of the cell and thus the sensitivity of the cell is brought back to normal, reestablishing homeostasis. Down-regulation occurs when a cell is overly stimulated by a neurotransmitter, hormone, or drug for a prolonged period of time and the expression of the receptor protein is decreased to protect the cell.
Why it matters: Parkinson's disease is marked by the loss of dopamine in the brain's nigrostriatal neural pathway, which is one of four major pathways for this hormone and neurotransmitter in the brain; the disease primarily affects part of the motor system involved in the production and coordination of movement. Defining the molecular changes in the striata of Parkinson's diseased brains is necessary to better understand the disorder and design new therapeutic approaches for its treatment. The striatum is a major input station of the basal ganglia system—the group of nuclei in the brain that are connected to the cerebral cortex, thalamus, and brainstem. The profiling methods used in this research to identify molecular changes may be a general approach for differentiating the molecular pathology of disease models resulting from agent-specific effects, such as the effects of the two neurotoxins used in this research.
Methods: To better understand the series of chemical reactions that occur in this particular neural pathway, team leads at UCLA, working with PNNL researchers, used two neurotoxins to induce changes in the structure, function, and abundance of proteins and the level of gene expression in mouse brain striata. The striatum of the brain in humans plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. To gain a deeper understanding of the cellular response of the two neurotoxins, the researchers applied global quantitative proteomics at the U.S. Department of Energy's national user facility—the Environmental Molecular Sciences Laboratory—and microarrays at UCLA to assay the protein and gene levels, respectively, for both neurotoxins. Proteomic analysis to profile protein abundance resulted in the identification and relative quantification for 912 proteins with two or more unique peptides and 86 proteins with significant abundance changes after treatment with the neurotoxins, while microarray analyses to profile gene expression revealed 181 genes with significant changes in mRNA after treatment. These techniques and functional analysis of the resulting data revealed a number of up- and down-regulated proteins and mRNAs; i.e., up-regulated by a signal (originating internal or external to the cell) that results in increased expression of one or more genes and as a result the protein(s) encoded by those genes, and down-regulated by a process resulting in decreased gene and corresponding protein expression. The revelation of proteins and mRNAs included some proteins associated with cellular conditions that play a role in the pathogenesis of Parkinson's disease, which may make them attractive candidates for development as biomarkers of the disease.
What's next: PNNL researchers are extending the quantitative proteomic methods developed in this work to the higher resolution investigation of disease models in mouse brains. To model and predict the behavior of biological systems researchers must address the temporal changes in biomolecule (RNA and protein) abundance levels as well as their spatial distribution. By applying the technique known as voxelation, developed by collaborators at UCLA, spatially defined regions (1 cubic millimeter in size) of the mouse brain can be characterized to develop three-dimensional (3D) relationships between cells and molecular networks. Brains that have been voxelated into ~700 cubes will be prepared using automated microscale sample processing and analyzed using high-throughput reversed-phase liquid chromatography coupled online with high-resolution mass spectrometry to obtain both the spatial localization and relative abundance of brain proteins. This 3D proteomics brain data can be integrated with parallel 3D transcriptomic studies to possibly provide insights to interesting targets for either therapeutic intervention or further mechanistic studies.
Acknowledgments: This work was supported by the National Institutes of Health, Staglin Music Festival and NARSAD Young Investigator Award, Tobacco-Related Disease Research Program, and Alzheimer's Association. Proteomic measurements were performed at the Environmental Molecular Sciences Laboratory, the DOE national scientific user facility located on the PNNL campus that provides integrated experimental and computational resources for discovery and innovation to support DOE and national needs.
Research Team: The research team included Wei-Jun Qian and Vladislav A. Petyuk, who were particularly instrumental in getting this collaborative research accomplished and published, along with Richard D. Smith, Haixing Wang, Diana J. Bigelow, and David G. Camp, II all of PNNL; and Mark H. Chin, Joshua S. Bloom, Daniel M. Sforca, Goran Lacan, Dahai Liu, Arshad H. Khan, Rita Cantor, William P. Melega, and Desmond J. Smith all of UCLA.
Reference: Chin MH, W Qian, H Wang, VA Petyuk, JS Bloom, DM Sforza, G Lacan, D Liu, AH Khan, RM Cantor, DJ Bigelow, WP Melega, DG Camp, II, RD Smith, and DJ Smith. 2008. "Mitochondrial dysfunction, oxidative stress and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson's disease. Journal of Proteome Research 7:666-677.