30 September 2012. Rarely do genetics, biology, and pathogenesis converge in a single study as they do in the September 25 Nature Communications. An unusually long α-synuclein mRNA identified by Asa Abeliovich and colleagues at Columbia University, New York, brandies an extended 3’ untranslated region (UTR) and thrives in the presence of dopamine and PD-linked gene variants. It also seems to steer synuclein protein away from synaptic terminals and toward mitochondria, where it accumulates, mimicking PD pathology. Synuclein is the major component of Lewy bodies, dense protein aggregates found in the brains of people with PD and related neurodegenerative diseases. The latest findings highlight a new mechanism for controlling α-synuclein and suggest that selective downregulation of the long isoforms could hold therapeutic value. “The manuscript and its data are outstanding,” noted Jörg Schulz of University Aachen, Germany, in an e-mail to Alzforum. “I believe it will change our view of the pathogenesis of Parkinson’s disease.”
Researchers have worked for decades to determine what drives sporadic PD. Though they have discovered genetic and environmental risk factors, how they provoke disease has been unclear. The new work now links both risk factors to a major hallmark of PD pathology.
To identify molecular pathways driving PD pathogenesis, the Columbia scientists initially tried genomewide expression analyses on patient brain tissue. “We could see it was going to be a rough road,” Abeliovich said. “The data we got were what you would expect with loss of dopamine neurons. They reflected 30 years of disease rather than telling us something about how the disease started.”
To distinguish secondary changes from causal events, first author Herve Rhinn and colleagues analyzed gene expression data using a new computational technique they call differential coexpression analysis (DCA), which is based on a method termed differential wiring that has been applied in cancer research (Hudson et al., 2009). Instead of simply looking for transcripts that go up or down in PD versus normal tissue, as is done in conventional whole-transcriptome analyses, they used bioinformatics to find “master regulator” transcripts that control expression of groups of downstream transcripts. The authors worked on the premise that when a master regulator goes awry, the whole network falls apart, and therefore the regulator likely represents a primary rather than a secondary event in disease. “We looked for the network that was most different between controls and patients. Then we looked for the center of that network,” Abeliovich said.
Using the bioinformatics method to analyze several independent datasets of PD patients and age-matched elderly, the researchers found that “center” to be an α-synuclein transcript with a long 3’UTR. Among 22 human brain regions analyzed, this isoform is expressed most abundantly in the substantia nigra of the midbrain, and people with PD had more of this extended transcript, relative to shorter α-synuclein species, than did age-matched controls. The ratio of the long transcript to total synuclein mRNA increased further in brain tissue from people with common variants in the 3’UTR that raise the risk of getting Parkinson’s. Even in unaffected individuals, risk variants boosted the ratio in a dose-dependent way. Abeliovich saw that as “overwhelming evidence that [the change] is not secondary to disease.”
More than genetics governs the production of this mRNA isoform. Environmental toxins, which are known risk factors for PD, also drove up expression of the long α-synuclein transcript—as did dopamine, whether exogenously applied to cultured rat neurons or injected into mice. Previous studies suggested that dopamine raises synuclein levels, but had not shown how, Abeliovich said.
Rhinn and colleagues also found that upregulation of the extended α-synuclein transcript, in turn, caused accumulation of synuclein protein—preferentially in mitochondria—as occurs in disease. In addition, they identified an miR-34b binding site in the 3’UTR of the α-synuclein long isoform, but not in shorter transcripts. Based on luciferase assays in SH-SY5Y cells transfected with the long synuclein isoform, miR-34b seems to drive translation of the transcript. However, the α-synuclein gene has PD risk variants and sites for binding other miRNAs, which likely add further complexity to the mechanisms regulating mRNA and protein expression, noted Owen Ross of the Mayo Clinic in Jacksonville, Florida (see comment below). Indeed, a recent microRNA profiling study found a dearth of miR-34b/c in PD brains, triggering transcript changes that underlie mitochondrial dysfunction and oxidative stress (Miñones-Moyano et al., 2011).
The findings “highlight the importance of abnormal RNA processing in PD research,” wrote Jesse McLean and Ole Isacson of McLean Hospital, Belmont, Massachusetts, in an e-mail to Alzforum (see full comment below). A prior analysis identified α-synuclein mRNA isoforms with alternatively spliced exons 3 and/or 5 (Beyer et al., 2008). “It would be interesting to know if these coding isoforms correlate with the 3’UTR isoforms in terms of expression,” noted Ross.
Abeliovich sees the extended 3’UTR as a “convergent point for environmental and genetic regulation of α-synuclein.” Compounds that preferentially curb expression of the long transcript may have therapeutic benefits, he suggested. The ratio of the long transcript to total synuclein also appears elevated in patient blood samples, compared to unaffected controls, suggesting it could serve as a disease biomarker, Abeliovich said.—Esther Landhuis.
Rhinn H, Qiang L, Yamashita T, Rhee D, Zolin A, Vanti W, Abeliovich A. Alternative α-synuclein transcript usage as a convergent mechanism in Parkinson’s disease pathology. Nat Comm. 25 Sep 2012. Abstract