Law, W. D. | Search bioRxiv

bioRxiv2018

Parkinson-associated SNCA enhancer variants revealed by open chromatin in mouse dopamine neurons

The progressive loss of midbrain (MB) dopaminergic (DA) neurons defines the motor features of Parkinson disease (PD) and modulation of risk by common variation in PD has been well established through GWAS. Anticipating that a fraction of PD-associated genetic variation mediates their effects within this neuronal population, we acquired open chromatin signatures of purified embryonic mouse MB DA neurons. Correlation with >2,300 putative enhancers assayed in mice reveals enrichment for MB cis-regulatory elements (CRE), data reinforced by transgenic analyses of six additional sequences in zebrafish and mice. One CRE, within intron 4 of the familial PD gene SNCA, directs reporter expression in catecholaminergic neurons of transgenic mice and zebrafish. Sequencing of this CRE in 986 PD patients and 992 controls reveals two common variants associated with elevated PD risk. To assess potential mechanisms of action, we screened >20,000 DNA interacting proteins and identify a subset whose binding is impacted by these enhancer variants. Additional genotyping across the SNCA locus identifies a single PD-associated haplotype, containing the minor alleles of both of the aforementioned PD-risk variants. Our work posits a model for how common variation at SNCA may modulate PD risk and highlights the value of cell context-dependent guided searches for functional non-coding variation.

genetics↗

bioRxiv2017

Temporal and spatial variation among single dopaminergic neuron transcriptomes informs cellular phenotype diversity and Parkinson’s Disease gene prioritization

Parkinsons disease (PD) is caused by the collapse of substantia nigra (SN) dopaminergic (DA) neurons of the midbrain (MB), while other DA populations remain relatively intact. Common variation influencing susceptibility to sporadic PD has been primarily identified through genome wide association studies (GWAS). However, like many other common genetic diseases, the genes impacted by common PD-associated variation remain to be elucidated. Here, we used single-cell RNA-seq to characterize DA neuron populations in the mouse brain at embryonic and early postnatal timepoints. These data allow for the unbiased identification of DA neuron subpopulations, including a novel postnatal neuroblast population and SN DA neurons. Comparison of SN DA neurons with other DA neurons populations in the brain reveals a unique transcriptional profile, novel marker genes, and specific gene regulatory networks. By integrating these cell population specific data with published GWAS, we develop a scoring system for prioritizing candidate genes in PD-associated loci. With this, we prioritize candidate genes in all 32 GWAS intervals implicated in sporadic PD risk, the first such systematically generated list. From this we confirm that the prioritized candidate gene CPLX1 disrupts the nigrostriatal pathway when knocked out in mice. Ultimately, this systematic rationale leads to the identification of biologically pertinent candidates and testable hypotheses for sporadic PD that will inform a new era of PD genetic research.

genetics↗