<i>Cis</i>-Acting SNP effects on gene expression for probes within 250 kb of the PD associated risk loci.

<p><i>Cis</i>-Acting SNP effects on gene expression for probes within 250 kb of the PD associated risk loci.</p

Brain Sample Characteristics.

*<p> <i>significantly different between cases and controls (p = 0.02).</i></p

Evaluation of Parkinson Disease Risk Variants as Expression-QTLs

<div><p>The recent Parkinson Disease GWAS Consortium meta-analysis and replication study reports association at several previously confirmed risk loci <em>SNCA</em>, <em>MAPT</em>, <em>GAK/DGKQ</em>, and <em>HLA</em> and identified a novel risk locus at <em>RIT2</em>. To further explore functional consequences of these associations, we investigated modification of gene expression in prefrontal cortex brain samples of pathologically confirmed PD cases (N = 26) and controls (N = 24) by 67 associated SNPs in these 5 loci. Association between the eSNPs and expression was evaluated using a 2-degrees of freedom test of both association and difference in association between cases and controls, adjusted for relevant covariates. SNPs at each of the 5 loci were tested for <em>cis</em>-acting effects on all probes within 250 kb of each locus. <em>Trans</em>-effects of the SNPs on the 39,122 probes passing all QC on the microarray were also examined. From the analysis of <em>cis</em>-acting SNP effects, several SNPs in the <em>MAPT</em> region show significant association to multiple nearby probes, including two strongly correlated probes targeting the gene <em>LOC644246</em> and the duplicated genes <em>LRRC37A</em> and <em>LRRC37A2</em>, and a third uncorrelated probe targeting the gene <em>DCAKD</em>. Significant <em>cis</em>-associations were also observed between SNPs and two probes targeting genes in the HLA region on chromosome 6. Expanding the association study to examine <em>trans</em> effects revealed an additional 23 SNP-probe associations reaching statistical significance (p<2.8×10⁻⁸) including SNPs from the <em>SNCA, MAPT</em> and <em>RIT2</em> regions. These findings provide additional context for the interpretation of PD associated SNPs identified in recent GWAS as well as potential insight into the mechanisms underlying the observed SNP associations.</p> </div

<i>Trans</i>-Acting SNP effects on gene expression.

<p><i>Trans</i>-Acting SNP effects on gene expression.</p

HLA region probes and SNPs involved in significant <i>cis</i> eSNP relationships.

<p>Two probes in the HLA region on chromosme 6 showing significant association with PD risk SNPs are shown on the alternative sequence haplotype chr6_ssto_hap7. Six PD risk SNPs (shown in green) showed significant association to A_24_P326084 located in <i>HLA-DQA1</i>, while four SNPs (shown in red) had significant association to A_24P852756, located in <i>HLA-DQA2</i>.</p

<i>MAPT</i> region probes and SNPs involved in significant <i>cis</i> eSNP relationships.

<p>Three probes in the <i>MAPT</i> region on chromosme 17 showing significant association with PD risk SNPs are displayed. Significant SNP associations with A_24_P110521 located in the duplicated genes <i>LRRC37A</i> and <i>LRRC37A2</i> are shown in blue, while SNPs associated with A_24_P221327 located in <i>LOC644246</i> are shown in green and SNPs associated with A_24_P58331 (in <i>DCAKD</i>) are shown in red.</p

The 4p16.3 Parkinson Disease Risk Locus Is Associated with <i>GAK</i> Expression and Genes Involved with the Synaptic Vesicle Membrane

<div><p>Genome-wide association studies (GWAS) have identified the <i>GAK</i>/<i>DGKQ</i>/<i>IDUA</i> region on 4p16.3 among the top three risk loci for Parkinson’s disease (PD), but the specific gene and risk mechanism are unclear. Here, we report transcripts containing the 3’ clathrin-binding domain of <i>GAK</i> identified by RNA deep-sequencing in post-mortem human brain tissue as having increased expression in PD. Furthermore, carriers of 4p16.3 PD GWAS risk SNPs show decreased expression of one of these transcripts, <i>GAK25</i> (Gencode Transcript 009), which correlates with the expression of genes functioning in the synaptic vesicle membrane. Together, these findings provide strong evidence for <i>GAK</i> clathrin-binding- and J-domain transcripts’ influence on PD pathogenicity, and for a role for <i>GAK</i> in regulating synaptic function in PD.</p></div

<i>GAK</i> exons significantly associated to case status primarily encode for the clathrin-binding and J domains of <i>GAK</i> protein.

<p><i>GAK</i> exon 25 (<i>GAK25)</i>, which was found to be associated to both case status and the risk SNP, is highlighted in magenta (under Gene), while <i>GAK</i> exons associated with case status only are highlighted in blue. All Gencode transcripts are shown below the gene structure, with transcript functionality listed below each contig. <i>GAK25</i> represents the 5’UTR of Gencode transcript 009 (Boxed in red). The <i>GAK</i> protein domains (under Protein) are denoted by color: J domain (green), clathrin-binding domain (yellow), phosphatase/tensin domain (blue), and kinase domain (red). Transcript data from <a href="http://www.ensembl.org/" target="_blank">http://www.ensembl.org</a>.</p

Genes Associated with <i>GAK25</i> Expression in PD brain are Significantly Enriched in GO Terms Related to Synaptic and Mitochondrial Structure.

<p>Genes Associated with <i>GAK25</i> Expression in PD brain are Significantly Enriched in GO Terms Related to Synaptic and Mitochondrial Structure.</p

<i>GAK</i> Gencode exons in the 3’ region are differentially expressed in PD.

<p>(A) The mean normalized expression for PD cases and controls is plotted for each of the 71 <i>GAK</i> exon feature bins (x-axis). Exon 1 corresponds to the 3’ end of the gene, while Exon 71 corresponds to the 5’ end. Brackets indicate groups of exons significantly increased in PD relative to control (* = <i>q</i>-value < 0.05). (B) The mean normalized expression of <i>GAK</i> exon 25 (<i>GAK25</i>) is plotted for each stratified group. The samples are stratified by case status (Control and PD) and by genotype in an additive fashion (CC = Major allele homozygote, CT = Heterozygote, TT = Risk allele homozygote). (C and D) -ΔΔCT (log2 fold change) of <i>GAK</i> normalized to <i>PPIA</i> is plotted for all control and PD samples for (<b>c</b>) <i>GAK</i> 3’ exons and (<b>d</b>) <i>GAK</i> 5’ exons.</p