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Genome-wide association studies have identified genetic variation in genomic loci associated with susceptibility to Parkinson’s disease (PD), the most common neurodegenerative movement disorder worldwide. We used allelic expression profiling of genes located within PD-associated loci to identify  cis -regulatory variation affecting gene expression. DNA and RNA were extracted from post-mortem superior frontal gyrus tissue and whole blood samples from PD patients and controls. The relative allelic expression of transcribed SNPs in 12 GWAS risk genes was analysed by real-time qPCR. Allele-specific expression was identified for 9 out of 12 genes tested ( GBA ,  TMEM175 ,  RAB7L1 ,  NUCKS1 ,  MCCC1 ,  BCKDK ,  ZNF646 ,  LZTS3 , and  WDHD1 ) in brain tissue samples. Three genes ( GPNMB ,  STK39  and  SIPA1L2 ) did not show significant allele-specific effects. Allele-specific effects were confirmed in whole blood for three genes ( BCKDK ,  LZTS3  and  MCCC1 ), whereas two genes ( RAB7L1  and  NUCKS1 ) showed brain-specific allelic expression. Our study supports the hypothesis that changes to the  cis -regulation of gene expression is a major mechanism behind a large proportion of genetic associations in PD. Interestingly, allele-specific expression was also observed for coding variants believed to be causal variants ( GBA  and  TMEM175 ), indicating that splicing and other regulatory mechanisms may be involved in disease development.

Allele-specific expression of Parkinson’s disease susceptibility genes in human brain