Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

Abstract

Genome-wide association studies (GWAS) have identified numerous genetic variants associated with complex diseases but mechanistic insights are impeded by the lack of understanding of how specific risk variants functionally contribute to the underlying pathogenesis1. It has been proposed that cis-acting effects of non-coding risk variants on gene expression are a major factor for phenotypic variation of complex traits and disease susceptibility. Recent genome-scale chromatin mapping studies have highlighted the enrichment of GWAS variants in regulatory DNA elements of disease-relevant cell types2–6. Furthermore, single nucleotide polymorphism (SNP)-specific changes in transcription factor (TF) binding are correlated with heritable alterations in chromatin state and considered a major mediator of sequence-dependent regulation of gene expression7–10. Here we describe a novel strategy to functionally dissect the cis-acting effect of genetic risk variants in regulatory elements on gene expression by combining genome-wide epigenetic information with clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9 genome editing in human pluripotent stem cells (hPSCs). By generating a genetically precisely controlled experimental system we identify a common Parkinson’s disease (PD)-associated risk variant in a non-coding distal enhancer element that regulates the expression of alpha-synuclein (SNCA), a key gene implicated in the pathogenesis of PD. Our data suggest that the transcriptional deregulation of SNCA is associated with sequence-dependent binding of the brain-specific TFs EMX2 and NKX6-1. This work establishes an experimental paradigm to functionally connect genetic variation with disease relevant phenotypes.

In Vitro Modeling of Complex Neurological Diseases

“…As a proof of principle, we describe below how we recently applied the aboveelucidated approach to sporadic Parkinson's disease as a prototypical complex disorder, to identify common risk variants in non-coding distal enhancer elements that functionally modulate the risk to develop the disease (Soldner et al 2016). Parkinson's disease is the second most common chronic progressive neurodegenerative disease, with a prevalence of more than 1% in the population over the age of 60.…”

“…As for SNCA, a gene known to be variable between neuronal cell types such as astrocytes, oligodendrocytes and neurons and to be regulated during development and terminal differentiation, cellular heterogeneity and incomplete maturation significantly interfere with the detection of subtle differences in gene expression between distinct risk-genotypes or patient compared to control cells, respectively. Indeed, individual in vitro differentiation experiments from genetically identical sub-clones resulted in up to fourfold differences in SNCA expression (Soldner et al 2016). To address this problem, we recently described an experimental approach that is based on determining the effect of individual regulatory elements on the transcription of the cis-regulated gene by analyzing allele-specific gene expression (Soldner et al 2016).…”

“…Indeed, individual in vitro differentiation experiments from genetically identical sub-clones resulted in up to fourfold differences in SNCA expression (Soldner et al 2016). To address this problem, we recently described an experimental approach that is based on determining the effect of individual regulatory elements on the transcription of the cis-regulated gene by analyzing allele-specific gene expression (Soldner et al 2016). The deletion of just a single copy (heterozygous) of a candidate regulatory element or its exchange with an alternative disease-associated element affects only the gene expression of the cis-regulated gene on the same allele while maintaining the expression of the other, homologous allele, unaltered.…”

“…By combining human pluripotent stem cell (hPSC)-technology with genome editing and genome-scale epigenetic and genome-wide association studies (GWAS) data to identify disease-associated risk variants, we will provide a blueprint to create genetically defined experimental model systems that allow the functional analysis of disease-associated risk variants. As a proof of principle, we describe how we applied this approach to sporadic Parkinson's disease and identified a common risk variant in a non-coding distal enhancer element that regulates the expression of SNCA, a key gene implicated in the pathogenesis of Parkinson's disease (Soldner et al 2016). …”

Finding the ‘Guilty’ Gene Variant of Sporadic Parkinson’s Disease Via CRISPR/Cas9

“…Soldner et al [4] used clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9 (CRISPR-associated protein 9), a powerful gene-editing technique, to analyze variants in the SNCA gene which encodes a-synuclein. They found that a common variant in a non-coding distal enhancer element increases the expression of SNCA by affecting the sequence-dependent binding of transcription factors (TFs).…”